GRID2 p.Pro624=
c.1872G>A · rs188016557 · VCV2067224
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.478%, eas)
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 -3.6 |
| Overall | ||
| CADD | 0.737 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.478%
East Asian · 214/44,744 alleles
Filtering AF
0.426%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.405%
Overall
0.0267%
429/1,608,008 alleles · rare
exomes 387/1,456,184 · genomes 42/151,824 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.478% | 209 |
| South Asian | 0.106% | 946 |
| Remaining individualsnot grpmax-eligible | 0.0643% | 1,555 |
| Middle Eastern | 0.0332% | 3,010 |
| European (non-Finnish) | 0.00621% | 16,103 |
| African / African-American | 0.00535% | 18,691 |
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.Pro624=
- Coding
- c.1872G>A
- MANE Select
- NM_001510
- dbSNP
- rs188016557
- Type
- single nucleotide variant
- Location
- chr4:93490652 (GRCh38)
- Gene constraint
- LOEUF 0.332 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.07 · 6 PDB
Similar variants
- GRID2 p.Pro624Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro624 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown