GRM5 p.Ser1041=
c.3123G>C · rs1012015295 · VCV2642258
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00119%, 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 -0.31 | GERP -1.4, phastCons 0.018 |
| Overall | ||
| CADD | 8.564 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00119%
South Asian · 1/83,988 alleles
Filtering AF
0.000369%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000268%
Overall
0.000646%
10/1,547,014 alleles · very rare
exomes 9/1,394,934 · genomes 1/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00119% | 83,988 |
| European (non-Finnish) | 0.000785% | 127,360 |
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.Ser1041=
- Coding
- c.3123G>C
- MANE Select
- NM_001143831
- dbSNP
- rs1012015295
- Type
- single nucleotide variant
- Location
- chr11:88509108 (GRCh38)
- Gene constraint
- LOEUF 0.43 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 30 PDB
- Residue 1041
- 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-ser1041 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown