AVP p.Cys58=
c.174C>T · rs1489047363 · VCV3010989
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00192%, 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 9.3 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 13.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00192%
Admixed American · 1/52,100 alleles
Overall
6.52e-05%
1/1,534,628 alleles · very rare
exomes 1/1,382,292 · genomes 0/152,336 · joint denominator
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.Cys58=
- Coding
- c.174C>T
- MANE Select
- NM_000490
- dbSNP
- rs1489047363
- Type
- single nucleotide variant
- Location
- chr20:3083125 (GRCh38)
- Gene constraint
- LOEUF 1.923 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.83 · 5 PDB
- Residue 58
- a UniProt-annotated variant site (in ndi); a disulfide bond
Similar variants
- AVP p.Cys58Ter Likely pathogenic ★ same residue
- AVP p.Cys58Arg Uncertain significance ★ ⚠ 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
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-cys58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown