AVPR2 p.Pro159=
c.477G>A · rs377293345 · VCV2961429
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00625%, nfe)
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 -9.5 | GERP -3.4 |
| Overall | ||
| CADD | 0.013 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00625%
European (non-Finnish) · 56/895,515 alleles
Filtering AF
0.00494%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00444%
Overall
0.0049%
59/1,204,948 alleles · very rare
exomes 54/1,091,256 · genomes 5/113,692 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00625% | 15,991 |
| Admixed American | 0.00434% | 23,037 |
| African / African-American | 0.00173% | 57,782 |
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.Pro159=
- Coding
- c.477G>A
- MANE Select
- NM_000054
- dbSNP
- rs377293345
- Type
- single nucleotide variant
- Location
- chrX:153905983 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
- Residue 159
- an α-helix
Similar variants
- AVPR2 p.Pro159Leu Likely benign ★ same residue
- AVPR2 p.Pro159fs Likely pathogenic ★ same residue
- 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
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-pro159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown