AVPR1B p.Pro90=
c.270A>G · rs202134542 · VCV757827
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0268%, 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 0.93 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 9.139 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0268%
European (non-Finnish) · 316/1,179,980 alleles
Filtering AF
0.0243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0234%
Overall
0.0211%
341/1,614,024 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0268% | 3,734 |
| Finnishnot grpmax-eligible | 0.0203% | 4,919 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| African / African-American | 0.00266% | 37,535 |
| Admixed American | 0.00167% | 60,024 |
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
- AVPR1B
- Protein
- p.Pro90=
- Coding
- c.270A>G
- MANE Select
- NM_000707
- dbSNP
- rs202134542
- Type
- single nucleotide variant
- Location
- chr1:206116621 (GRCh38)
- Gene constraint
- LOEUF 1.194 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.18
Similar variants
- AVPR1B p.Leu113Val Uncertain significance ★★ ⚠ same type
- AVPR1B p.Thr129= Likely benign ★★ same type
- AVPR1B p.Trp187Arg Likely benign ★★ same type
- AVPR1B p.Ala319Thr Uncertain significance ★ ⚠ same type
- AVPR1B p.Ala34Thr Uncertain significance ★ ⚠ same type
- AVPR1B p.Arg132Cys Uncertain significance ★ ⚠ same type
- AVPR1B p.Arg141His Uncertain significance ★ ⚠ same type
- AVPR1B p.Arg175Trp Uncertain significance ★ ⚠ 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/avpr1b-p-pro90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown