RIN2 p.Arg310=
c.928A>C · rs1287779748 · VCV695396
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.11%, nfe)
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 1.4 | GERP -0.054, phastCons 1 |
| Overall | ||
| CADD | 8.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.11%
European (non-Finnish) · 6,987/331,662 alleles
Filtering AF
2.07%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.05%
Overall
1.54%
7,882/511,866 alleles · low-frequency
exomes 7,702/437,506 · genomes 180/74,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.11% | 47 |
| Remaining individualsnot grpmax-eligible | 1.55% | 65 |
| Ashkenazi Jewishnot grpmax-eligible | 0.555% | 180 |
| African / African-American | 0.531% | 188 |
| South Asian | 0.403% | 248 |
| Middle Eastern | 0.391% | 256 |
| Admixed American | 0.302% | 331 |
| Finnishnot grpmax-eligible | 0.28% | 357 |
| East Asian | 0.237% | 421 |
| Amishnot grpmax-eligible | 0.217% | 460 |
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.Arg310=
- Coding
- c.928A>C
- MANE Select
- NM_018993
- dbSNP
- rs1287779748
- Type
- single nucleotide variant
- Location
- chr20:19974953 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.30
- Residue 310
- the 'disordered' region
Similar variants
- RIN2 p.Arg310Met Uncertain significance ★ ⚠ same residue
- RIN2 p.Arg310fs 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
- RIN2 p.Arg255Thr 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-arg310 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown