Intellectual disability syndromic and non-syndromic
Gene: SATB1

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

Created: 8 Nov 2024, 3:20 a.m.
Last Modified: 8 Nov 2024, 3:20 a.m.
Panel version: 0.6651

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

PMID: 33513338
33057194

Mode of pathogenicity
Other

Created: 1 Feb 2021, 4:52 a.m.
Last Modified: 1 Feb 2021, 4:52 a.m.
Panel version: 0.3420

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

33057194

Created: 4 Nov 2020, 5:07 a.m.

Panel version: 0.3538

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