GRM5 p.Ser1050=
c.3150C>T · rs201338353 · VCV738980
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0713%, sas)
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 7.8 | GERP -0.42, phastCons 1 |
| Overall | ||
| CADD | 13.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0713%
South Asian · 60/84,170 alleles
Filtering AF
0.0568%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0515%
Overall
0.00503%
78/1,551,056 alleles · ultra-rare
exomes 76/1,398,964 · genomes 2/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0713% | 1,403 |
| Remaining individualsnot grpmax-eligible | 0.00666% | 15,007 |
| Admixed American | 0.00195% | 51,218 |
| European (non-Finnish) | 0.00113% | 88,285 |
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.Ser1050=
- Coding
- c.3150C>T
- MANE Select
- NM_001143831
- dbSNP
- rs201338353
- Type
- single nucleotide variant
- Location
- chr11:88509081 (GRCh38)
- Gene constraint
- LOEUF 0.43 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 30 PDB
- Residue 1050
- the 'disordered' region
Similar variants
- 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
- GRM5 p.Lys678= Benign/Likely 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-ser1050 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown