AOPEP p.Cys131=
c.393C>T · VCV3388353
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0512%, eas)
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 2.1 | GERP -0.25, phastCons 1 |
| Overall | ||
| CADD | 8.989 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0512%
East Asian · 23/44,900 alleles
Filtering AF
0.035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.00427%
69/1,614,076 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0512% | 1,952 |
| Middle Eastern | 0.0164% | 6,084 |
| South Asian | 0.00439% | 22,773 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.0033% | 30,257 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
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
- AOPEP
- Protein
- p.Cys131=
- Coding
- c.393C>T
- MANE Select
- NM_001193329
- Type
- single nucleotide variant
- Location
- chr9:94760176 (GRCh38)
- Gene constraint
- LOEUF 0.979 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.36
Similar variants
- 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
- FANCC c.844-1G>C 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-cys131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown