SIN3A p.Leu484=
c.1452A>G · rs143312992 · VCV717738
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, 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 -0.64 | GERP -2.8, phastCons 0.009 |
| Overall | ||
| CADD | 5.097 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/74,880 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00989%
Overall
0.00149%
24/1,613,774 alleles · ultra-rare
exomes 14/1,461,676 · genomes 10/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 4,992 |
| South Asian | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000678% | 147,483 |
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.Leu484=
- Coding
- c.1452A>G
- MANE Select
- NM_001145358
- dbSNP
- rs143312992
- Type
- single nucleotide variant
- Location
- chr15:75401926 (GRCh38)
- Gene constraint
- LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.67
- Residue 484
- the 'interaction with sap30' region; the pah 3 domain
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-leu484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown