RIN2 p.Thr332=
c.996G>A · rs368257270 · VCV1966778
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.216%, eas)
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 2.3 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 6.724 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.216%
East Asian · 92/42,646 alleles
Filtering AF
0.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.171%
Overall
0.0203%
323/1,588,866 alleles · rare
exomes 311/1,439,902 · genomes 12/148,964 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.216% | 464 |
| South Asian | 0.204% | 489 |
| Middle Eastern | 0.0169% | 5,934 |
| Remaining individualsnot grpmax-eligible | 0.0115% | 8,731 |
| European (non-Finnish) | 0.00309% | 32,378 |
| African / African-American | 0.00272% | 36,818 |
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
- RIN2
- Protein
- p.Thr332=
- Coding
- c.996G>A
- MANE Select
- NM_018993
- dbSNP
- rs368257270
- Type
- single nucleotide variant
- Location
- chr20:19975021 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.30
- Residue 332
- the 'disordered' region
Similar variants
- RIN2 p.Thr332Lys Uncertain significance ★★ ⚠ same residue
- RIN2 p.Thr332Ala Uncertain significance ★ ⚠ same residue
- RIN2 p.Thr332Met Uncertain significance ★ ⚠ same residue
- RIN2 p.Ala205Val Uncertain significance ★★ ⚠ same type
- RIN2 p.Ala72Thr Uncertain significance ★★ ⚠ same type
- RIN2 p.Ala8Thr Uncertain significance ★★ ⚠ same type
- RIN2 p.Arg135Cys Uncertain significance ★★ ⚠ same type
- RIN2 p.Arg170Trp 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/rin2-p-thr332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown