AVP p.Pro7=
c.21C>T · VCV4696384
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -11 | GERP -4.2 |
| Overall | ||
| CADD | 1.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.00112%
18/1,613,378 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| Finnishnot grpmax-eligible | 0.00316% | 31,663 |
| African / African-American | 0.00267% | 37,472 |
| Admixed American | 0.00167% | 60,008 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 0.000932% | 107,276 |
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.Pro7=
- Coding
- c.21C>T
- MANE Select
- NM_001243133 · reported on NM_000490
- Type
- single nucleotide variant
- Location
- chr20:3084654 (GRCh38)
- Structure
- AlphaFold pLDDT 81.16 · 27 PDB
- Residue 7
- the pyrin domain; an α-helix
Similar variants
- AVP p.Pro7Leu Pathogenic ⚠ 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
- AVP p.Ser87Phe Pathogenic/Likely pathogenic ★★ ⚠ same type
- NLRP3 p.Ala352Thr 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-pro7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown