GRM6 p.Phe799=
c.2397C>T · rs17078875 · VCV99644
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 7.5%, nfe) — too common for a highly-penetrant pathogenic allele
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 -1 | GERP -4.2 |
| Overall | ||
| CADD | 10.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.5%
European (non-Finnish) · 88,470/1,179,846 alleles
Filtering AF
7.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.44%
Overall
6.29%
101,443/1,614,008 alleles · common
exomes 94,738/1,461,676 · genomes 6,705/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 7.5% | 13 |
| Finnishnot grpmax-eligible | 6.58% | 15 |
| Remaining individualsnot grpmax-eligible | 5.45% | 18 |
| Ashkenazi Jewishnot grpmax-eligible | 3.68% | 27 |
| Admixed American | 2.47% | 41 |
| South Asian | 2.05% | 49 |
| Amishnot grpmax-eligible | 1.54% | 65 |
| African / African-American | 1.11% | 90 |
| Middle Eastern | 1.04% | 96 |
| East Asian | 0.0111% | 8,976 |
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
- GRM6
- Protein
- p.Phe799=
- Coding
- c.2397C>T
- MANE Select
- NM_000843
- dbSNP
- rs17078875
- Type
- single nucleotide variant
- Location
- chr5:178982949 (GRCh38)
- Gene constraint
- LOEUF 1.229 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.90 · 5 PDB
Similar variants
- GRM6 p.Phe799Leu Uncertain significance ★ ⚠ same residue
- GRM6 c.722-2A>C Likely pathogenic ★★ same type
- GRM6 p.Arg238Ter Pathogenic ★★ same type
- GRM6 p.Arg446Ter Pathogenic ★★ same type
- GRM6 p.Arg621Ter Pathogenic ★★ same type
- GRM6 p.Gln488Ter Pathogenic ★★ same type
- GRM6 p.Gln681Ter Pathogenic/Likely pathogenic ★★ same type
- GRM6 p.Gln708Ter Pathogenic ★★ 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/grm6-p-phe799 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown