RNF31 p.Arg485=
c.1455G>T · rs1213234913 · VCV2898524
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000606%, 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 -0.37 | GERP -4.6, phastCons 0.004 |
| Overall | ||
| CADD | 5.978 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000606%
European (non-Finnish) · 7/1,155,558 alleles
Filtering AF
0.000252%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000162%
Overall
0.000447%
7/1,567,240 alleles · very rare
exomes 5/1,415,010 · genomes 2/152,230 · joint denominator
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.Arg485=
- Coding
- c.1455G>T
- MANE Select
- NM_017999
- dbSNP
- rs1213234913
- Type
- single nucleotide variant
- Location
- chr14:24150855 (GRCh38)
- Gene constraint
- LOEUF 0.37 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.39 · 36 PDB
- Residue 485
- the 'polyubiquitin-binding' region
Similar variants
- RNF31 p.Arg485Gln Uncertain significance ★★ ⚠ same residue
- RNF31 p.Arg485Trp Uncertain significance ★★ ⚠ same residue
- 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
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-arg485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown