AVPR2 p.Leu53=
c.159G>C · rs2064958435 · VCV2699737
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00172%, 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 2 | GERP -0.82, phastCons 1 |
| Overall | ||
| CADD | 6.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00172%
African / African-American · 1/58,066 alleles
Overall
9.11e-05%
1/1,097,188 alleles · very rare
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.Leu53=
- Coding
- c.159G>C
- MANE Select
- NM_000054
- dbSNP
- rs2064958435
- Type
- single nucleotide variant
- Location
- chrX:153905665 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
- Residue 53
- an α-helix; a UniProt-annotated variant site (in ndi1)
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-leu53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown