RNF31 p.Arg577Ter
c.1729C>T · rs755821957 · VCV2877176
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 21 |
| Splicing | ||
| SpliceAI | Δ0.85 | donor gain · deltas |
| Pangolin | Δ0.46 | gain · loss 0.25 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 43.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,878 |
| European (non-Finnish) | 8.47e-05% | 1,180,011 |
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.Arg577Ter
- Coding
- c.1729C>T
- MANE Select
- NM_017999
- dbSNP
- rs755821957
- Type
- single nucleotide variant
- Location
- chr14:24151371 (GRCh38)
- Gene constraint
- LOEUF 0.37 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.39 · 36 PDB
- Residue 577
- an α-helix; the 'interaction with rbck1' region; the uba domain
Similar variants
- RNF31 p.Arg577Gln 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
- RNF31 p.Ala539Val 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-arg577ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown