SIN3A

Chr 15AD

SIN3 transcription regulator family member A

Also known as: CHR15DELq24, DEL15Q24, WITKOS

NCBI Gene: 25942ENSG00000169375UniProt: Q96ST3OMIM: 607776

The protein encoded by this gene is a transcriptional regulatory protein. It contains paired amphipathic helix (PAH) domains, which are important for protein-protein interactions and may mediate repression by the Mad-Max complex. [provided by RefSeq, Jul 2008]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Witteveen-Kolk syndromeMIM #613406
AD

Clinical highlights

Gene-disease validity (ClinGen)
SIN3A-related intellectual disability syndrome · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
45
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.07
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — SIN3A
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.07LOEUF
pLI 1.000
Z-score 7.50
OE 0.01 (0.00–0.07)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
4.39Z-score
OE missense 0.54 (0.49–0.59)
386 obs / 717.0 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.01 (0.00–0.07)
0≤0.351.4
Missense OE?0.54 (0.49–0.59)
0≤0.61.4
Synonymous OE?0.98
0≤1.21.6
LoF obs/exp: 1 / 67.4Missense obs/exp: 386 / 717.0Syn Z: 0.19

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SIN3A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients