GPR82 p.Val170=
c.510T>C · rs141461559 · VCV2660355
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0185%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 3.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0185%
European (non-Finnish) · 165/890,575 alleles
Filtering AF
0.0162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0152%
Overall
0.0145%
175/1,204,894 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0185% | 5,397 |
| Remaining individualsnot grpmax-eligible | 0.0105% | 9,481 |
| Finnishnot grpmax-eligible | 0.00429% | 23,287 |
| African / African-American | 0.0035% | 28,534 |
| Admixed American | 0.00219% | 45,736 |
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
- GPR82
- Protein
- p.Val170=
- Coding
- c.510T>C
- MANE Select
- NM_001367721 · reported on NM_080817
- dbSNP
- rs141461559
- Type
- single nucleotide variant
- Location
- chrX:41727536 (GRCh38)
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/gpr82-p-val170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown