AVP p.Cys65=
c.195C>T · VCV3609324
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00183%, amr)
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 8 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 14.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00183%
Admixed American · 1/54,760 alleles
Overall
0.000143%
2/1,399,486 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00183% | 54,760 |
| European (non-Finnish) | 8.63e-05% | 1,158,946 |
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
- AVP
- Protein
- p.Cys65=
- Coding
- c.195C>T
- MANE Select
- NM_001243133 · reported on NM_000490
- Type
- single nucleotide variant
- Location
- chr20:3083104 (GRCh38)
- Structure
- AlphaFold pLDDT 81.16 · 27 PDB
- Residue 65
- the pyrin domain; an α-helix; a disulfide bond
Similar variants
- AVP p.Cys65Ter Uncertain significance ★ same residue
- NLRP3 p.Ala65Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- NLRP3 p.Ala65= Likely benign ★ same residue
- AVP p.Ala19Thr Pathogenic ★★ ⚠ same type
- AVP p.Cys92Tyr Likely pathogenic ★★ same type
- AVP p.Glu108Ter Pathogenic ★★ same type
- AVP p.Gly54Arg Pathogenic ★★ same type
- AVP p.Gly96Asp 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/avp-p-cys65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown