RNF31 p.Ser515=
c.1545G>A · rs368285865 · VCV1078596
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.111%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -5.6 |
| Overall | ||
| CADD | 3.872 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
South Asian · 101/91,078 alleles
Filtering AF
0.0933%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0868%
Overall
0.0704%
1,137/1,614,136 alleles · rare
exomes 1,076/1,461,796 · genomes 61/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.111% | 902 |
| European (non-Finnish) | 0.0817% | 1,224 |
| Middle Eastern | 0.0495% | 2,020 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Finnishnot grpmax-eligible | 0.0344% | 2,908 |
| Admixed American | 0.0167% | 6,003 |
| African / African-American | 0.00933% | 10,722 |
| East Asian | 0.00669% | 14,957 |
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
- RNF31
- Protein
- p.Ser515=
- Coding
- c.1545G>A
- MANE Select
- NM_017999
- dbSNP
- rs368285865
- Type
- single nucleotide variant
- Location
- chr14:24151187 (GRCh38)
- Gene constraint
- LOEUF 0.37 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.39 · 36 PDB
Similar variants
- RNF31 p.Ala251Val Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala350Gly Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala45Val Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala501Thr Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala503Ser Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala503Thr Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala539Val Uncertain significance ★★ ⚠ same type
- RNF31 p.Ala904Thr 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/rnf31-p-ser515 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown