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Intellectual disability

Gene: SART3

Amber List (moderate evidence)
SART3 (squamous cell carcinoma antigen recognized by T-cells 3)
EnsemblGeneIds (GRCh38): ENSG00000075856
EnsemblGeneIds (GRCh37): ENSG00000075856
OMIM: 611684, Gene2Phenotype
SART3 is in 8 panels

1 review

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are six unrelated families reported with biallelic SART3 variants and Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis. Hence, this gene can be promoted to green rating in the next GMS update.
Created: 3 Nov 2026, 8:19 p.m. | Last Modified: 3 Nov 2026, 8:19 p.m.
Panel Version: 11.79
PMID:37296101 (2023) reported nine individuals from six different families presenting with a congenital syndrome characterised by gonadal dysgenesis in 46,XY individuals, intellectual disability, global developmental delay and overlapping neurological findings, including hypoplasia of the corpus callosum, cerebral and cerebellar anomalies. They were identified with either homozygous or compound heterozygous variants in the SART3 gene.

Severity of ID was severe in four patients, profound in one, moderate in one, mild-moderate in two and unreported in one. The age of patients at first examination ranged from 1 month to 7 years of age. Spasticity was reported in three patients (mild in two), mild ataxia reported in two and three patients were not walking on last examination. Cerebellar vermis atrophy was reported in six patients, of which it was mild in four.

Knockdown of the Drosophila orthologue of SART3 revealed a conserved role in testicular and neuronal development and human induced pluripotent stem cells carrying patient variants in SART3 demonstrated aberrant gonadal and neuronal differentiation in vitro. The authors tentatively termed this a spliceosomopathy as INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis).

This gene has been associated with relevant phenotype in Gene2Phenotype (with 'moderate' rating on the DD panel), but not yet in OMIM (last accessed 03 November 2026).
Sources: Literature
Created: 3 Nov 2026, 8:15 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
neurodevelopmental disorder, MONDO:0700092; 46 XY differences of sex development, MONDO:0020040

Publications

Created: 3 Nov 2026, 8:15 p.m.

Panel version: 11.78

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • neurodevelopmental disorder, MONDO:0700092
  • 46 XY differences of sex development, MONDO:0020040
Tags
Q4_26_promote_green
OMIM
611684
Clinvar variants
Variants in SART3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

3 Nov 2026, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: sart3 has been classified as Amber List (Moderate Evidence).

3 Nov 2026, Gel status: 1

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q4_26_promote_green tag was added to gene: SART3.

3 Nov 2026, Gel status: 1

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

Achchuthan Shanmugasundram (Genomics England Curator)

gene: SART3 was added gene: SART3 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: SART3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SART3 were set to 37296101 Phenotypes for gene: SART3 were set to neurodevelopmental disorder, MONDO:0700092; 46 XY differences of sex development, MONDO:0020040 Review for gene: SART3 was set to GREEN