GRM7 p.Pro40=
c.120G>T · rs752485323 · VCV2164556
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, amr)
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 2.3 | GERP -0.032, phastCons 1 |
| Overall | ||
| CADD | 12.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
Admixed American · 8/54,298 alleles
Filtering AF
0.00731%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00526%
Overall
0.000697%
11/1,577,888 alleles · ultra-rare
exomes 9/1,425,664 · genomes 2/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0147% | 6,787 |
| European (non-Finnish) | 0.000258% | 387,899 |
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
- GRM7
- Protein
- p.Pro40=
- Coding
- c.120G>T
- MANE Select
- NM_000844
- dbSNP
- rs752485323
- Type
- single nucleotide variant
- Location
- chr3:6861508 (GRCh38)
- Gene constraint
- LOEUF 0.549 · pLI 0.37 (gnomAD)
- Structure
- AlphaFold pLDDT 84.48 · 12 PDB
Similar variants
- GRM7 p.Pro40Leu Uncertain significance ★ ⚠ same residue
- GRM7 p.Ala29Thr Uncertain significance ★★ ⚠ same type
- GRM7 p.Arg493His Uncertain significance ★★ ⚠ same type
- GRM7 p.Arg614Cys Uncertain significance ★★ ⚠ same type
- GRM7 p.Arg9His Uncertain significance ★★ ⚠ same type
- GRM7 p.Asn505Ser Uncertain significance ★★ ⚠ same type
- GRM7 p.Cys770Ser Uncertain significance ★★ ⚠ same type
- GRM7 p.Glu140Gln 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/grm7-p-pro40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown