RNF168 p.Arg477=
c.1431C>T · rs143993777 · VCV1160151
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0658%, mid)
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 -0.19 | GERP -3.8 |
| Overall | ||
| CADD | 0.708 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0658%
Middle Eastern · 4/6,082 alleles
Filtering AF
0.0466%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0421%
Overall
0.00874%
141/1,613,744 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0658% | 1,521 |
| South Asian | 0.0593% | 1,685 |
| Admixed American | 0.0284% | 3,527 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| European (non-Finnish) | 0.00449% | 22,263 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,590 |
| East Asian | 0.00223% | 44,898 |
| African / African-American | 0.00134% | 74,888 |
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
- RNF168
- Protein
- p.Arg477=
- Coding
- c.1431C>T
- MANE Select
- NM_152617
- dbSNP
- rs143993777
- Type
- single nucleotide variant
- Location
- chr3:196472104 (GRCh38)
- Gene constraint
- LOEUF 1.406 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.97 · 39 PDB
- Residue 477
- the 'disordered' region
Similar variants
- RNF168 p.Arg477Cys Uncertain significance ★ ⚠ same residue
- RNF168 p.Arg477Gly Uncertain significance ★ ⚠ same residue
- RNF168 p.Arg477His Uncertain significance ★ ⚠ same residue
- RNF168 p.Arg131Ter Pathogenic/Likely pathogenic ★★ same type
- RNF168 p.Arg165Ter Pathogenic/Likely pathogenic ★★ same type
- RNF168 p.Glu138Ter Pathogenic/Likely pathogenic ★★ same type
- RNF168 p.Ala141Val Uncertain significance ★★ ⚠ same type
- RNF168 p.Ala7Ser 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/rnf168-p-arg477 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown