GRM2 p.Val865=
c.2595G>A · rs147758967 · VCV786879
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.389%, 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 |
|---|---|---|
| Pangolin | Δ0.23 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.23 | GERP -3.4, phastCons 0.026 |
| Overall | ||
| CADD | 0.771 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.389%
African / African-American · 292/75,024 alleles
Filtering AF
0.352%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.338%
Overall
0.0219%
353/1,614,070 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.389% | 257 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| Admixed American | 0.045% | 2,223 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 8.47e-05% | 1,179,948 |
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
- GRM2
- Protein
- p.Val865=
- Coding
- c.2595G>A
- MANE Select
- NM_000839
- dbSNP
- rs147758967
- Type
- single nucleotide variant
- Location
- chr3:51718088 (GRCh38)
- Gene constraint
- LOEUF 0.75 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.17 · 31 PDB
Similar variants
- GRM2 p.Asn824= Benign ★★ same type
- GRM2 p.Ala127Glu Uncertain significance ★ ⚠ same type
- GRM2 p.Ala275Val Uncertain significance ★ same type
- GRM2 p.Ala281Val Uncertain significance ★ ⚠ same type
- GRM2 p.Ala287Val Uncertain significance ★ ⚠ same type
- GRM2 p.Ala363Thr Uncertain significance ★ ⚠ same type
- GRM2 p.Ala430Val Uncertain significance ★ same type
- GRM2 p.Ala47Val 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/grm2-p-val865 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown