RIN1 p.Ala261=
c.783C>T · rs144796211 · VCV2641986
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9 | GERP -2.5 |
| Overall | ||
| CADD | 0.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
African / African-American · 12/72,392 alleles
Filtering AF
0.00951%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00745%
Overall
0.00227%
35/1,539,150 alleles · ultra-rare
exomes 23/1,386,934 · genomes 12/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0166% | 6,033 |
| European (non-Finnish) | 0.00192% | 52,053 |
| South Asian | 0.00127% | 78,764 |
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
- RIN1
- Protein
- p.Ala261=
- Coding
- c.783C>T
- MANE Select
- NM_004292
- dbSNP
- rs144796211
- Type
- single nucleotide variant
- Location
- chr11:66335016 (GRCh38)
- Gene constraint
- LOEUF 1.22 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.78
- Residue 261
- the 'disordered' region
Similar variants
- RIN1 p.Ala690= Benign ★★ same type
- RIN1 p.Gly737= Benign ★★ same type
- RIN1 p.Thr643= Benign/Likely benign ★★ same type
- RIN1 p.Val700Ile Benign ★★ same type
- RIN1 p.Ala111Thr Uncertain significance ★ ⚠ same type
- RIN1 p.Ala168Thr Uncertain significance ★ ⚠ same type
- RIN1 p.Ala221Ser Uncertain significance ★ ⚠ same type
- RIN1 p.Ala31Val Uncertain significance ★ ⚠ 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/rin1-p-ala261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown