AOPEP p.Val402=
c.1206C>G · rs2538539280 · VCV2659320
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 0.56 | GERP 0.57, phastCons 0.99 |
| Overall | ||
| CADD | 2.281 | 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
- AOPEP
- Protein
- p.Val402=
- Coding
- c.1206C>G
- MANE Select
- NM_001193329
- dbSNP
- rs2538539280
- Type
- single nucleotide variant
- Location
- chr9:94800844 (GRCh38)
- Gene constraint
- LOEUF 0.979 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.36
- Residue 402
- a UniProt-annotated variant site (in dyt31)
Similar variants
- FANCC p.Gly402= Likely benign ★★ same residue
- AOPEP p.Gln235Ter Likely pathogenic ★★ same type
- FANCC c.1072+2T>A Likely pathogenic ★★ same type
- FANCC c.1155-2A>G Likely pathogenic ★★ same type
- FANCC c.522-1G>C Likely pathogenic ★★ same type
- FANCC c.687-1G>A Likely pathogenic ★★ same type
- FANCC c.843+1G>A Pathogenic/Likely pathogenic ★★ same type
- FANCC c.844-1G>A Pathogenic/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/aopep-p-val402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown