GRM5 p.Val709=
c.2127T>A · rs139898033 · VCV716425
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.19%, 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 -2.6 | GERP -5.5 |
| Overall | ||
| CADD | 0.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.19%
African / African-American · 892/75,054 alleles
Filtering AF
1.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1%
Overall
0.0633%
1,021/1,614,122 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.19% | 84 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| Admixed American | 0.065% | 1,539 |
| South Asian | 0.00439% | 22,770 |
| European (non-Finnish) | 0.00237% | 42,141 |
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
- GRM5
- Protein
- p.Val709=
- Coding
- c.2127T>A
- MANE Select
- NM_001143831
- dbSNP
- rs139898033
- Type
- single nucleotide variant
- Location
- chr11:88567556 (GRCh38)
- Gene constraint
- LOEUF 0.43 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 30 PDB
- Residue 709
- an α-helix
Similar variants
- GRM5 p.Val709Leu Uncertain significance ★ ⚠ same residue
- GRM5 c.1691-4G>T Likely benign ★★ same type
- GRM5 p.Arg925= Likely benign ★★ same type
- GRM5 p.Asn402= Benign ★★ same type
- GRM5 p.Gln63= Benign ★★ same type
- GRM5 p.Gly926= Benign ★★ same type
- GRM5 p.Gly978Ser Benign ★★ same type
- GRM5 p.Lys396= Benign ★★ 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/grm5-p-val709 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown