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Prepair 1000+ v1.1566 SLC6A5 Andrew Coventry changed review comment from: Affected individuals cab present with neonatal hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea episodes. In some cases, symptoms resolved in the first year of life (PMID: 16751771).
Well established gene-disease association, especially for bi-allelic variants, including animal model.

AD association also reported, however, limited evidence in literature for mono-allelic cause of disease.; to: Affected individuals can present with neonatal hypertonia, an exaggerated startle response to tactile or acoustic stimuli, and life-threatening neonatal apnea episodes. In some cases, symptoms resolved in the first year of life (PMID: 16751771).
Well established gene-disease association, especially for bi-allelic variants, including animal model.

AD association also reported, however, limited evidence in literature for mono-allelic cause of disease.
Prepair 1000+ v1.1480 UROS Zornitza Stark Phenotypes for gene: UROS were changed from Porphyria, congenital erythropoietic, 263700 (3) to Porphyria, congenital erythropoietic MIM#263700, cutaneous porphyria MONDO:0009902
Prepair 1000+ v1.1460 MED23 Andrew Coventry changed review comment from: Intellectual developmental disorder, autosomal recessive 18, with or without epilepsy is a syndromic intellectual disability, including early onset epilepsy, spasticity, microcephaly and, less frequently, delayed myelination and thin corpus callosum. Variants in MED23 have been reported in at least 11 affected individuals from at least 6 unrelated families. Congenital/early onset. Functional studies and animal models present.; to: Intellectual developmental disorder, autosomal recessive 18, with or without epilepsy is a syndromic intellectual disability, including early onset epilepsy, spasticity, microcephaly and, less frequently, delayed myelination and thin corpus callosum. Variants in MED23 have been reported in at least 11 affected individuals from at least 6 unrelated families. Congenital/early onset. Functional studies and animal models present. Variants reported include nonsense and missense.
Prepair 1000+ v1.1460 UROS Marta Cifuentes Ochoa reviewed gene: UROS: Rating: GREEN; Mode of pathogenicity: None; Publications: 30685241, 24027798, 28334762, 27512208, 34187847, 34828434, 15065102; Phenotypes: Porphyria, congenital erythropoietic MIM#263700, cutaneous porphyria MONDO:0009902; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1460 TRMU Marta Cifuentes Ochoa commented on gene: TRMU: Acute infantile liver failure resulting from variants in TRMU is a transient disorder of hepatic function. In addition to elevated liver enzymes, jaundice, vomiting, coagulopathy, and hyperbilirubinemia, the presence of increased serum lactate is consistent with a defect in mitochondrial respiratory function.

HGNC approved symbol/name: TRMU
Is the phenotype(s) severe and onset <18yo? Y
Known technical challenges? N
Gene reported in >3 independent families

Yemenite Jewish founder variant, p.Tyr77His.
Prepair 1000+ v1.1457 MTHFR Lauren Thomas changed review comment from: Methylenetetrahydrofolate reductase deficiency is a common inborn error of folate metabolism. The phenotypic spectrum ranges from severe neurologic deterioration and early death to asymptomatic adults.

HGNC approved symbol/name: MTHFR
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes ; to: Methylenetetrahydrofolate reductase deficiency is a common inborn error of folate metabolism. The phenotypic spectrum ranges from severe neurologic deterioration and early death to asymptomatic adults.

HGNC approved symbol/name: MTHFR
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes

NOTE: there are two very common variants in this gene that are not associated with severe disease (665C>T & 1286A>C)
Prepair 1000+ v1.1456 UGT1A1 Zornitza Stark Phenotypes for gene: UGT1A1 were changed from Crigler-Najjar syndrome, type I, 218800 (3) to Bilirubin UDP-glucuronosyltransferase 1 deficiency (Disorders of bile acid metabolism and transport); Crigler-Najjar syndrome, type I MIM#218800; Crigler-Najjar syndrome, type II MIM#606785
Prepair 1000+ v1.1397 UGT1A1 Clare Hunt reviewed gene: UGT1A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 12983120, 37585628, 1734381, 5411133, 9413009; Phenotypes: Bilirubin UDP-glucuronosyltransferase 1 deficiency (Disorders of bile acid metabolism and transport), Crigler-Najjar syndrome, type I MIM#218800, Crigler-Najjar syndrome, type II MIM#606785; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.1367 MUT Lauren Thomas changed review comment from: Isolated methylmalonic aciduria is found in patients with mutations in the MUT gene causing partial, mut(-), or complete, mut(0), enzyme deficiency. Variable severity and age of onset:
• Infantile completely deficient (mut0) or non-B12-responsive (clbB) is the most common phenotype and presents during infancy. Infants are normal at birth, but develop lethargy, vomiting, and dehydration within the first few months of life. They may also exhibit hepatomegaly, hypotonia, encephalopathy, metabolic acidosis, ketosis and ketonuria, hyperammonemia, and hyperglycemia.
• Partially deficient (mut-) or B12-responsive (cblA, cblD, rarely cblB) is an intermediate phenotype that can occur in the first few months or years of life. Symptoms include feeding problems, failure to thrive, hypotonia, and developmental delay. Some have protein aversion and vomiting, and lethargy after protein intake.

HGNC approved symbol/name: MMUT *
Is the phenotype(s) severe and onset <18yo? Yes
Treatments available: cobalamin, N-carbamylglutamate, carnitine, diet, liver transplant
Known technical challenges? No
Gene reported in 3 independent families: Yes

* NOTE: gene previously called MUT; to: Isolated methylmalonic aciduria is found in patients with mutations in the MUT gene causing partial, mut(-), or complete, mut(0), enzyme deficiency. Variable severity and age of onset:

• Infantile completely deficient (mut0) or non-B12-responsive (clbB) is the most common phenotype and presents during infancy. Infants are normal at birth, but develop lethargy, vomiting, and dehydration within the first few months of life. They may also exhibit hepatomegaly, hypotonia, encephalopathy, metabolic acidosis, ketosis and ketonuria, hyperammonemia, and hyperglycemia.

• Partially deficient (mut-) or B12-responsive (cblA, cblD, rarely cblB) is an intermediate phenotype that can occur in the first few months or years of life. Symptoms include feeding problems, failure to thrive, hypotonia, and developmental delay. Some have protein aversion and vomiting, and lethargy after protein intake.

HGNC approved symbol/name: MMUT *
Is the phenotype(s) severe and onset <18yo? Yes
Treatments available: cobalamin, N-carbamylglutamate, carnitine, diet, liver transplant
Known technical challenges? No
Gene reported in 3 independent families: Yes

* NOTE: gene previously called MUT
Prepair 1000+ v1.1367 MTHFR Lauren Thomas changed review comment from: Methylenetetrahydrofolate reductase deficiency is a common inborn error of folate metabolism. The phenotypic spectrum ranges from severe neurologic deterioration and early death to asymptomatic adults.

HGNC approved symbol/name: MTHFR
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes

NOTE: common variants not associated with severe disease are not reported; to: Methylenetetrahydrofolate reductase deficiency is a common inborn error of folate metabolism. The phenotypic spectrum ranges from severe neurologic deterioration and early death to asymptomatic adults.

HGNC approved symbol/name: MTHFR
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes
Prepair 1000+ v1.1357 DCLRE1C Lauren Thomas changed review comment from: The majority of individuals present within the first months of life with oral thrush, diarrhea, fever, pneumonia, and/or failure to thrive as well as hypogammmaglobulinaemia, absent T and B lymphocytes and increased radiosensitivity.

Homozygous and compound heterozygous (missense, in-frame indel, nonsense, frameshift, and large deletion) variants have been reported; with the most common being gross deletions exons 1-3.
*c.597C>A p.Tyr199X founder variant (Athabascan/ European Origin)

HGNC approved symbol/name: DCLRE1C
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges: ?most common variant is a deletion
Gene reported in 3 independent families: Yes

Note: ClinGen groups the 2 OMIM phenotypes into "severe combined immunodeficiency due to DCLRE1C deficiency"; to: The majority of individuals present within the first months of life with oral thrush, diarrhea, fever, pneumonia, and/or failure to thrive as well as hypogammmaglobulinaemia, absent T and B lymphocytes and increased radiosensitivity.

Homozygous and compound heterozygous (missense, in-frame indel, nonsense, frameshift, and large deletion) variants have been reported; with the most common being gross deletions exons 1-3 (~59%)
*c.597C>A p.Tyr199X founder variant (Athabascan/ European Origin)

HGNC approved symbol/name: DCLRE1C
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges: ?most common variant is a deletion
Gene reported in 3 independent families: Yes

Note: ClinGen groups the 2 OMIM phenotypes into "severe combined immunodeficiency due to DCLRE1C deficiency"
Prepair 1000+ v1.1326 COL4A5 Zornitza Stark Phenotypes for gene: COL4A5 were changed from Alport syndrome 1, X-linked to Alport syndrome 1, X-linked, MIM#301050
Prepair 1000+ v1.1268 GJA1 Michelle Torres changed review comment from: The GJA1 gene is associated with both AD & AR conditions (OMIM).

For carrier screening testing, the only relevant conditions are the AR disorders: Craniometaphyseal dysplasia MIM#218400; Oculodentodigital dysplasia MIM#257850.

Craniometaphyseal dysplasia (CMD) is a rare sclerosing skeletal disorder with progressive hyperostosis of craniofacial bones. Characteristic ocular and dental features of ODDD as well as syndactyly are absent in patients with CMD (PMID: 23951358). Reports are rare and individuals are homozygous for the p.(Arg239Gln), located in the C-terminus of the GJA1 gene; at least 4x families reported (PMID: 23951358).

Oculodentodigital dysplasia (ODDD) is a rare condition characterised by a typical facial appearance and variable findings of the eyes, teeth, and fingers (PMID: 29902798). ODDD is generally AD (DN and GoF suggested), but rare AR cases have been identified. LoF is associated with AR ODDD (PMID: 29902798), and most variants reported are PTV within the connexin domain (PMID: 34035645).

NB: the association with Hypoplastic left heart syndrome 1, MIM#241550 isn't listed in OMIM anymore, variants associated have been re-classified VUS (OMIM). Pfitzer C 2024 concludes that researchers must move beyond the expectation that a single disease-causing variant can be found (PMID 38884762).; to: The GJA1 gene is associated with both AD & AR conditions (OMIM).

For carrier screening testing, the only relevant conditions are the AR disorders: Craniometaphyseal dysplasia MIM#218400; Oculodentodigital dysplasia MIM#257850.

Craniometaphyseal dysplasia (CMD) is a rare sclerosing skeletal disorder with progressive hyperostosis of craniofacial bones. Characteristic ocular and dental features of ODDD as well as syndactyly are absent in patients with CMD (PMID: 23951358). Reports are rare and individuals are homozygous for the p.(Arg239Gln), located in the C-terminus of the GJA1 gene; at least 4x families reported (PMID: 23951358).

Oculodentodigital dysplasia (ODDD) is a rare condition characterised by a typical facial appearance and variable findings of the eyes, teeth, and fingers (PMID: 29902798). ODDD is generally AD (DN and GoF suggested), but rare AR cases have been identified. LoF is associated with AR ODDD (PMID: 29902798), and most variants reported are PTV within the connexin domain (PMID: 34035645).

NB: the association with Hypoplastic left heart syndrome 1, MIM#241550 isn't listed in OMIM anymore, variants associated have been re-classified VUS (OMIM; PMID 38884762).
Prepair 1000+ v1.1268 COL7A1 Michelle Torres changed review comment from: The COL7A1 gene is associated with dystrophic epidermolysis bullosa (DEB), a genetic skin disorder affecting skin and nails that usually presents at birth.

There are 2 main subtypes: dominant (DDEB) and recessive (RDEB), both with many clinical subtypes. For carrier screening testing, the only relevant subtypes are AR.

Genotype-phenotype correlation is unclear (PMID: 31670143), but variants resulting in complete absence of protein are usually associated with the most severe RDEB (PMID: 32506467). The recessive exon skipping variants are scattered throughout the gene (PMID: 31670143).

NB: Transient bullous of the newborn MIM#131705 is predominantly AD, but AR cases have been reported (PMID: 25639640 Table 1). It has onset at birth, but skin lesions resolve between 6 months and 2 years of age. Some patients have milder persistent blistering.; to: The COL7A1 gene is associated with dystrophic epidermolysis bullosa (DEB), a genetic skin disorder affecting skin and nails that usually presents at birth.

There are 2 main subtypes: dominant (DDEB) and recessive (RDEB), both with many clinical subtypes. For carrier screening testing, the only relevant subtypes are AR.

Genotype-phenotype correlation is unclear (PMID: 31670143), but variants resulting in complete absence of protein are usually associated with the most severe RDEB (PMID: 32506467). The recessive exon skipping variants are scattered throughout the gene (PMID: 31670143).

NB: Transient bullous of the newborn MIM#131705 is predominantly AD, but AR cases have been reported (PMID: 25639640 Table 1). It has onset at birth, but skin lesions resolve between 6 months and 2 years of age. Some patients have milder persistent blistering. As noted above, genotype-phenotype correlation is unclear.
Prepair 1000+ v1.1268 COL7A1 Michelle Torres changed review comment from: The COL7A1 gene is associated with dystrophic epidermolysis bullosa (DEB), a genetic skin disorder affecting skin and nails that usually presents at birth.

There are 2 main subtypes: dominant (DDEB) and recessive (RDEB), both with many clinical subtypes. For carrier screening testing, the only relevant subtypes are AR.

Genotype-phenotype correlation is unclear (PMID: 31670143), but variants resulting in complete absence of protein are usually associated with the most severe RDEB (PMID: 32506467). The recessive exon skipping variants are scattered throughout the gene (PMID: 31670143).

NB: Transient bullous of the newborn MIM#131705 is predominantly AD, but AR cases have been reported (PMID: 25639640 Table 1). It has onset at birth, but skin lesions resolve between 6 months and 2 years of age. Some patients have milder persistent blistering. Relevance for Prepair requires discussion.; to: The COL7A1 gene is associated with dystrophic epidermolysis bullosa (DEB), a genetic skin disorder affecting skin and nails that usually presents at birth.

There are 2 main subtypes: dominant (DDEB) and recessive (RDEB), both with many clinical subtypes. For carrier screening testing, the only relevant subtypes are AR.

Genotype-phenotype correlation is unclear (PMID: 31670143), but variants resulting in complete absence of protein are usually associated with the most severe RDEB (PMID: 32506467). The recessive exon skipping variants are scattered throughout the gene (PMID: 31670143).

NB: Transient bullous of the newborn MIM#131705 is predominantly AD, but AR cases have been reported (PMID: 25639640 Table 1). It has onset at birth, but skin lesions resolve between 6 months and 2 years of age. Some patients have milder persistent blistering.
Prepair 1000+ v1.1257 COL4A5 Crystle Lee reviewed gene: COL4A5: Rating: GREEN; Mode of pathogenicity: None; Publications: 36531881, 19965530, 36341250; Phenotypes: Alport syndrome 1, X-linked, MIM#301050; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Prepair 1000+ v1.1257 TWNK Crystle Lee changed review comment from: Gene also know as C10ORF2.

MTDPS7 is characterized by primarily by hypotonia, ataxia, ophthalmoplegia, hearing loss, seizures, and sensory axonal neuropathy (OMIM)

PMID: 35035228: Reported an 11yo girl with delayed gonadal development, sensorineural hearing loss, and neurologic manifestations

Allelic conditions, Perrault syndrome is less severe than MTDPS7.; to: Gene also know as C10ORF2.

MTDPS7 is characterized by primarily by hypotonia, ataxia, ophthalmoplegia, hearing loss, seizures, and sensory axonal neuropathy (OMIM)

PMID: 35035228: Reported an 11yo girl with delayed gonadal development, sensorineural hearing loss, and neurologic manifestations

Allelic conditions, Perrault syndrome is less severe than MTDPS7.
Prepair 1000+ v1.1105 POR Zornitza Stark Marked gene: POR as ready
Prepair 1000+ v1.1105 POR Zornitza Stark Gene: por has been classified as Green List (High Evidence).
Prepair 1000+ v1.1105 POR Zornitza Stark Publications for gene: POR were set to
Prepair 1000+ v1.992 STIL Ee Ming Wong changed review comment from: - More than 10 unrelated families reported.
- Onset at birth
- PMID: 24485834; 29352115: Complete loss of STIL is not compatible with life. Genetic mutations in human STIL result in
1. residual expression or
2. stabilization of STIL: PTCs that delete of the critical C-terminal KEN Box domain involved in Anaphase-Promoting-Complex/Cyclosome (APC/C)-mediated degradation of STIL5 were shown to result in mutant STIL stabilization and accumulation and subsequent centriole amplification. Demonstrated for p.(Val1219X) and p.(Gln1239X), suggested gain of function.; to: - More than 10 unrelated families reported.
- Onset at birth
- PMID: 24485834; 29352115: Complete loss of STIL is not compatible with life. Genetic mutations in human STIL result in
1. residual expression or
2. stabilization of mutant STIL: PTCs that delete of the critical C-terminal KEN Box domain involved in Anaphase-Promoting-Complex/Cyclosome (APC/C)-mediated degradation of STIL5 were shown to result in mutant STIL stabilization and accumulation and subsequent centriole amplification. Demonstrated for p.(Val1219X) and p.(Gln1239X), suggested gain of function.
Prepair 1000+ v1.992 TBX22 Ee Ming Wong changed review comment from: 1. Cleft palate with ankyloglossia (MIM# 303400)
- More than 10 families reported with cleft palate/ankyloglossia and variants in this gene.
- PMID:36901693 - Characterised by a cleft palate phenotype that is most often present in males and ranges from a high-arched palate, bifid uvula, submucous cleft palate, soft cleft palate, to complete cleft palate
- OMIM, PMID:36901693 - Ankyloglossia/ bifid uvula/cleft palate reported in heterozygous females
- Overall mild phenotype although PMID: 21375406 describes 1x TBX22 hemizygous individual with unilateral complete cleft lip and palate, ankyloglossia, hypodontia of the left maxillary second premolar, carpal bone anomalies, and hypoplastic thumb of the right hand. No other genes were tested.

2. Abruzzo-Erickson syndrome, MIM# 302905
PMID:22784330 - Single family reported with Abruzzo-Erickson syndrome, a syndromic form of cleft palate. Did not find additional reports on this phenotype; to: 1. Cleft palate with ankyloglossia (MIM# 303400)
- More than 10 families reported with cleft palate/ankyloglossia and variants in this gene.
- PMID:36901693 - Characterised by a cleft palate phenotype that is most often present in males and ranges from a high-arched palate, bifid uvula, submucous cleft palate, soft cleft palate, to complete cleft palate
- OMIM, PMID:36901693 - Ankyloglossia/ bifid uvula/cleft palate reported in heterozygous females
- Overall mild phenotype although PMID: 21375406 describes 1x TBX22 hemizygous individual with unilateral complete cleft lip and palate, ankyloglossia, hypodontia of the left maxillary second premolar, carpal bone anomalies, and hypoplastic thumb of the right hand. No other genes were tested.

2. Abruzzo-Erickson syndrome, MIM# 302905
PMID:22784330 - Single family reported with Abruzzo-Erickson syndrome, a syndromic form of cleft palate. Did not find additional reports on this phenotype
Prepair 1000+ v1.992 ELP1 Clare Hunt changed review comment from: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age.

HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31. Also previously referred to as Riley-Day syndrome.
From Mendeliome; AR dysautonomia: the condition is predominantly caused by homozygosity of c.2204+6T>C (major familial dysautonomia AJ haplotype - causes tissue-specific exon 20 skipping) in Ashkenazi Jewish individuals. Other variants have been reported in association with the disease.; to: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age.

HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31.

From Mendeliome; AR dysautonomia: the condition is predominantly caused by homozygosity of c.2204+6T>C (major familial dysautonomia AJ haplotype - causes tissue-specific exon 20 skipping) in Ashkenazi Jewish individuals. Other variants have been reported in association with the disease.
Prepair 1000+ v1.992 ELP1 Clare Hunt changed review comment from: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age. HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31. Also previously referred to as Riley-Day syndrome.; to: From OMIM; Hereditary sensory and autonomic neuropathy type III (HSAN3) is an autosomal recessive neurodegenerative disorder with onset soon after birth. Affected individuals show progressive symptoms resulting from depletion of sensory proprioceptive and autonomic neurons. Features include gastrointestinal dysfunction, gastroesophageal reflux, vomiting crises, recurrent pneumonia, seizures, gait abnormalities with loss of ambulation, kyphoscoliosis, postural hypotension, hypertension crises, absence of fungiform papillae on the tongue, decreased deep tendon reflexes, defective lacrimation, and impaired pain and temperature perception. The disorder is inevitably fatal, with only 50% of patients reaching 40 years of age.

HSAN3 has a high carrier frequency in the Ashkenazi Jewish population (summary by Morini et al., 2016).

Gene previously referred to as IKBKAP gene (ELP1; 603722) located on chromosome 9q31. Also previously referred to as Riley-Day syndrome.
From Mendeliome; AR dysautonomia: the condition is predominantly caused by homozygosity of c.2204+6T>C (major familial dysautonomia AJ haplotype - causes tissue-specific exon 20 skipping) in Ashkenazi Jewish individuals. Other variants have been reported in association with the disease.
Prepair 1000+ v1.992 ISCA1 Lauren Thomas changed review comment from: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes; to: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes

Most recent case report: PMID 32092383 (4th independent family)
Prepair 1000+ v1.992 ISCA1 Lauren Thomas changed review comment from: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes; to: Multiple mitochondrial dysfunctions syndrome-5 (MMDS5) is an autosomal recessive disorder characterized mainly by progressive neurologic deterioration beginning in early infancy. Affected individuals have essentially no psychomotor development and have early-onset seizures with neurologic decline and spasticity. Brain imaging shows severe leukodystrophy with evidence of dys- or delayed myelination. Death usually occurs in early childhood.

HGNC approved symbol/name: ISCA1
Is the phenotype(s) severe and onset <18yo? Yes
Known technical challenges? No
Gene reported in 3 independent families: Yes
Prepair 1000+ v1.992 DGUOK Clare Hunt reviewed gene: DGUOK: Rating: GREEN; Mode of pathogenicity: None; Publications: 12874104, 15887277, 23043144; Phenotypes: Mitochondrial DNA depletion syndrome 3 (hepatocerebral type), MIM# 251880, Portal hypertension, noncirrhotic, 1, MIM# 617068, Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 4, MIM# 617070; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.992 POR Ee Ming Wong changed review comment from: - PORD (P450 oxidoreductase deficiency) is associated with disorders of sex development in both sexes, where Antley-Bixler (ABS) syndrome is the name given to the severe form
- Skeletal abnormalities of the ABS phenotype are frequently observed in individuals with PORD, characterised by craniosynostosis, brachycephaly, radio-ulnar or radio-humeral synostosis, bowed femora, arachnodactyly, midface hypoplasia, proptosis, and choanal stenosis. The severity of malformations varies from mild to moderate and severe.

NB: Only the more severe MIM# has been added to this gene list.; to: - PORD (P450 oxidoreductase deficiency) is associated with disorders of sex development in both sexes, where Antley-Bixler (ABS) syndrome is the name given to the severe form
- Skeletal abnormalities of the ABS phenotype are frequently observed in individuals with PORD, characterised by craniosynostosis, brachycephaly, radio-ulnar or radio-humeral synostosis, bowed femora, arachnodactyly, midface hypoplasia, proptosis, and choanal stenosis. The severity of malformations varies from mild to moderate and severe.
- Congenital onset

NB: Only the more severe MIM# has been added to this gene list.
Prepair 1000+ v1.992 POR Ee Ming Wong reviewed gene: POR: Rating: GREEN; Mode of pathogenicity: None; Publications: 27604308, 20301592, 35842891; Phenotypes: Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis (MIM#201750); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Prepair 1000+ v1.992 PC Ee Ming Wong changed review comment from: - Well-established gene disease association
- Age of onset: neonatal to early childhood
- Severity: variable severity - three subtypes

1. Type A (infantile form aka North American form): characterized by infantile onset of metabolic and lactic acidosis, delayed motor development, intellectual disability, poor linear growth and/or weight gain, and neurologic findings. Brain anomalies can be noted. Most affected children die in infancy or early childhood.

2. Type B (severe neonatal form aka French form): characterized by neonatal or infantile onset of hypothermia, respiratory distress/failure, vomiting, severe lactic acidosis, hyperammonemia, and often hypoglycemia. Neurologic findings include brain abnormalities, lethargy, hypotonia, and pyramidal and extrapyramidal signs. Death typically occurs by age eight months.

3. Type C (intermittent/attenuated form aka Benign form): characterized by relatively normal or mildly delayed neurologic
development, motor and/or gait abnormalities, (rarely) seizures, episodic movement disorders, and metabolic
acidosis. Life span is unknown but survival into adulthood has been reported.; to: - Well-established gene disease association
- Age of onset: neonatal to early childhood
- Severity: variable severity - three subtypes

1. Type A (infantile form aka North American form): characterized by infantile onset of metabolic and lactic acidosis, delayed motor development, intellectual disability, poor linear growth and/or weight gain, and neurologic findings. Brain anomalies can be noted. Most affected children die in infancy or early childhood.

2. Type B (severe neonatal form aka French form): characterized by neonatal or infantile onset of hypothermia, respiratory distress/failure, vomiting, severe lactic acidosis, hyperammonemia, and often hypoglycemia. Neurologic findings include brain abnormalities, lethargy, hypotonia, and pyramidal and extrapyramidal signs. Death typically occurs by age eight months.

3. Type C (intermittent/attenuated form aka Benign form): characterized by relatively normal or mildly delayed neurologic development, motor and/or gait abnormalities, (rarely) seizures, episodic movement disorders, and metabolic acidosis. Life span is unknown but survival into adulthood has been reported.
Prepair 1000+ v1.992 NMNAT1 Ee Ming Wong changed review comment from: Syndromic and non-syndromic causes of LCA are associated with bi-allelic variants in this gene.

Non-syndromic LCA: multiple affected families reported, p.Glu257Lys is a common founder variant.

Syndromic disorder: three families reported, but two are distantly related (shared haplotype). The affected children in those two families were homozygous for 7.4-kb duplication involving the last 2 exons of the NMNAT1 gene, spanning the beginning of intron 3 to the middle of the 3-prime UTR (chr1:10,036,359-10,043,727, GRCh37). The third affected individual was compound het for the duplication and a splicing variant.

Green for non-syndromic LCA (MIM# added to review). No additional affected individuals in the literature (Amber? MIM# has not been added to review).; to: Syndromic and non-syndromic causes of LCA are associated with bi-allelic variants in this gene.

Non-syndromic LCA: multiple affected families reported, p.Glu257Lys is a common founder variant.

Syndromic disorder: three families reported, but two are distantly related (shared haplotype). The affected children in those two families were homozygous for 7.4-kb duplication involving the last 2 exons of the NMNAT1 gene, spanning the beginning of intron 3 to the middle of the 3-prime UTR (chr1:10,036,359-10,043,727, GRCh37). The third affected individual was compound het for the duplication and a splicing variant.

Green for non-syndromic LCA (MIM# added to review). No additional affected individuals in the literature for syndromic LCA (Amber? MIM# has not been added to review).
Prepair 1000+ v1.992 CHST14 Michelle Torres edited their review of gene: CHST14: Added comment: Musculocontractural EDS type 1 (mcEDS) is a rare type of EDS caused by biallelic loss-of-function variants in CHST14 (PMID: 34815299).

Major features are: congenital multiple contractures and characteristic craniofacial features at birth or in early infancy; congenital multiple contractures and characteristic cutaneous features in adolescence and in adulthood (PMID: 34815299).

The CHST14 gene has only 1 exon, therefore PTV variants escape NMD. Missense and in-frame deletion have also been reported with a similar phenotype to that caused by PTV (PMID: 34815299).; Changed rating: GREEN
Prepair 1000+ v1.992 TCAP Crystle Lee changed review comment from: Established for LGMD. Rare muscle disorder characterised by proximal and distal lower limb weakness, calf hypertrophy and loss of ambulation.

Mean age at onset 12.5 years (range 2 to 15 years). Progression to wheelchair in fourth decade (OMIM)
PMID: 37216648: Onset range from 6-35.
PMID: 25724973: Onset in teens. Wheelchair bound by 44.
PMID: 25055047: Reported PTCs in 2 families. In at least one family, with 3 affected family members, one was wheelchair bound state at 21 years of age.

Other similar/more severe LDMG phenotypes included in panel.; to: Established for LGMD. Rare muscle disorder characterised by proximal and distal lower limb weakness, calf hypertrophy and loss of ambulation.

Mean age at onset 12.5 years (range 2 to 15 years). Progression to wheelchair in fourth decade (OMIM)
PMID: 37216648: Onset range from 6-35.
PMID: 25724973: Onset in teens. Wheelchair bound by 44.
PMID: 25055047: Reported PTCs in 2 families. In at least one family, with 3 affected family members, one was wheelchair bound state at 21 years of age.

Other similar/more severe LGMD phenotypes included in panel.
Prepair 1000+ v1.992 TCAP Crystle Lee changed review comment from: Established for LGMD. Rare muscle disorder characterised by proximal and distal lower limb weakness, calf
hypertrophy and loss of ambulation.

Mean age at onset 12.5 years (range 2 to 15 years). Progression to wheelchair in fourth decade (OMIM)
PMID: 37216648: Onset range from 6-35.
PMID: 25724973: Onset in teens. Wheelchair bound by 44.
PMID: 25055047: Reported PTCs in 2 families. In at least one family, with 3 affected family members, one was wheelchair bound state at 21 years of age.

Other similar/more severe LDMG phenotypes included in panel.; to: Established for LGMD. Rare muscle disorder characterised by proximal and distal lower limb weakness, calf hypertrophy and loss of ambulation.

Mean age at onset 12.5 years (range 2 to 15 years). Progression to wheelchair in fourth decade (OMIM)
PMID: 37216648: Onset range from 6-35.
PMID: 25724973: Onset in teens. Wheelchair bound by 44.
PMID: 25055047: Reported PTCs in 2 families. In at least one family, with 3 affected family members, one was wheelchair bound state at 21 years of age.

Other similar/more severe LDMG phenotypes included in panel.
Prepair 1000+ v1.978 PGAP2 Shakira Heerah changed review comment from: Strong gene-disease association, multiple unrelated families reported severe intellectual disability.; to: Strong gene-disease association, multiple unrelated families reported severe intellectual disability.
Prepair 1000+ v1.978 PGAP2 Shakira Heerah changed review comment from: Strong gene-disease association, multiple unrelated families reported severe intellectual disability..; to: Strong gene-disease association, multiple unrelated families reported severe intellectual disability.
Prepair 1000+ v1.978 NSDHL Kate Scarff changed review comment from: X-linked recessive disorder characterized by mild to severe cognitive impairment, seizures, microcephaly, cerebral cortical malformations, dysmorphic facial features, and thin body habitus. 25 affected males from three unrelated families have been reported. Heterozygous females are typically unaffected; however, some may experience mild behavior problems such as irritability or aggression. The NSDHL pathogenic variants c.455G>A, c.696_698delGAA, and c.1098dupT have been consistently associated with CK syndrome.

Other phenotype associated with this gene is CHILD syndrome (MIM #308050) not reportable for Prepair1000 as is X-linked dominant, only affects females, lethal before birth in hemizygous males.; to: X-linked recessive disorder characterized by mild to severe cognitive impairment, seizures, microcephaly, cerebral cortical malformations, dysmorphic facial features, and thin body habitus. 25 affected males from three unrelated families have been reported. Heterozygous females are typically unaffected; however, some may experience mild behavior problems such as irritability or aggression. The NSDHL pathogenic variants c.455G>A, c.696_698delGAA, and c.1098dupT have been consistently associated with CK syndrome.

Other phenotype associated with this gene is CHILD syndrome (MIM #308050) not reportable for Prepair1000 as is X-linked dominant, only affects females, lethal before birth in hemizygous males.

See also GeneReviews PMID: 21290788
Prepair 1000+ v1.836 GUCY2D Kate Scarff changed review comment from: LCA1 is a congenital eye disorder that primarily affects the retina and causes vision loss, nystagmus, and severe retinal dysfunction. People with this disorder typically have severe visual impairment beginning at birth or shortly afterward. The visual impairment tends to be severe and may worsen over time.

Cone-rod dystrophy 6, MIM #601777 is a dominant condition due to heterozygous mutations in GUCY2D, not reportable for Prepair1000+.
Autosomal recessive GUCY2D mutations may cause congenital night blindness with normal acuity and refraction, and unique electroretinography. Progression to mild retinitis pigmentosa may occur. See PMID: 29559409. Not reportable for Prepair1000+ (severity).; to: LCA1 is a congenital eye disorder that primarily affects the retina and causes vision loss, nystagmus, and severe retinal dysfunction. People with this disorder typically have severe visual impairment beginning at birth or shortly afterward. The visual impairment tends to be severe and may worsen over time.

Cone-rod dystrophy 6, MIM #601777 is a dominant condition due to heterozygous mutations in GUCY2D, not reportable for Prepair1000+. See PMID: 35205358
Autosomal recessive GUCY2D mutations may cause congenital night blindness with normal acuity and refraction, and unique electroretinography. Progression to mild retinitis pigmentosa may occur. See PMID: 29559409. Not reportable for Prepair1000+ (severity).
Prepair 1000+ v1.761 TPRKB Lucy Spencer changed review comment from: Gene is red on Mackenzie's mission panel but the review itself is green and says "Three unrelated families reported with renal-neurologic disease characterized by early-onset nephrotic syndrome associated with microcephaly." this is refering to 3 families all with homozygous missense, p.Lys65Met, p.Tyr149Cys, and p.Leu136Pro.

There has been at least one more individual reported PMID: 38628357: a three-year-old male with developmental delay, regression, microcephaly, distinctive facial features, skeletal abnormalities, and epilepsy. He also had relapsing nephrotic proteinuria exacerbated by upper respiratory tract infections and progressive renal function decline. He was compound heterozygous for p.(Ser76IlefsTer3) and c.247C>T, p.(Leu83Phe).

Severe early-onset and reported in at least 4 individuals (also green on mendeliome), upgrading to green here.; to: Gene is red on Mackenzie's mission panel but the review itself is green and says "Three unrelated families reported with renal-neurologic disease characterized by early-onset nephrotic syndrome associated with microcephaly." this is refering to 3 families all with homozygous missense, p.Lys65Met, p.Tyr149Cys, and p.Leu136Pro (PMIDs: 28805828, 30053862).

There has been at least one more individual reported PMID: 38628357: a three-year-old male with developmental delay, regression, microcephaly, distinctive facial features, skeletal abnormalities, and epilepsy. He also had relapsing nephrotic proteinuria exacerbated by upper respiratory tract infections and progressive renal function decline. He was compound heterozygous for p.(Ser76IlefsTer3) and c.247C>T, p.(Leu83Phe).

Severe early-onset and reported in at least 4 individuals (also green on mendeliome), upgrading to green here.
Prepair 1000+ v1.745 SLC16A1 Zornitza Stark Phenotypes for gene: SLC16A1 were changed from Monocarboxylate transporter 1 deficiency, 616095 (3) to Monocarboxylate transporter 1 deficiency, MIM#616095
Prepair 1000+ v1.633 SLC9A6 Andrew Coventry changed review comment from: Established gene-disease association. Childhood onset, multi-system, Angelman-like disorder.
Characterised by microcephaly, impaired ocular movements, progressive severe global developmental delay, developmental regression, hypotonia, abnormal movements, and early-onset seizures of variable types.

Female carriers may be either asymptomatic, or more mildly affected than males.
PMID 31192222: describes 20 female carriers from 9 families. Presentations included impairments in visuospatial function, attention, and executive function. Cohort features: Intellectual disability/developmental delay (20%), learning difficulties (31%), speech/language delays (30%), and attention-deficit/hyperactivity disorder (20%).
PMID 35198730: Japanese family where SLC9A6 variant in female carriers segregated with atypical parkinsonism and intellectual disability.

More than 20 unrelated families reported. Functional data including mouse model.; to: Established gene-disease association. Childhood onset, multi-system, Angelman-like disorder in affected males -
characterised by microcephaly, impaired ocular movements, progressive severe global developmental delay, developmental regression, hypotonia, abnormal movements, and early-onset seizures of variable types.

Female carriers may be either asymptomatic, or more mildly affected than males.
PMID 31192222: describes 20 female carriers from 9 families. Presentations included impairments in visuospatial function, attention, and executive function. Cohort features: Intellectual disability/developmental delay (20%), learning difficulties (31%), speech/language delays (30%), and attention-deficit/hyperactivity disorder (20%).
PMID 35198730: Japanese family where SLC9A6 variant in female carriers segregated with atypical parkinsonism and intellectual disability.

More than 20 unrelated families reported. Functional data including mouse model.
Prepair 1000+ v1.633 SLC26A2 Andrew Coventry changed review comment from: Well established gene disease association causing skeletal abnormalities of varying severity.
Variants in this gene have been shown to cause achondrogenesis type 1B, atelosteogenesis type 2, diastrophic dysplasia, and recessive multiple epiphyseal dysplasia, which comprise a spectrum of phenotypes (depending on level of residual sulfate transport). Onset/features can often be observed neonatally.
Mouse models present for some phenotypes, and functional studies are present.

Homozygosity or compound heterozygosity for stop codons or transmembrane domain substitutions mostly result in achondrogenesis type IB, whereas other structural or regulatory mutations usually result in one of the less severe phenotypes (PMID: 8723100)

Unsure of phenotypes to list under condition. Clingen includes curations for:
diastrophic dysplasia MONDO:0009107
multiple epiphyseal dysplasia MONDO:0016648
atelosteogenesis type II MONDO:0009727
achondrogenesis type IB MONDO:0010966
OMIM phenotypes (6) listed above.; to: Well established gene disease association causing skeletal abnormalities of varying severity.
Variants in this gene have been shown to cause achondrogenesis type 1B, atelosteogenesis type 2, diastrophic dysplasia, and recessive multiple epiphyseal dysplasia, which comprise a spectrum of phenotypes (depending on level of residual sulfate transport). Onset/features can often be observed neonatally.
Mouse models present for some phenotypes, and functional studies are present.

Homozygosity or compound heterozygosity for stop codons or transmembrane domain substitutions mostly result in achondrogenesis type IB, whereas other structural or regulatory variants usually result in one of the less severe phenotypes (PMID: 8723100)

Unsure of phenotypes to list under condition. Clingen includes curations for:
diastrophic dysplasia MONDO:0009107
multiple epiphyseal dysplasia MONDO:0016648
atelosteogenesis type II MONDO:0009727
achondrogenesis type IB MONDO:0010966
OMIM phenotypes (6) listed above.
Prepair 1000+ v1.633 SLC26A2 Andrew Coventry changed review comment from: Well established gene disease association causing skeletal abnormalities of varying severity.
Variants in this gene have been shown to cause achondrogenesis type 1B, atelosteogenesis type 2, diastrophic dysplasia, and recessive multiple epiphyseal dysplasia, which comprise a spectrum of phenotypes (depending on level of residual sulfate transport). Onset can be neonatal.
Mouse models present for some phenotypes, and functional studies are present.

Homozygosity or compound heterozygosity for stop codons or transmembrane domain substitutions mostly result in achondrogenesis type IB, whereas other structural or regulatory mutations usually result in one of the less severe phenotypes (PMID: 8723100)

Unsure of phenotypes to list under condition. Clingen includes curations for:
diastrophic dysplasia MONDO:0009107
multiple epiphyseal dysplasia MONDO:0016648
atelosteogenesis type II MONDO:0009727
achondrogenesis type IB MONDO:0010966
OMIM phenotypes (6) listed above.; to: Well established gene disease association causing skeletal abnormalities of varying severity.
Variants in this gene have been shown to cause achondrogenesis type 1B, atelosteogenesis type 2, diastrophic dysplasia, and recessive multiple epiphyseal dysplasia, which comprise a spectrum of phenotypes (depending on level of residual sulfate transport). Onset/features can often be observed neonatally.
Mouse models present for some phenotypes, and functional studies are present.

Homozygosity or compound heterozygosity for stop codons or transmembrane domain substitutions mostly result in achondrogenesis type IB, whereas other structural or regulatory mutations usually result in one of the less severe phenotypes (PMID: 8723100)

Unsure of phenotypes to list under condition. Clingen includes curations for:
diastrophic dysplasia MONDO:0009107
multiple epiphyseal dysplasia MONDO:0016648
atelosteogenesis type II MONDO:0009727
achondrogenesis type IB MONDO:0010966
OMIM phenotypes (6) listed above.
Prepair 1000+ v1.633 SLC16A1 Andrew Coventry reviewed gene: SLC16A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 25390740, 20301549, 36082648, 35729663; Phenotypes: Monocarboxylate transporter 1 deficiency MIM#616095; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Prepair 1000+ v1.633 L2HGDH Crystle Lee changed review comment from: Well established gene-disease association.

Onset typically in infancy or early childhood, however, reports of milder, adult onset cases have been reported. Patients may present with a wide variety of clinical manifestations.; to: Well established gene-disease association.

Onset typically in infancy or early childhood, however, reports of milder, adult onset cases have been reported. Patients may present with a wide variety of clinical manifestations.
Prepair 1000+ v1.592 GCH1 Lilian Downie Added comment: Comment when marking as ready: Biallelic variants in GCH1 typically result in severe deficiency of GTPCH activity, and result in hyperphenylalaninemia due to secondary PAH deficiency. This can be identified by newborn screening. However, patients with phenotypes that are intermediate between the classic DRD and severe GTPCH deficiency symptoms have been described, such those with severe DRD and additional neurological features but without hyperphenylalaninemia (for review, see Table in Brüggemann et al 2012, PMID 22473768). Because the mechanism of disease in both the monoallelic and biallelic cases is loss of function of GTPCH, and there is a range of GTPCH activity that can cause disease, the decision was made to curate GCH1 for GTPCH deficiency with semi-dominant inheritance. Note that heterozygous parents of biallelic individuals are usually reported as unaffected, although there are some exceptions (Furukawa et al, 1998, PMID 9667588; Bodzioch et al, 2010, PMID 20842687). Reduced penetrance has been reported for individuals with monoallelic GCH1 variants, with penetrance varying according to age and diagnostic criteria. In addition, some variants (e.g. p.Arg184His and p.Lys224Arg) have been reported in monallelic and biallelic individuals. This data was presented to the ClinGen Lumping and Splitting Working Group on November 3, 2020 and there was agreement that GTPCH deficiency should be curated as a semi-dominant trait, including individuals with monoallelic and biallelic GCH1 variants.
Prepair 1000+ v1.546 IFNGR1 Andrew Coventry changed review comment from: Multiple families with recessive disease reported, reviewed in PMID 15589309.
Patients with complete IFNGR1 deficiency have a severe clinical phenotype characterized by early and often fatal mycobacterial infections. The disorder can thus be categorized as a form of mendelian susceptibility to mycobacterial disease (MSMD). Bacillus Calmette-Guerin (BCG) and environmental mycobacteria are the most frequent pathogens, and infection typically begins before the age of 3 years. Recessive deficiency is thought to result in complete loss of cellular response to IFNG and absence of surface IFNGR1 expression. Animal models present.

Note: AD condition associated with this gene - Immunodeficiency 27B, mycobacteriosis, MIM#615978.
Dominant deficiency is typically due to cytoplasmic domain truncations resulting in accumulation of non-functional IFNGR1 proteins that may impede the function of molecules encoded by the wildtype allele, thereby leading to diminished but not absent responsiveness to IFNG. Common deletions at and around nucleotide 818. (PMID: 10192386); to: Multiple families with recessive disease reported, reviewed in PMID 15589309.
Patients with complete IFNGR1 deficiency have a severe clinical phenotype characterized by early and often fatal mycobacterial infections. The disorder can thus be categorized as a form of mendelian susceptibility to mycobacterial disease (MSMD). Bacillus Calmette-Guerin (BCG) and environmental mycobacteria are the most frequent pathogens, and infection typically begins before the age of 3 years. Recessive deficiency is thought to result in complete loss of cellular response to IFNG and absence of surface IFNGR1 expression. Animal models present.

Note: AD condition associated with this gene - Immunodeficiency 27B, mycobacteriosis, MIM#615978.
Dominant deficiency is typically due to cytoplasmic domain truncations resulting in accumulation of non-functional IFNGR1 proteins that may impede the function of molecules encoded by the wildtype allele, thereby leading to diminished but not absent responsiveness to IFNG. Deletions including nucleotide 818 reported. (PMID: 10192386)
Prepair 1000+ v1.503 FOLR1 Zornitza Stark Phenotypes for gene: FOLR1 were changed from Neurodegeneration due to cerebral folate transport deficiency, 613068 (3) to Neurodegeneration due to cerebral folate transport deficiency, MIM#613068
Prepair 1000+ v1.486 FOLR1 Andrew Coventry reviewed gene: FOLR1: Rating: GREEN; Mode of pathogenicity: None; Publications: 19732866 30420205 27743887; Phenotypes: Neurodegeneration due to cerebral folate transport deficiency MIM#613068; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.384 TSPYL1 Lilian Downie Added comment: Comment when marking as ready: Originally reported only in Amish community, founder variant
subsequently reported in 3 unrelated families, non amish - GREEN AT UPGRADE
2 cohort studies looking for variants in this gene in SIDS cohorts but it's very rare and presents with more of a progressive neurological phenotype in the non Amish families
Prepair 1000+ v1.371 PNKP Lilian Downie Added comment: Comment on phenotypes: CMT phenotype is usually onset in 30's but childhood onset has been reported.
Prepair 1000+ v1.322 AARS2 Clare Hunt edited their review of gene: AARS2: Added comment: At least 6 families presenting with a severe COXPD phenotype in infancy, primarily with cardiac, muscle and neurological features in addition to lactic acidosis. Further 6 reported with a progressive neurodegenerative disorder characterised by loss of motor and cognitive skills, usually with onset in young adulthood. Some had a history of delayed motor development or learning difficulties in early childhood. Neurologic decline was severe, usually resulting in gait difficulties, ataxia, spasticity, and cognitive decline and dementia. Most individuals lost speech and become wheelchair-bound or bedridden. Brain MRI showed progressive white matter signal abnormalities in the deep white matter. Affected females developed premature ovarian failure. These likely represent a spectrum of severity of a single mitochondrial disorder.
Created: 29 Aug 2020, 4:55 a.m. | Last Modified: 29 Aug 2020, 4:55 a.m.
Panel Version: 0.3999; Changed publications: 27839525
Prepair 1000+ v1.322 ALAD Lauren Thomas reviewed gene: ALAD: Rating: GREEN; Mode of pathogenicity: None; Publications: 16343966, 30724374, 2063868, 1569184, 15303011; Phenotypes: Porphyria, acute hepatic, MIM#612740; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.304 ERCC2 Ee Ming Wong changed review comment from: - Bi-allelic inactivation of XPD protein, a nucleotide excision repair (NER) signaling pathway component encoded by ERCC2 gene, has been associated with several defective DNA repair phenotypes, including xeroderma pigmentosum, photosensitive trichothiodystrophy, and cerebro-oculo-facio-skeletal syndrome.
- Severe, early onset of all three phenotypes have been reported
- Variable expressivity has been reported for Xeroderma pigmentosum, group D, MIM# 278730 where individuals can present with or without mild or severe neurologic abnormalities (GeneReviews)
- OMIM: The location of variants (mutagenic pattern) is consistent in determining the phenotype. Variants shared by both phenotypes are functionally null alleles, and the second / compound heterozygous variant then determines the phenotype. Changes at p.Arg683 are clearly associated with XP, whereas p.Arg112His, p.Arg722Trp, and changes at p.Arg658 are associated with TTD.; to: - Bi-allelic inactivation of XPD protein, a nucleotide excision repair (NER) signaling pathway component encoded by ERCC2 gene, has been associated with several defective DNA repair phenotypes, including xeroderma pigmentosum, photosensitive trichothiodystrophy, and cerebro-oculo-facio-skeletal syndrome.
- Severe, early onset of all three phenotypes have been reported
- Variable expressivity has been reported for Xeroderma pigmentosum, group D, MIM# 278730 where individuals can present with or without mild or severe neurologic abnormalities (GeneReviews)
- OMIM: The location of variants (mutagenic pattern) is consistent in determining the phenotype. Variants shared by both phenotypes are functionally null alleles, and the second / compound heterozygous variant then determines the phenotype. Changes at p.Arg683 are clearly associated with XP, whereas p.Arg112His, p.Arg722Trp, and changes at p.Arg658 are associated with TTD.
Prepair 1000+ v1.287 LRP5 Andrew Coventry reviewed gene: LRP5: Rating: GREEN; Mode of pathogenicity: None; Publications: 9056564 9831343 11719191 15346351 18602879; Phenotypes: Exudative vitreoretinopathy 4 MIM#601813, Osteoporosis-pseudoglioma syndrome MIM#259770; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Prepair 1000+ v1.258 COL4A4 Kate Scarff reviewed gene: COL4A4: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 20301386; Phenotypes: Alport syndrome 2, autosomal recessive MIM# 203780; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.248 F2 Marta Cifuentes Ochoa changed review comment from: Prothrombin deficiency type I, known as true prothrombin deficiency or 'hypoprothrombinemia,' is defined as plasma levels of prothrombin being less than 10% of normal with a concomitant decrease in activity. These patients have severe bleeding from birth, including umbilical cord hemorrhage, hematomas, ecchymoses, hematuria, mucosal bleeding, hemarthroses, intracranial bleeding, gastrointestinal bleeding, and menorrhagia.

HGNC approved symbol/name: F2
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges? N
Gene reported in >3 independent families

Type II deficiency, known as 'dysprothrombinemia,' is characterized by normal or low-normal synthesis of a dysfunctional protein; to: Prothrombin deficiency type I, known as true prothrombin deficiency or 'hypoprothrombinemia,' is defined as plasma levels of prothrombin being less than 10% of normal with a concomitant decrease in activity. These patients have severe bleeding from birth, including umbilical cord hemorrhage, hematomas, ecchymoses, hematuria, mucosal bleeding, hemarthroses, intracranial bleeding, gastrointestinal bleeding, and menorrhagia.

HGNC approved symbol/name: F2
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges? N
Gene reported in >3 independent families

Type II deficiency, known as 'dysprothrombinemia,' is characterized by normal or low-normal synthesis of a dysfunctional protein

AD forms and multifactorial conditions described for this gene not reportable in screening context
Prepair 1000+ v1.248 GNE Andrew Coventry changed review comment from: Nonaka myopathy - Well established gene disease relationship. However, age of onset of myopathy reported to usually occur between age 20 and 40. Marginal for childhood onset condition.

Thrombocytopenia - well reported association of affected individuals experiencing bleeding episodes that commence from neonatal to early childhood. Myopathy variably reported in those affected - possibly due to young age of individuals presenting with bleeding symptoms. Myopathy, when reported, occurs at similar age of onset to Nonaka. Publication (25257349) indicates myopathy onset in affected sibs at mid-late teens. Also reported renal complications at age 7. Mouse model for GNE knockout shows renal involvement (PMID: 17549255). Condition reported to have caused cerebral haemorrhages in neonatal period (PMID:29941673). Unsure if phenotypic variability of condition, and isolated bleeding phenotype (as in ClinGen) suitable or adequate for screening context.; to: Nonaka myopathy - Well established gene disease relationship. However, age of onset of myopathy reported to usually occur between age 20 and 40. Myopathy then progresses, usually over ~10 year period to then require wheelchair assistance for mobility. Severe condition but onset is marginal for childhood onset screening context.

Thrombocytopenia - well reported association of affected individuals experiencing bleeding episodes that commence from neonatal to early childhood. Myopathy variably reported in those affected - possibly due to young age of individuals presenting with bleeding symptoms. Myopathy, when reported, occurs at similar age of onset to Nonaka. Publication (25257349) indicates myopathy onset in affected sibs at mid-late teens. Also reported renal complications at age 7. Mouse model for GNE knockout shows renal involvement (PMID: 17549255). Condition reported to have caused cerebral haemorrhages in neonatal period (PMID:29941673). Unsure if phenotypic variability of condition, and isolated bleeding phenotype (as in ClinGen) suitable or adequate for screening context.
Prepair 1000+ v1.229 DYSF Marta Cifuentes Ochoa commented on gene: DYSF: Miyoshi myopathy (MM) is the most common form of recessive distal myopathy in populations with founder mutations such as Libyan and Israeli Jewish population, Italian and Spanish populations.The typical age of onset of MM lies between 15 and 30 years

Autosomal recessive limb-girdle muscular dystrophy type 2B (LGMD2B) is a subtype of autosomal recessive limb-girdle muscular dystrophy characterized by an onset in late adolescence or early adulthood of slowly progressive, proximal weakness and atrophy of shoulder and pelvic girdle muscles. Cardiac and respiratory muscles are not involved. Hypertrophy of the calf muscles and highly elevated serum creatine kinase levels are frequently observed.

Myopathy, distal, with anterior tibial onset is a rare genetic neuromuscular disease with characteristics of a progressive muscle weakness starting in the anterior tibial muscles, later involving lower and upper limb muscles, associated with an increased serum creatine kinase levels and absence of dysferlin on muscle biopsy. Patients become wheelchair dependent.

HGNC approved symbol/name: DYSF
Is the phenotype(s) severe and onset <18yo ? ? chidhood, early adulthood to late onset
Known technical challenges? N but large‐scale copy number variants have been identified.
Gene reported in >3 independent families

Unsure due genotype/phenotype correlation and onset
Prepair 1000+ v1.219 COL4A3 Zornitza Stark Phenotypes for gene: COL4A3 were changed from Alport syndrome, autosomal recessive, 203780 (3) to Alport syndrome 3b, autosomal recessive MIM#620536; MONDO:0957811
Prepair 1000+ v1.187 CEP152 Marta Cifuentes Ochoa changed review comment from: Primary microcephaly (head circumference more than 3 standard deviations below the age- and sex-matched population mean). Causes Intellectual disability.

Seckel syndrome is a rare autosomal recessive inherited disorder, which is mainly characterized by intrauterine and postnatal growth restrictions, microcephaly, intellectual disability, and a typical “bird-head” facial appearance.

Established gene-disease association.

Congenital onset, severe disorder

HGNC approved symbol/name: CEP152

Is the phenotype(s) severe and onset <18yo ? Y

Known technical challenges? N

Gene reported in >3 independent families; to: Primary microcephaly (head circumference more than 3 standard deviations below the age- and sex-matched population mean). Causes Intellectual disability.

Seckel syndrome is a rare autosomal recessive inherited disorder, which is mainly characterized by intrauterine and postnatal growth restrictions, microcephaly, intellectual disability, facial dysmorphic features.

Established gene-disease association.

Congenital onset, severe disorder

HGNC approved symbol/name: CEP152

Is the phenotype(s) severe and onset <18yo ? Y

Known technical challenges? N

Gene reported in >3 independent families
Prepair 1000+ v1.187 COLQ Marta Cifuentes Ochoa changed review comment from: Patients with congenital myasthenic syndromes present clinically with onset of variable muscle weakness between infancy and adulthood.

Well established gene-disease association, more than 10 families reported.
HGNC approved symbol/name: COLQ
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges?N; to: Patients with congenital myasthenic syndromes present clinically with onset of variable muscle weakness between infancy and adulthood.
Presentations:
-neonatal: respiratory insufficiency, multiple joint contractures (often described as arthrogryposis multiplex congenita) resulting from a lack of fetal movement in utero. Feeding difficulties, poor suck and cry, choking spells, eyelid ptosis, and facial, bulbar, and generalized weakness.In some individuals, long face, narrow jaw, and a high-arched palate have been reported
-childhood: delayed motr milestones, fluctuating eyelid ptosis and fixed or fluctuating extraocular muscle weakness. Ptosis may involve one or both eyelids. Facial and bulbar weakness with nasal speech and difficulties in coughing and swallowing may be present.Spinal deformity or muscle atrophy may occur
-limb-girdle

Well established gene-disease association, more than 10 families reported.
HGNC approved symbol/name: COLQ
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges?N
Prepair 1000+ v1.187 COL4A3 Marta Cifuentes Ochoa reviewed gene: COL4A3: Rating: GREEN; Mode of pathogenicity: None; Publications: 24052634, 35419377, 39071776; Phenotypes: Alport syndrome 3b, autosomal recessive MIM#620536, MONDO:0957811; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.187 CLN3 Marta Cifuentes Ochoa commented on gene: CLN3: Well established gene disease association.

Severe neurodegenerative disorder.

HGNC approved symbol/name: CLN3
Is the phenotype(s) severe and onset <18yo ? Y
Known technical challenges? N
Gene reported in >3 independent families
Prepair 1000+ v1.168 YIF1B Zornitza Stark edited their review of gene: YIF1B: Added comment: DEFINITIVE gene-disease association by ClinGen. Over 20 individuals now reported in the literature.; Changed publications: 33103737, 32006098, 36948290, 34373908
Prepair 1000+ v1.143 CSMD1 Krithika Murali gene: CSMD1 was added
gene: CSMD1 was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: CSMD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CSMD1 were set to PMID:38816421
Phenotypes for gene: CSMD1 were set to complex neurodevelopmental disorder MONDO:0100038
Review for gene: CSMD1 was set to GREEN
Added comment: PMID 38816421 Werren et al 2024 report 8 individuals from 6 families with biallelic missense CSMD1 variants identified through exome sequencing and subsequent gene-sharing efforts. Shared phenotypic features included: GDD, ID, microcephaly and polymicrogyria. Other features included dysmorphism, IUGR, hypotonia, arthrogryposis, seizures, opthalmological anomalies and other brain white matter anomalies Heterozygous parents were unaffected.

Loss of function is the postulated mechanism based on experimental data involving early-stage forebrain organoids differentiated from CSMD1 knockout human embryonic stem cells. ClinGen haploinsufficiency score of 1, however, this curation was last reviewed in 2018. This gene is within the scope of review for the ClinGen Autism and ID GCEP.
Sources: Literature
Prepair 1000+ v1.142 MFRP Zornitza Stark gene: MFRP was added
gene: MFRP was added to Prepair 1000+. Sources: Expert Review
Mode of inheritance for gene: MFRP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MFRP were set to 17167404; 18554571; 20361016
Phenotypes for gene: MFRP were set to Microphthalmia, isolated 5, MIM# 611040
Review for gene: MFRP was set to GREEN
Added comment: More than 10 unrelated families reported with bi-allelic variants in this gene associated with posterior microphthalmia with retinitis pigmentosa, foveoschisis, and optic disc drusen. Causes congenital visual impairment.
Sources: Expert Review
Prepair 1000+ v1.88 RMRP Lilian Downie Added comment: Comment when marking as ready: A range of phenotypes from mild skeletal dysplasia to a severe (anauxetic dysplasia), there is not a clear genotype phenotype correlation, however loss of function variants are more often reported in the severe phenotypes
Prepair 1000+ v1.82 AKR1D1 Ee Ming Wong changed review comment from: Well established gene-disease association.
Inborn error of bile acid metabolism. At least 6 cases (with 5 variants) in 5 families reported.
Severe condition with congenital onset, leads to liver failure.; to: Well established gene-disease association.
Inborn error of bile acid metabolism. At least 6 cases (with 5 variants) in 5 families reported.
Severe condition with congenital onset, leads to liver failure.
Prepair 1000+ v1.82 CYP17A1 Andrew Coventry changed review comment from: Established gene-disease association. Congenital onset. More than 100 families reported. Mechanism impacts hormone production in gonads and adrenal glands. Phenotype typically includes hypertension, low blood potassium, and abnormal development of sexual characteristics including genitalia (disorder of sexual development) in both males and females. Phenotypic spectrum for those affected is variable.; to: Established gene-disease association. Congenital onset. More than 100 families reported. Mechanism impacts hormone production in gonads and adrenal glands. Phenotype typically includes hypertension, low blood potassium, and abnormal development of sexual characteristics including genitalia (disorder of sexual development) in both males and females. Phenotypic spectrum of severity for those affected is variable.
Prepair 1000+ v1.76 CLCNKB Lilian Downie Added comment: Comment when marking as ready: The digenic inheritance is not clearly proven, patients with variants in both genes also had biallelic variants in this gene which is just as likely to have been the cause. Not enough evidence to report in carrier screening as a digenic condition. PMID: 18310267
Prepair 1000+ v1.76 ADAT3 Cassandra Muller changed review comment from: 20+ unrelated Arab families reported in the literature with the same homozygous missense variant in this gene causing intellectual disability (p.(Val128Met))
Other features can include microcephaly, growth failure, epilepsy.; to: 20+ unrelated Arab families reported in the literature with the same homozygous missense variant in this gene causing intellectual disability (p.(Val128Met)). One known family with a different variant in the same gene.
Other features can include microcephaly, growth failure, epilepsy.
Prepair 1000+ v1.67 ATM Lilian Downie Added comment: Comment when marking as ready: NB for reporting carrier mother may need additional breast cancer surveillance
Prepair 1000+ v1.65 MMADHC Lauren Rogers reviewed gene: MMADHC: Rating: ; Mode of pathogenicity: None; Publications: 33552904; Phenotypes: Homocystinuria, cblD type, variant 1 MIM#277410, Methylmalonic aciduria and homocystinuria, cblD type MIM#277410, Methylmalonic aciduria, cblD type, variant 2 MIM#277410, Disorders of cobalamin absorption, transport and metabolism; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Prepair 1000+ v1.65 CLCNKB Lucy Spencer changed review comment from: Is the phenotype(s) severe and onset <18yo? YES. CLCNKB mutations cause Bartter syndrome type 3 also called classic Bartter syndrome with renal salt wasting, hypokalemia, metabolic alkalosis, polyuria, polydipsia, and failure to thrive. It typically manifests in early childhood but late childhood or adulthood onset cases have been reported. Classic Bartter syndrome has a heterogeneous presentation from severe to very mild (PMIDs: 25810436, 24965226)

There is also a digenic inheritance known for this gene with variants in CLCNKA causing Bartter syndrome type 4b.; to: Is the phenotype(s) severe and onset <18yo? YES. CLCNKB mutations cause Bartter syndrome type 3 also called classic Bartter syndrome with renal salt wasting, hypokalemia, metabolic alkalosis, polyuria, polydipsia, and failure to thrive. It typically manifests in early childhood but late childhood or adulthood onset cases have been reported. Classic Bartter syndrome has a heterogeneous presentation from severe to very mild (PMIDs: 25810436, 24965226)

There is also a digenic inheritance known for this gene with variants in CLCNKA causing Bartter syndrome type 4b.
Prepair 1000+ v1.43 COQ4 Lauren Rogers changed review comment from: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.; to: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.
Prepair 1000+ v1.43 COQ4 Lauren Rogers changed review comment from: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.; to: At least 9 unrelated families reported.

Primary coenzyme Q10 deficiency-7 (COQ10D7) is an autosomal recessive disorder resulting from mitochondrial dysfunction. Most patients have onset of severe cardiac or neurologic symptoms soon after birth. IUGR reported.

Treatment: CoQ10 supplementation can limit disease progression and reverse some clinical manifestations.
Prepair 1000+ v1.7 ABCB7 Andrew Coventry changed review comment from: HGNC approved symbol/name: ABCB7
Reported cases of ataxia are typically childhood onset and progressive, anaemia reported to be mostly mild.; to: HGNC approved symbol/name: ABCB7
Reported cases of ataxia are typically childhood onset and progressive, anaemia reported to be mostly mild.
Prepair 1000+ v1.5 ADPRHL2 Zornitza Stark changed review comment from: Fourteen unrelated families reported with stress-induced childhood-onset neurodegeneration with variable ataxia and seizures (CONDSIAS), an autosomal recessive neurodegenerative disorder with onset in the first years of life following normal early development. The disorder is characterised by cyclic episodic deterioration in response to stress, such as infection or febrile illness. The severity is highly variable: some individuals develop seizures early in life that are associated with loss of developmental milestones and early sudden death in childhood, whereas others present at a later age with muscle weakness, gait ataxia, impaired speech, more subtle clinical deterioration, and cognitive decline. Neurologic involvement includes gait ataxia, cerebellar signs associated with cerebellar atrophy, generalized brain atrophy, impaired intellectual development, hearing loss, and peripheral neuropathy.

New HGNC approved name is ADPRS.; to: Fourteen unrelated families reported with stress-induced childhood-onset neurodegeneration with variable ataxia and seizures (CONDSIAS), an autosomal recessive neurodegenerative disorder with onset in the first years of life following normal early development. The disorder is characterised by cyclic episodic deterioration in response to stress, such as infection or febrile illness. The severity is highly variable: some individuals develop seizures early in life that are associated with loss of developmental milestones and early sudden death in childhood, whereas others present at a later age with muscle weakness, gait ataxia, impaired speech, more subtle clinical deterioration, and cognitive decline. Neurologic involvement includes gait ataxia, cerebellar signs associated with cerebellar atrophy, generalized brain atrophy, impaired intellectual development, hearing loss, and peripheral neuropathy.

New HGNC approved name is ADPRS.

To be upgraded to GREEN in next version of panel.
Prepair 1000+ v1.4 PIEZO1 Crystle Lee gene: PIEZO1 was added
gene: PIEZO1 was added to Prepair 1000+. Sources: Literature
Mode of inheritance for gene: PIEZO1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIEZO1 were set to PMID: 26333996
Phenotypes for gene: PIEZO1 were set to Lymphatic malformation 6, MIM#616843
Review for gene: PIEZO1 was set to GREEN
Added comment: Biallelic mutations in PIEZO1 reported in 10 patients from 6 families with generalized lymphatic dysplasia (GLD) This is characterized by a uniform, widespread lymphedema affecting all segments of the body, with systemic involvement such as intestinal and/or pulmonary lymphangiectasia, pleural effusions, chylothoraces and/or pericardial effusions.
Sources: Literature
Prepair 1000+ v1.3 POR Seb Lunke Added phenotypes Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis, 201750 (3) for gene: POR
Prepair 1000+ v1.3 COL4A5 Seb Lunke Added phenotypes Alport syndrome 1, X-linked for gene: COL4A5
Prepair 1000+ v1.3 COL4A4 Seb Lunke Added phenotypes Alport syndrome, autosomal recessive, 203780 (3) for gene: COL4A4
Prepair 1000+ v1.3 COL4A3 Seb Lunke Added phenotypes Alport syndrome, autosomal recessive, 203780 (3) for gene: COL4A3
Prepair 1000+ v0.168 HERC2 Crystle Lee edited their review of gene: HERC2: Added comment: Mapping issues reviewed: Majority of exons in this gene are well covered and there is no evidence of any recurrent variants. Insufficient mapping issues to exclude gene.

Note: most SNVs reported as VUS. Lots of multigenic CNVs reported.; Changed rating: GREEN
Prepair 1000+ v0.164 RYR1 Zornitza Stark commented on gene: RYR1: Hard to predict outcome in a screening context. However, multiple reports of severe perinatal outcomes.
Prepair 1000+ v0.135 PRKRA Zornitza Stark changed review comment from: Founder variant but multiple other families reported.

Pseudogene is a processed pseudogene and therefore false positives can be identified on manual inspection.; to: Founder variant but multiple other families reported.

Pseudogene is a processed pseudogene and therefore false positives can be identified on manual inspection. Risk of false negatives is low.
Prepair 1000+ v0.126 MPZ Zornitza Stark changed review comment from: More than 3 families reported with biallelic variants.; to: More than 3 families reported with biallelic variants. Childhood/congenital onset.
Prepair 1000+ v0.85 TECPR2 Crystle Lee gene: TECPR2 was added
gene: TECPR2 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: TECPR2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TECPR2 were set to 23176824; 26542466; 35130874
Phenotypes for gene: TECPR2 were set to Neuropathy, hereditary sensory and autonomic, type IX, with developmental delay, MIM#615031
Review for gene: TECPR2 was set to GREEN
Added comment: SPG49 is an autosomal recessive complicated form of spastic paraplegia. PMID 23176824 reported 4 Jewish Bukharian individuals homozygous for same founder variant and delayed psychomotor development, intellectual disability, and onset of spastic paraplegia in the first decade. Affected individuals also had dysmorphic features, thin corpus callosum on brain imaging, and episodes of central apnea, some of which were fatal. Three additional patients from unrelated non-Bukharian families reported in PMID 26542466, harboring two novel variants (c.1319delT, c.C566T) in this gene. In addition to intellectual disability and evolving spasticity, autonomic-sensory neuropathy accompanied by chronic respiratory disease and paroxysmal autonomic events were prominent
Sources: Literature
Prepair 1000+ v0.85 RS1 Crystle Lee gene: RS1 was added
gene: RS1 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: RS1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: RS1 were set to 15932525; 23453514; 23847049
Phenotypes for gene: RS1 were set to Retinoschisis (MIM#312700)
Review for gene: RS1 was set to AMBER
Added comment: - This gene is known to be associated with X-linked recessive disease, however, some affected females have been reported (OMIM).
- May not clinically manifest until middle life (OMIM)
- Many PTCs and missense reported. All result in same XLRS phenotype (although expression can be variable). Also a knockout mouse with similar phenotype.
- PTCs and missense involving cysteines tend to result in a more severe phenotype, whereas other missense can vary widely in severity (PMID: 23847049).
Sources: Literature
Prepair 1000+ v0.85 PYGM Crystle Lee gene: PYGM was added
gene: PYGM was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: PYGM was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: PYGM were set to McArdle disease (MIM#232600)
Review for gene: PYGM was set to AMBER
Added comment: Gene-disease association for bi-allelic variants is well established.

McCardle disease: glycogen storage disease type V (GSD5), characterized by onset of exercise intolerance and muscle cramps in childhood or adolescence. Transient myoglobinuria may occur after exercise, due to rhabdomyolysis. Severe myoglobinuria may lead to acute renal failure. Patients may report muscle weakness, myalgia, and lack of endurance since childhood or adolescence. Later in adult life, there is persistent and progressive muscle weakness and atrophy with fatty replacement. McArdle disease is a relatively benign disorder, except for possible renal failure as a complication of myoglobinuria

Clinical heterogeneity exists; about 10% of all affected individuals have mild manifestations (e.g., fatigue or poor stamina without contractures) and remain virtually asymptomatic during daily activities of living(Gene Reviews)
Sources: Literature
Prepair 1000+ v0.85 MCCC2 Crystle Lee gene: MCCC2 was added
gene: MCCC2 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: MCCC2 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: MCCC2 were set to 3-Methylcrotonyl-CoA carboxylase 2 deficiency (MIM#210210)
Review for gene: MCCC2 was set to RED
Added comment: Variants in this gene cause a biochemical defect. Relationship to clinical features is less certain.

Variants in this gene have been reported in multiple individuals with ID/regression/neurological phenotypes. However, ascertainment through NBS programs indicates most individuals remain asymptomatic and therefore caution should be applied in interpreting the clinical significance of variants in this gene (though they undoubtedly cause a biochemical phenotype).
Sources: Literature
Prepair 1000+ v0.61 HYAL1 Crystle Lee gene: HYAL1 was added
gene: HYAL1 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: HYAL1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HYAL1 were set to 10339581; 18344557; 21559944
Phenotypes for gene: HYAL1 were set to Mucopolysaccharidosis type IX (MIM#601492)
Review for gene: HYAL1 was set to RED
Added comment: Two families reported: in one, multiple soft tissue masses were the predominant clinical manifestation, and in the second, juvenile arthritis. Mouse model.

>15 pLoF variants reported as pathogenic in ClinVar. All submitted by a single lab and evidence suggests that the variant has not been previously reported.

Insufficient gene disease association. Not suitable for inclusion in a carrier screening panel
Sources: Literature
Prepair 1000+ v0.61 GRHPR Crystle Lee gene: GRHPR was added
gene: GRHPR was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: GRHPR was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GRHPR were set to 28569194; 10484776; 10484776; 24116921
Phenotypes for gene: GRHPR were set to Hyperoxaluria, primary, type II (MIM#260000)
Review for gene: GRHPR was set to AMBER
Added comment: Well established gene-disease association, more than 10 families reported.
Onset usually in infancy or early childhood, variable severity and some patients may be asymptomatic (OMIM; Gene Reviews)
Sources: Literature
Prepair 1000+ v0.61 GP9 Crystle Lee gene: GP9 was added
gene: GP9 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: GP9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GP9 were set to 8049428; 33553065; 32030720; 31484196
Phenotypes for gene: GP9 were set to Bernard-Soulier syndrome, type C (MIM#231200)
Review for gene: GP9 was set to AMBER
Added comment: Bernard-Soulier syndrome is a bleeding disorder caused by a defect in or deficiency of the platelet membrane von Willebrand factor receptor complex, glycoprotein Ib (GP Ib). GP Ib is composed of 4 subunits encoded by 4 separate genes: GP1BA, GP1BB, GP9, and GP5.

At least 3 unrelated families reported, animal model.
Sources: Literature
Prepair 1000+ v0.61 GJB1 Crystle Lee gene: GJB1 was added
gene: GJB1 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: GJB1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Phenotypes for gene: GJB1 were set to Charcot-Marie-Tooth neuropathy, X-linked dominant, 1 (MIM#302800)
Review for gene: GJB1 was set to AMBER
Added comment: CMTX has both demyelinating and axonal features. Well established gene-disease association, over 100 families reported. Variable phenotype with incomplete penetrance (OMIM)

PMID 31842800: Three unrelated males with GJB1 variants and recurrent episodes of reversible posterior leukoencephalopathy reported.
Sources: Literature
Prepair 1000+ v0.61 G6PD Crystle Lee gene: G6PD was added
gene: G6PD was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: G6PD was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Phenotypes for gene: G6PD were set to Hemolytic anemia, G6PD deficient (favism) (MIM#300908)
Review for gene: G6PD was set to AMBER
Added comment: Well established gene disease association. Most G6PD-deficient patients are asymptomatic throughout their life, but G6PD deficiency can be life-threatening

Note: OMIM states this is XLD, however it is males that a repeatedly reported affected and just carrier females; females are affected when HOMOZYGOUS, meaning this is primarily an XLR condition
Sources: Literature
Prepair 1000+ v0.61 F11 Crystle Lee gene: F11 was added
gene: F11 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: F11 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: F11 were set to 18446632; 15026311; 27723456
Phenotypes for gene: F11 were set to Factor XI deficiency, autosomal dominant (MIM#612416); Factor XI deficiency, autosomal recessive, (MIM#612416)
Review for gene: F11 was set to AMBER
Added comment: Recessive cases are more severe than heterozygous carriers, who may be asymptomatic despite having FXI deficiency (PMID:18446632). Dominant negative missense tend to have dominant inheritance patterns (PMID:15026311), while PTCs are generally recessive, though symptomatic carriers have been reported (OMIM).

PMID: 27723456 - "Bleeding due to FXI deficiency is variable and does not correlate with the plasma FXI level or FXI coagulant activity1"
Sources: Literature
Prepair 1000+ v0.61 CERKL Crystle Lee changed review comment from: More than 20 families reported, though some variants are recurrent (founder). This gene causes nonsyndromic retinal disease. Highly variable age of onset (7-45 years) and severity. There is also evidence of phenotypic intra- and inter-familial variability between patients with the same genotype.
Sources: Literature; to: More than 20 families reported, though some variants are recurrent (founder). This gene causes nonsyndromic retinal disease. Highly variable age of onset (7-45 years) and severity. There is also evidence of phenotypic intra- and inter-familial variability between patients with the same genotype.
Sources: Literature
Prepair 1000+ v0.61 CERKL Crystle Lee gene: CERKL was added
gene: CERKL was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: CERKL was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CERKL were set to 33322828
Phenotypes for gene: CERKL were set to Retinitis pigmentosa 26 (MIM#608380)
Review for gene: CERKL was set to RED
Added comment: More than 20 families reported, though some variants are recurrent (founder). This gene causes nonsyndromic retinal disease. Highly variable age of onset (7-45 years) and severity. There is also evidence of phenotypic intra- and inter-familial variability between patients with the same genotype.
Sources: Literature
Prepair 1000+ v0.61 AIRE Crystle Lee gene: AIRE was added
gene: AIRE was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: AIRE was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AIRE were set to 35521792; 28323927
Phenotypes for gene: AIRE were set to Autoimmune polyendocrinopathy syndrome , type I, with or without reversible metaphyseal dysplasia (MIM#240300)
Review for gene: AIRE was set to AMBER
Added comment: Well established gene disease association. Onset in childhood however phenotype can vary even between siblings with the same genotype. Therefore, it may be difficult (?impossible) to predict the severity/age of onset from the genotype

Most reported individuals have bi-allelic variants. AD inheritance has been reported in a single family (OMIM) p.G228W has been shown to have a dominant-negative effect by binding to WT AIRE (OMIM)
Sources: Literature
Prepair 1000+ v0.50 PROC Crystle Lee changed review comment from: Gene is associated AD and AR thrombophilia 3 due to protein C deficiency

AR form of condition is associated with variable severity and occasional late-onset of symptoms with homozygosity

Heterozygous 'carriers' of pathogenic variants in the PROC gene are said to have mild protein C deficiency which is often asymptomatic, but may involve recurrent venous thrombosis.

Difficult to define penetrance as represents risk factor for thrombophilia.

Challenge in interpretation and reporting in a carrier screening context; to: Gene is associated AD and AR thrombophilia 3 due to protein C deficiency

AR form of condition is associated with variable severity and occasional late-onset of symptoms with homozygosity

Heterozygous 'carriers' of pathogenic variants in the PROC gene are said to have mild protein C deficiency which is often asymptomatic, but may involve recurrent venous thrombosis.

Difficult to define penetrance as represents risk factor for thrombophilia.

Challenge in interpretation and reporting in a carrier screening context
Prepair 1000+ v0.31 ALG2 Crystle Lee commented on gene: ALG2: One additional variant reported in association with CDG on top of the previously reviewed patients reported with CDG/congenital myasthenia

PMID: 33644825: R251L reported in 3 probands from 2 families with CDG (same patients in PMID: 30397276)
Prepair 1000+ v0.0 SEC23A Crystle Lee changed review comment from: Amber in Mendeliome. Insufficient evidence for inclusion.

There is only one family reported with convincing evidence for gene-disease association, and we have downgraded this gene on other panels.; to: Amber in Mendeliome. Insufficient evidence for inclusion.

There is only one family reported with convincing evidence for gene-disease association, and we have downgraded this gene on other panels.
Prepair 1000+ v0.0 PIBF1 Crystle Lee gene: PIBF1 was added
gene: PIBF1 was added to Reproductive Carrier Screen_VCGS. Sources: Literature
Mode of inheritance for gene: PIBF1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIBF1 were set to 26167768; 30858804; 29695797; 33004012
Phenotypes for gene: PIBF1 were set to Joubert syndrome 33 (MIM#617767)
Review for gene: PIBF1 was set to AMBER
Added comment: Green gene to be considered for inclusion

Three unrelated families plus three Hutterite families reported with bi-allelic variants in this gene.
Sources: Literature
Prepair 1000+ v0.0 UROS Zornitza Stark gene: UROS was added
gene: UROS was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: UROS was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: UROS were set to Porphyria, congenital erythropoietic, 263700 (3)
Prepair 1000+ v0.0 SLC16A1 Zornitza Stark gene: SLC16A1 was added
gene: SLC16A1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: SLC16A1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SLC16A1 were set to Monocarboxylate transporter 1 deficiency, 616095 (3)
Prepair 1000+ v0.0 POR Zornitza Stark gene: POR was added
gene: POR was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: POR was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: POR were set to Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis, 201750 (3)
Prepair 1000+ v0.0 LRP5 Zornitza Stark gene: LRP5 was added
gene: LRP5 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: LRP5 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: LRP5 were set to Osteoporosis-pseudoglioma syndrome, 259770 (3)
Prepair 1000+ v0.0 LAMA1 Zornitza Stark gene: LAMA1 was added
gene: LAMA1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: LAMA1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: LAMA1 were set to Poretti-Boltshauser syndrome, 615960 (3)
Prepair 1000+ v0.0 FOLR1 Zornitza Stark gene: FOLR1 was added
gene: FOLR1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: FOLR1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: FOLR1 were set to Neurodegeneration due to cerebral folate transport deficiency, 613068 (3)
Prepair 1000+ v0.0 COL4A5 Zornitza Stark gene: COL4A5 was added
gene: COL4A5 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: COL4A5 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Phenotypes for gene: COL4A5 were set to Alport syndrome 1, X-linked
Prepair 1000+ v0.0 COL4A4 Zornitza Stark gene: COL4A4 was added
gene: COL4A4 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: COL4A4 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: COL4A4 were set to Alport syndrome, autosomal recessive, 203780 (3)
Prepair 1000+ v0.0 COL4A3 Zornitza Stark gene: COL4A3 was added
gene: COL4A3 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: COL4A3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: COL4A3 were set to Alport syndrome, autosomal recessive, 203780 (3)
Prepair 1000+ v0.0 ALAD Zornitza Stark gene: ALAD was added
gene: ALAD was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ALAD was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ALAD were set to Porphyria, acute hepatic, 612740 (3)
Prepair 1000+ v0.0 ACTA1 Zornitza Stark gene: ACTA1 was added
gene: ACTA1 was added to Reproductive Carrier Screen_VCGS. Sources: Mackenzie's Mission,Expert Review Green
Mode of inheritance for gene: ACTA1 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ACTA1 were set to Myopathy, congenital, with fiber-type disproportion 1, 255310 (3)