SIN3A p.Val663=
c.1989C>T · rs149841231 · VCV3013169
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.076%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 6.238 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.076%
African / African-American · 57/75,034 alleles
Filtering AF
0.0601%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0545%
Overall
0.00378%
61/1,614,116 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.076% | 1,316 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| Admixed American | 0.00167% | 60,006 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SIN3A
- Protein
- p.Val663=
- Coding
- c.1989C>T
- MANE Select
- NM_001145358
- dbSNP
- rs149841231
- Type
- single nucleotide variant
- Location
- chr15:75396362 (GRCh38)
- Gene constraint
- LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.67
- Residue 663
- the 'interaction with ncor1' region
Similar variants
- SIN3A p.Arg1140Ter Pathogenic ★★ same type
- SIN3A p.Arg471Ter Pathogenic ★★ same type
- SIN3A p.Arg537Ter Pathogenic ★★ same type
- SIN3A p.Arg553Ter Pathogenic/Likely pathogenic ★★ same type
- SIN3A p.Arg559Ter Pathogenic/Likely pathogenic ★★ same type
- SIN3A p.Arg718Ter Pathogenic/Likely pathogenic ★★ same type
- SIN3A p.Arg897Ter Pathogenic ★★ same type
- SIN3A p.Arg935Ter Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/sin3a-p-val663 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown