AVPR2 p.Ala140=
c.420C>T · rs1278343735 · VCV2711737
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0158%, sas)
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 4.8 | GERP -0.41, phastCons 1 |
| Overall | ||
| CADD | 13.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0158%
South Asian · 9/57,001 alleles
Filtering AF
0.0082%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00615%
Overall
0.000914%
11/1,203,201 alleles · ultra-rare
exomes 10/1,089,458 · genomes 1/113,743 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0158% | 6,333 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,789 |
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
- AVPR2
- Protein
- p.Ala140=
- Coding
- c.420C>T
- MANE Select
- NM_000054
- dbSNP
- rs1278343735
- Type
- single nucleotide variant
- Location
- chrX:153905926 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
- Residue 140
- an α-helix
Similar variants
- AVPR2 p.Arg104Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AVPR2 p.Arg113Trp Pathogenic ★★ same type
- AVPR2 p.Arg137Cys Pathogenic ★★ same type
- AVPR2 p.Arg137His Pathogenic ★★ same type
- AVPR2 p.Arg181Cys Pathogenic ★★ same type
- AVPR2 p.Arg202Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AVPR2 p.Arg337Ter Pathogenic ★★ same type
- AVPR2 p.Asp85Asn 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/avpr2-p-ala140 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown