RNF31 p.Pro169=
c.507A>G · VCV3716471
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, amr)
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 0.97 | GERP -1.8, phastCons 0.98 |
| Overall | ||
| CADD | 9.508 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
Admixed American · 15/60,002 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.000929%
15/1,614,076 alleles · ultra-rare
exomes 14/1,461,878 · genomes 1/152,198 · 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.Pro169=
- Coding
- c.507A>G
- MANE Select
- NM_017999
- Type
- single nucleotide variant
- Location
- chr14:24148653 (GRCh38)
- Gene constraint
- LOEUF 0.37 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.39 · 36 PDB
- Residue 169
- the 'polyubiquitin-binding' region
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-pro169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown