RFC2 p.Pro260=
c.780A>C · rs782078961 · VCV1879690
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, sas)
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 -4 | GERP -7.5 |
| Overall | ||
| CADD | 6.813 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
South Asian · 13/88,276 alleles
Filtering AF
0.00869%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00691%
Overall
0.0009%
13/1,444,142 alleles · ultra-rare
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
- RFC2
- Protein
- p.Pro260=
- Coding
- c.780A>C
- MANE Select
- NM_181471
- dbSNP
- rs782078961
- Type
- single nucleotide variant
- Location
- chr7:74237422 (GRCh38)
- Gene constraint
- LOEUF 1.394 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63 · 16 PDB
- Residue 260
- an α-helix
Similar variants
- RFC2 p.Ala196Thr Uncertain significance ★★ ⚠ same type
- RFC2 c.759+8C>T Benign ★★ same type
- RFC2 p.Ala232Val Likely benign ★★ same type
- RFC2 p.Arg201= Benign ★★ same type
- RFC2 p.His33= Benign ★★ same type
- RFC2 p.Thr129= Benign ★★ same type
- RFC2 p.Ala150Val Uncertain significance ★ ⚠ same type
- RFC2 p.Ala15Val 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/rfc2-p-pro260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown