GRM5 p.Val203=
c.609G>A · rs199881528 · VCV756535
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0175%, nfe)
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 3.3 | GERP 4.7, phastCons 1 |
| Overall | ||
| CADD | 11.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0175%
European (non-Finnish) · 206/1,179,952 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.0138%
222/1,613,900 alleles · ultra-rare
exomes 217/1,461,744 · genomes 5/152,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0175% | 5,728 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| African / African-American | 0.00801% | 12,484 |
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.Val203=
- Coding
- c.609G>A
- MANE Select
- NM_001143831
- dbSNP
- rs199881528
- Type
- single nucleotide variant
- Location
- chr11:89047264 (GRCh38)
- Gene constraint
- LOEUF 0.43 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.16 · 30 PDB
- Residue 203
- an α-helix
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-val203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown