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Intellectual disability syndromic and non-syndromic

Gene: SATB1

Green List (high evidence)

SATB1 (SATB homeobox 1)
EnsemblGeneIds (GRCh38): ENSG00000182568
EnsemblGeneIds (GRCh37): ENSG00000182568
OMIM: 602075, Gene2Phenotype
SATB1 is in 4 panels

3 reviews

Sangavi Sivagnanasundram (Melbourne Health)

Green List (high evidence)

Classified as DEFINITIVE by ClinGen ID and Autism GCEP on 17/09/2024 - https://search.clinicalgenome.org/CCID:008481
Created: 8 Nov 2024, 3:20 a.m. | Last Modified: 8 Nov 2024, 3:20 a.m.
Panel Version: 0.6651

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
complex neurodevelopmental disorder MONDO:0100038

Publications

  • https://search.clinicalgenome.org/CCID:008481

Elena Savva (Victorian Clinical Genetics Services)

Green List (high evidence)

PMID: 33513338: 42 patients with SNVs. 28 de novo, 3 inherited from an affected parent.
Missense variants - more severe, profound ID
NMD PTCs - milder disease

Functional studies show missense variants have a STRONGER binding to downstream targets
Created: 1 Feb 2021, 4:52 a.m. | Last Modified: 1 Feb 2021, 4:52 a.m.
Panel Version: 0.3420

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Neurodevelopmental disorders

Publications

Mode of pathogenicity
Other

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Green List (high evidence)

Kohlschutter-Tonz syndrome-like (KTZSL) is characterized by global developmental delay with moderately to severely impaired intellectual development, poor or absent speech, and delayed motor skills. Although the severity of the disorder varies, many patients are nonverbal and have hypotonia with inability to sit or walk. Early-onset epilepsy is common and may be refractory to treatment, leading to epileptic encephalopathy and further interruption of developmental progress. Most patients have feeding difficulties with poor overall growth and dysmorphic facial features, as well as significant dental anomalies resembling amelogenesis imperfecta. This phenotype was reported in 28 patients (patients 13 to 40, PMID 33513338), including 9 patients from 3 families. Most variants were de novo, though some were inherited, suggestive of incomplete penetrance and variable expressivity.

Developmental delay with dysmorphic facies and dental anomalies (DEFDA) is characterized by generally mild global developmental delay with variably impaired intellectual development, walking by 2 to 3 years, and slow language acquisition. The severity of the disorder ranges from moderate cognitive deficits to mild learning difficulties or behavioral abnormalities. Most patients have dysmorphic facial features, often with abnormal dentition and nonspecific visual defects, such as myopia, astigmatism, and strabismus. Although rare, involvement of other systems, such as skeletal, cardiac, and gastrointestinal, may be present. 12 individuals from 11 families reported (one inherited variant, affected parent).
Created: 21 Mar 2021, 7:15 a.m. | Last Modified: 21 Mar 2021, 7:15 a.m.
Panel Version: 0.3538
PMID: 33057194 - Has been identified as a gene with significant de novo enrichment in a large trio study from the Deciphering Developmental Disorders study. 12 de novo (2 frameshift, 7 missense, 1 stopgain, 2 synonymous) identified in ~10,000 cases with developmental disorders (no other phenotype info provided hence Amber rating).
Sources: Literature
Created: 4 Nov 2020, 5:07 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Kohlschutter-Tonz syndrome-like, MIM# 619229; Developmental delay with dysmorphic facies and dental anomalies, MIM# 619228; Developmental disorders

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Kohlschutter-Tonz syndrome-like, MIM# 619229
  • Developmental delay with dysmorphic facies and dental anomalies, MIM# 619228
  • Neurodevelopmental disorder
  • intellectual disability
  • epilepsy
  • microcephaly
OMIM
602075
Clinvar variants
Variants in SATB1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

21 Mar 2021, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SATB1 were changed from Developmental delay with dysmorphic facies and dental anomalies, MIM# 619228; Neurodevelopmental disorder; intellectual disability; epilepsy; microcephaly to Kohlschutter-Tonz syndrome-like, MIM# 619229; Developmental delay with dysmorphic facies and dental anomalies, MIM# 619228; Neurodevelopmental disorder; intellectual disability; epilepsy; microcephaly

20 Mar 2021, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SATB1 were changed from Neurodevelopmental disorder; intellectual disability; epilepsy; microcephaly to Developmental delay with dysmorphic facies and dental anomalies, MIM# 619228; Neurodevelopmental disorder; intellectual disability; epilepsy; microcephaly

1 Feb 2021, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: SATB1 were changed from Developmental disorders to Neurodevelopmental disorder; intellectual disability; epilepsy; microcephaly

1 Feb 2021, Gel status: 3

Set publications

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Publications for gene: SATB1 were set to 33057194

1 Feb 2021, Gel status: 3

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: satb1 has been classified as Green List (High Evidence).

4 Nov 2020, Gel status: 2

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: satb1 has been classified as Amber List (Moderate Evidence).

4 Nov 2020, Gel status: 2

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: satb1 has been classified as Amber List (Moderate Evidence).

4 Nov 2020, Gel status: 1

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

gene: SATB1 was added gene: SATB1 was added to Intellectual disability syndromic and non-syndromic. Sources: Literature Mode of inheritance for gene: SATB1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SATB1 were set to 33057194 Phenotypes for gene: SATB1 were set to Developmental disorders Review for gene: SATB1 was set to AMBER