AVP p.Ser34=
c.102C>T · VCV3644925
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0786%, afr)
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 -7.9 | GERP -4.2 |
| Overall | ||
| CADD | 5.084 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0786%
African / African-American · 59/75,070 alleles
Filtering AF
0.0625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0567%
Overall
0.00812%
131/1,613,972 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0786% | 1,272 |
| Admixed American | 0.0117% | 8,574 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| European (non-Finnish) | 0.005% | 20,001 |
| East Asian | 0.00223% | 44,882 |
| South Asian | 0.0011% | 91,086 |
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.Ser34=
- Coding
- c.102C>T
- MANE Select
- NM_001243133 · reported on NM_000490
- Type
- single nucleotide variant
- Location
- chr20:3084573 (GRCh38)
- Structure
- AlphaFold pLDDT 81.16 · 27 PDB
- Residue 34
- the pyrin domain; a β-strand; a disulfide bond
Similar variants
- NLRP3 p.Lys34= 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
- 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-ser34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown