SIN3B p.Pro1115=
c.3345C>G · VCV4534284
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0172%, mid)
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 -16 | GERP -3.7 |
| Overall | ||
| CADD | 0.217 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0172%
Middle Eastern · 1/5,822 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.000744%
12/1,612,336 alleles · ultra-rare
exomes 11/1,460,104 · genomes 1/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0172% | 5,822 |
| South Asian | 0.00879% | 11,374 |
| European (non-Finnish) | 0.000254% | 393,226 |
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
- SIN3B
- Protein
- p.Pro1115=
- Coding
- c.3345C>G
- MANE Select
- NM_001297595
- Type
- single nucleotide variant
- Location
- chr19:16878679 (GRCh38)
- Gene constraint
- LOEUF 0.245 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.07 · 4 PDB
Similar variants
- SIN3B p.Ala534Thr Uncertain significance ★★ same type
- SIN3B p.Glu258Asp Uncertain significance ★★ ⚠ same type
- SIN3B p.His91Tyr Uncertain significance ★★ ⚠ same type
- SIN3B p.Pro281Ala Uncertain significance ★★ ⚠ same type
- SIN3B p.Val160Met Uncertain significance ★★ ⚠ same type
- SIN3B p.Val873Ile Uncertain significance ★★ ⚠ same type
- SIN3B c.1266+354G>A Benign ★★ same type
- SIN3B c.2954+6A>G Benign ★★ 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/sin3b-p-pro1115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown