GRM7 p.Ser253=
c.759C>T · rs144380165 · VCV728651
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -4.8 |
| Overall | ||
| CADD | 8.586 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
East Asian · 579/44,864 alleles
Filtering AF
1.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.17%
Overall
0.0461%
744/1,613,324 alleles · low-frequency
exomes 687/1,461,150 · genomes 57/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.29% | 77 |
| South Asian | 0.0923% | 1,084 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,471 |
| Admixed American | 0.00667% | 14,997 |
| European (non-Finnish) | 0.00466% | 21,444 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,588 |
| African / African-American | 0.00267% | 37,486 |
| Finnishnot grpmax-eligible | 0.00156% | 63,994 |
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.Ser253=
- Coding
- c.759C>T
- MANE Select
- NM_000844
- dbSNP
- rs144380165
- Type
- single nucleotide variant
- Location
- chr3:7298706 (GRCh38)
- Gene constraint
- LOEUF 0.549 · pLI 0.37 (gnomAD)
- Structure
- AlphaFold pLDDT 84.48 · 12 PDB
- Residue 253
- a β-strand
Similar variants
- 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
- GRM7 p.Glu501Lys 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-ser253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown