GRM6 p.Gly485=
c.1455C>T · rs149519053 · VCV498251
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.122%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.85 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.69 | gain · loss 0.38 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.99 | GERP -3.5 |
| Overall | ||
| CADD | 21.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.122%
South Asian · 111/91,080 alleles
Filtering AF
0.103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0965%
Overall
0.0367%
593/1,614,110 alleles · rare
exomes 547/1,461,776 · genomes 46/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.122% | 821 |
| Admixed American | 0.05% | 2,001 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,404 |
| European (non-Finnish) | 0.0343% | 2,914 |
| Middle Eastern | 0.033% | 3,031 |
| African / African-American | 0.0147% | 6,825 |
| East Asian | 0.0111% | 8,974 |
| Finnishnot grpmax-eligible | 0.00469% | 21,319 |
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.Gly485=
- Coding
- c.1455C>T
- MANE Select
- NM_000843
- dbSNP
- rs149519053
- Type
- single nucleotide variant
- Location
- chr5:178986883 (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 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
- GRM6 p.Glu622Ter Pathogenic/Likely 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-gly485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown