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| Aminoacidopathy v1.133 | GCH1 | Bryony Thompson Mode of inheritance for gene: GCH1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Aminoacidopathy v1.113 | PYCR2 |
Sangavi Sivagnanasundram changed review comment from: Has been reported in 10 consanguineous families with different variants (frameshift, missense, splice). The affected individuals all had neurological clinical presentation however upon biochemical assessment, plasma proline levels were normal (showed no depletion). There is not enough evidence to indicate that these individuals have a phenotype consistent with an inborn error of amino acid metabolism. Sources: Other; to: Has been reported in 10 consanguineous families with different variants (frameshift, missense, splice). The affected individuals all had neurological clinical presentation along with other phenotypes including failure to thrive. Sources: Other |
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| Aminoacidopathy v1.113 | PYCR2 |
Sangavi Sivagnanasundram gene: PYCR2 was added gene: PYCR2 was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: PYCR2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PYCR2 were set to 25865492; 27130255 Phenotypes for gene: PYCR2 were set to Hypomyelinating leukodystrophy 10 MONDO:0014632; Disorders of ornithine, proline and hydroxyproline metabolism Review for gene: PYCR2 was set to RED Added comment: Has been reported in 10 consanguineous families with different variants (frameshift, missense, splice). The affected individuals all had neurological clinical presentation however upon biochemical assessment, plasma proline levels were normal (showed no depletion). There is not enough evidence to indicate that these individuals have a phenotype consistent with an inborn error of amino acid metabolism. Sources: Other |
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| Aminoacidopathy v1.113 | NFE2L2 |
Sangavi Sivagnanasundram gene: NFE2L2 was added gene: NFE2L2 was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: NFE2L2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: NFE2L2 were set to 29018201 Phenotypes for gene: NFE2L2 were set to Immunodeficiency, developmental delay, and hypohomocysteinemia MONDO:0060591; Disorders of glutathione metabolism Review for gene: NFE2L2 was set to GREEN Added comment: 4 unrelated patients with de novo missense variants affected with a multisystem disorder with failure to thrive, immunodeficiency and neurological symptoms including an inborn error of amino acid metabolism. Sources: Other |
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| Aminoacidopathy v1.113 | GPX4 |
Sangavi Sivagnanasundram gene: GPX4 was added gene: GPX4 was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: GPX4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GPX4 were set to 24706940; 32827718 Phenotypes for gene: GPX4 were set to Spondylometaphyseal dysplasia, Sedaghatian type MONDO:0009593; Disorders of glutathione metabolism Review for gene: GPX4 was set to GREEN Added comment: SSMD is an inborn error of gluthathione metabolism. Reports of four children (two were siblings from a consanguineous family) with SSMD. Parents were unaffected carriers. LoF is the mechanism of disease. Sources: Other |
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| Aminoacidopathy v1.113 | GSR |
Sangavi Sivagnanasundram gene: GSR was added gene: GSR was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: GSR was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GSR were set to 17185460; 31122244 Phenotypes for gene: GSR were set to Hemolytic anemia due to glutathione reductase deficiency MONDO:0019531; Disorders of glutathione metabolism Review for gene: GSR was set to AMBER Added comment: Not an established gene-disease association however there have been reports of two families reported with GR deficiency and there has been a report of functional evidence as well. More concrete evidence of biochemical abnormalities is required to promote the gene to green. Sources: Other |
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| Aminoacidopathy v1.113 | OPLAH |
Sangavi Sivagnanasundram gene: OPLAH was added gene: OPLAH was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: OPLAH was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: OPLAH were set to 27477828; 27604308 Phenotypes for gene: OPLAH were set to 5-oxoprolinase deficiency MONDO:0009825; Disorders of glutathione metabolism Review for gene: OPLAH was set to RED Added comment: Variants have been reported in individuals however it appears that this inborn error of glutathione metabolism appears to be of benign nature. Sources: Other |
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| Aminoacidopathy v1.113 | GCLC |
Sangavi Sivagnanasundram gene: GCLC was added gene: GCLC was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: GCLC was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GCLC were set to 28571779; 10515893; 18024385 Phenotypes for gene: GCLC were set to Gamma-glutamylcysteine synthetase deficiency MONDO:0009259; Disorders of glutathione metabolism Review for gene: GCLC was set to GREEN Added comment: Established gene-disease association with >3 unrelated probands reported with GCLC deficiency which is an inborn error of amino acid metabolism. Sources: Other |
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| Aminoacidopathy v1.101 | TAT | Zornitza Stark Marked gene: TAT as ready | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Aminoacidopathy v1.101 | TAT | Zornitza Stark Gene: tat has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Aminoacidopathy v1.101 | TAT | Zornitza Stark Classified gene: TAT as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Aminoacidopathy v1.101 | TAT | Zornitza Stark Gene: tat has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Aminoacidopathy v1.95 | TAT |
Sangavi Sivagnanasundram gene: TAT was added gene: TAT was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: TAT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TAT were set to 9544843; 16917729 Phenotypes for gene: TAT were set to tyrosinemia type II MONDO:0010160 Review for gene: TAT was set to GREEN Added comment: Well reported gene-disease association with affected individuals having reports of a deficiency in hepatic tyrosine aminotransferase (TAT). Classified Definitive by Aminoacidopathy GCEP on 29/06/2020 - https://search.clinicalgenome.org/CCID:006320 Sources: ClinGen |
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| Aminoacidopathy v1.95 | SUGCT |
Sangavi Sivagnanasundram gene: SUGCT was added gene: SUGCT was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SUGCT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SUGCT were set to 18926513; 28766179; 29421601 Phenotypes for gene: SUGCT were set to glutaric acidemia type 3 MONDO:0009283 Review for gene: SUGCT was set to AMBER Added comment: There is uncertain clinical relevance for this gene-disease association - reports of different clinical phenotypes between affected individuals and potentially a benign condition. Variants have been reported in >3 unrelated affected probands however their clinical presentations vary. Classified Moderate by Aminoacidopathy GCEP on 12/12/2022- https://search.clinicalgenome.org/CCID:006299 Sources: ClinGen |
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| Aminoacidopathy v1.95 | SLC6A8 |
Sangavi Sivagnanasundram gene: SLC6A8 was added gene: SLC6A8 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SLC6A8 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: SLC6A8 were set to 27604308; 16738945 Phenotypes for gene: SLC6A8 were set to creatine transporter deficiency MONDO:0010305 Review for gene: SLC6A8 was set to GREEN Added comment: Well-established gene disease association with reported individuals having error in creatine transport. Classified Definitive by Aminoacidopathy GCEP on 10/02/2020 - https://search.clinicalgenome.org/CCID:006200 Sources: ClinGen |
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| Aminoacidopathy v1.95 | SLC6A6 |
Sangavi Sivagnanasundram gene: SLC6A6 was added gene: SLC6A6 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SLC6A6 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC6A6 were set to 31903486; 31345061 Phenotypes for gene: SLC6A6 were set to hypotaurinemic retinal degeneration and cardiomyopathy MONDO:0007777 Review for gene: SLC6A6 was set to AMBER Added comment: 4 individuals reported with retinal degeneration while 2 (who are siblings) also reported cardiomyopathy. The proband (one of the siblings) was given oral taurine supplementation that reversed their phenotype (cardiomyopathy was reversed and the retinal degeneration was halted) (PMID: 31903486). Classified Limited by Aminoacidopathy GCEP on 10/03/2023 - https://search.clinicalgenome.org/CCID:006199 Sources: ClinGen |
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| Aminoacidopathy v1.95 | SLC6A19 |
Sangavi Sivagnanasundram gene: SLC6A19 was added gene: SLC6A19 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SLC6A19 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC6A19 were set to 15286787; 15286788; 18484095 Phenotypes for gene: SLC6A19 were set to Hartnup disease MONDO:0009324 Review for gene: SLC6A19 was set to GREEN Added comment: Established gene-disease association with >10 probands reported with clinical symptoms assocation with Hartnup disease. Mechanism of disease is LoF with affected individuals having a defect in amino acid transportation. Classified Definitive by Aminoacidopathy GCEP on 07/05/2020 - https://search.clinicalgenome.org/CCID:006196 Sources: ClinGen |
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| Aminoacidopathy v1.95 | SLC3A1 |
Sangavi Sivagnanasundram gene: SLC3A1 was added gene: SLC3A1 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SLC3A1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC3A1 were set to 8054986; 16374432; 8486766 Phenotypes for gene: SLC3A1 were set to cystinuria MONDO:0009067 Review for gene: SLC3A1 was set to GREEN Added comment: Established gene-disease association with reported individuals having biochemical abnormalities affecting cystine transportation. Classified Definitive by Aminoacidopathy GCEP on 29/06/2020 - https://search.clinicalgenome.org/CCID:006188 Sources: ClinGen |
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| Aminoacidopathy v1.95 | SLC25A13 |
Sangavi Sivagnanasundram gene: SLC25A13 was added gene: SLC25A13 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SLC25A13 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC25A13 were set to 18367750; 10369257; 19036621; 18392553; 11343053; 31607264 Phenotypes for gene: SLC25A13 were set to citrin deficiency MONDO:0016602 Review for gene: SLC25A13 was set to GREEN Added comment: Established gene-disease association with variants reported in >10 probands with reported biochemical abnormalities. Variants in this gene have been reported in both adult onset citrullinemia type 2 but also in individuals with neonatal intrahepatic cholestasis. Mechanism of disease is biallelic loss of function - significantly reduced or absent glutamate transport in and aspartate transport out of mitochondria depriving argininosuccinate synthetase leading to the accumulation of citrulline and ammonia. Classified Definitive by Aminoacidopathy GCEP on 23/07/2021 - https://search.clinicalgenome.org/CCID:006161 Sources: ClinGen |
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| Aminoacidopathy v1.66 | SLC1A3 |
Sangavi Sivagnanasundram gene: SLC1A3 was added gene: SLC1A3 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: SLC1A3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SLC1A3 were set to 27829685, 16116111, 29062094, 19139306, 29208948, 29066757, 32754645, 25497598 Phenotypes for gene: SLC1A3 were set to episodic ataxia type 6 MONDO:0012982 Mode of pathogenicity for gene: SLC1A3 was set to Other Review for gene: SLC1A3 was set to GREEN Added comment: Variants reported in 8 unrelated probands with reported errors in glutamate metabolism. Mechanism of disease varies depending on the mutation. The most severe variants (p.M128R, p.P290R, and p.T318A) appear to have gain of function mechanism. Classified as Definitive by ClinGen Aminoacidopathy GCEP on 09/10/2020 https://search.clinicalgenome.org/CCID:006154 Sources: ClinGen |
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| Aminoacidopathy v1.66 | OTC |
Sangavi Sivagnanasundram gene: OTC was added gene: OTC was added to Aminoacidopathy. Sources: Other Mode of inheritance for gene: OTC was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: OTC were set to 26059767 Phenotypes for gene: OTC were set to ornithine carbamoyltransferase deficiency MONDO:0010703 Review for gene: OTC was set to GREEN Added comment: Well established gene-disease association where affected individuals have a deficiency in carbamoyltransferase which affects the urea cycle. Classified as Definitive by ClinGen Aminoacidopathy GCEP on 29/10/2019 https://search.clinicalgenome.org/CCID:005712 Sources: Other |
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| Aminoacidopathy v1.66 | NAT8L |
Sangavi Sivagnanasundram gene: NAT8L was added gene: NAT8L was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: NAT8L was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NAT8L were set to 19807691 Phenotypes for gene: NAT8L were set to N-acetylaspartate deficiency MONDO:0013549 Review for gene: NAT8L was set to RED Added comment: Reported in one individual with N-acetylaspartate deficiency but also has other severe neurological features however the gene-disease association in this individual is unclear. Classified LIMITED by ClinGen Aminoacidopathy GCEP on 29/03/2024 - https://search.clinicalgenome.org/CCID:005565 Sources: ClinGen |
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| Aminoacidopathy v1.66 | MPST |
Sangavi Sivagnanasundram gene: MPST was added gene: MPST was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: MPST was set to Unknown Phenotypes for gene: MPST were set to encephalopathy due to beta-mercaptolactate-cysteine disulfiduria MONDO:0009585 Review for gene: MPST was set to RED Added comment: No reported individuals with deficiency in MPST enzymatic activity. No known disease relationship classification given by ClinGen Aminoacidopathy GCEP on 28/04/2023 - https://search.clinicalgenome.org/CCID:005413 Sources: ClinGen |
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| Aminoacidopathy v1.47 | GSTZ1 |
Sangavi Sivagnanasundram gene: GSTZ1 was added gene: GSTZ1 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: GSTZ1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GSTZ1 were set to 27876694 Phenotypes for gene: GSTZ1 were set to maleylacetoacetate isomerase deficiency MONDO:0060527 Review for gene: GSTZ1 was set to RED Added comment: Classified Moderate by ClinGen Aminoacidopathy GCEP on 09/09/2022 -https://search.clinicalgenome.org/CCID:005017 6 probands have been reported with mild hypersuccinylacetonaemia (MHSA). The reported individuals remained well without receiving any treatment or change in diet. Sources: ClinGen |
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| Aminoacidopathy v1.47 | GSS |
Sangavi Sivagnanasundram gene: GSS was added gene: GSS was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: GSS was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GSS were set to 17397529 Phenotypes for gene: GSS were set to inherited glutathione synthetase deficiency MONDO:0017909 Review for gene: GSS was set to GREEN Added comment: Classified Definitive by ClinGen Aminoacidopathy GCEP on 26/04/2019 -https://search.clinicalgenome.org/CCID:005016 Well established gene-disease association with reported individuals having errors in glutathione metabolism. Sources: ClinGen |
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| Aminoacidopathy v1.18 | GAMT |
Sangavi Sivagnanasundram gene: GAMT was added gene: GAMT was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: GAMT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GAMT were set to 20301745; 17466557; 16293431; 12701824; 2441567 Phenotypes for gene: GAMT were set to guanidinoacetate methyltransferase deficiency MONDO:0012999 Review for gene: GAMT was set to GREEN Added comment: Classified Definitive by ClinGen Aminoacidopathy GCEP on 25/01/2019 - https://search.clinicalgenome.org/CCID:004917 Well established gene-disease association. Reported as an inborn error of creatine metabolism. The two most commonly reported variants are p.Trp20Ser (c.59G>C) and c.327G>A (p.Lys109=). Both variants are pathogenic on ClinVar (>2 stars) and is classified pathogenic by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (FDA recognised database). Sources: ClinGen |
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| Aminoacidopathy v1.18 | CTH |
Sangavi Sivagnanasundram gene: CTH was added gene: CTH was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: CTH was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CTH were set to 20584029; 19428278; 12574942 Phenotypes for gene: CTH were set to cystathioninuria MONDO:0009058 Review for gene: CTH was set to GREEN Added comment: Classified Definitive by ClinGen Aminoacidopathy GCEP on 14/06/2019 - https://search.clinicalgenome.org/CCID:004594 Inborn error of cystathionine gamma-lyase metabolism and has been reported in >5 affected individuals. Sources: ClinGen |
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| Aminoacidopathy v1.9 | ARG1 |
Sangavi Sivagnanasundram gene: ARG1 was added gene: ARG1 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: ARG1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ARG1 were set to 16747805, 23859858, 1463019, 1598908, 12052859, 23920045 Phenotypes for gene: ARG1 were set to hyperargininemia MONDO:0008814 Review for gene: ARG1 was set to GREEN Added comment: Classified Definitive by ClinGen Aminoacidopathy GCEP on 29/06/2020 - https://search.clinicalgenome.org/CCID:004163 Reported in >5 unrelated probands with manifestations of hyperammonemia and hyperargininemia. It is an inborn error of L-arginine metabolism. Two knock out mouse models have been conducted attesting to the LoF mechanism of disease. Sources: ClinGen |
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| Aminoacidopathy v1.9 | ALDH18A1 |
Sangavi Sivagnanasundram gene: ALDH18A1 was added gene: ALDH18A1 was added to Aminoacidopathy. Sources: ClinGen Mode of inheritance for gene: ALDH18A1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: ALDH18A1 were set to 32017139, 26026163, 26320891 Phenotypes for gene: ALDH18A1 were set to P5CS deficiency MONDO:0100126 Added comment: Classified Definitive on 18/05/2021 by ClinGen Aminoacidopathy GCEP - https://search.clinicalgenome.org/CCID:004093 P5CS is an important enzyme in several amino acid pathways. >10 Individuals with abnormal biochemistry and function studies have been conducted. Mechanism of disease is variable LOF depending on the mutation present which results in the spectrum of severity in the phenotype. Dominant negative mutations have a less severe phenotype (AD cutis laxa/hsp) to the severely affected proteins having no activity (AR cutis laxa/hsp) (PMID: 32017139). Sources: ClinGen |
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| Aminoacidopathy v0.49 |
Bryony Thompson Panel status changed from internal to public Panel types changed to Royal Melbourne Hospital; Rare Disease |
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| Aminoacidopathy v0.0 | TAZ |
Bryony Thompson gene: TAZ was added gene: TAZ was added to Disorders of branched chain amino acid metabolism. Sources: Literature Mode of inheritance for gene: TAZ was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: TAZ were set to 29152456 Phenotypes for gene: TAZ were set to 3-methylglutaconic aciduria MONDO:0017359 |
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