RNF2 p.Ser20=
c.60T>C · VCV4923514
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 2.8 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 11.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- RNF2
- Protein
- p.Ser20=
- Coding
- c.60T>C
- MANE Select
- NM_007212
- Type
- single nucleotide variant
- Location
- chr1:185087613 (GRCh38)
- Gene constraint
- LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.27 · 28 PDB
- Residue 20
- the 'interaction with hip2' region; an α-helix
Similar variants
- BAP1 p.Glu20= Benign/Likely benign ★★ same residue
- BAP1 p.Glu20Lys Uncertain significance ★ ⚠ same residue
- BAP1 p.Glu20fs Pathogenic ★ same residue
- BAP1 c.1117-1G>A Likely pathogenic ★★ same type
- BAP1 c.122+1G>A Pathogenic ★★ same type
- BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same type
- BAP1 c.122+5G>A Pathogenic/Likely pathogenic ★★ same type
- BAP1 c.122+5G>C Likely pathogenic ★★ 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/rnf2-p-ser20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown