GRID2 p.Gln775=
c.2325A>G · rs139320203 · VCV2654952
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0827%, afr)
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 -0.041 | GERP -4.8, phastCons 0.071 |
| Overall | ||
| CADD | 2.076 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0827%
African / African-American · 62/74,968 alleles
Filtering AF
0.0661%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0602%
Overall
0.00546%
88/1,611,790 alleles · ultra-rare
exomes 43/1,459,468 · genomes 45/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0827% | 1,209 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,201 |
| Admixed American | 0.0134% | 7,481 |
| European (non-Finnish) | 0.000509% | 196,415 |
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
- GRID2
- Protein
- p.Gln775=
- Coding
- c.2325A>G
- MANE Select
- NM_001510
- dbSNP
- rs139320203
- Type
- single nucleotide variant
- Location
- chr4:93626400 (GRCh38)
- Gene constraint
- LOEUF 0.332 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.07 · 6 PDB
Similar variants
- GRID2 p.Ala654Thr Pathogenic/Likely pathogenic ★★ same type
- GRID2 p.Thr649Ala Pathogenic/Likely pathogenic ★★ same type
- GRID2 p.Ala196Glu Uncertain significance ★★ ⚠ same type
- GRID2 p.Ala21Val Uncertain significance ★★ ⚠ same type
- GRID2 p.Ala574Ser Uncertain significance ★★ ⚠ same type
- GRID2 p.Arg229Gln Uncertain significance ★★ ⚠ same type
- GRID2 p.Arg297Gln Uncertain significance ★★ ⚠ same type
- GRID2 p.Arg300His 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/grid2-p-gln775 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown