GRIA3 p.Pro625=
c.1875A>G · VCV3689644
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00355%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.44 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8 | GERP 0.6, phastCons 1 |
| Overall | ||
| CADD | 15.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00355%
African / African-American · 2/56,297 alleles
Filtering AF
0.000589%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000221%
Overall
0.000253%
3/1,185,881 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00355% | 28,148 |
| Remaining individualsnot grpmax-eligible | 0.00215% | 46,602 |
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
- GRIA3
- Protein
- p.Pro625=
- Coding
- c.1875A>G
- MANE Select
- NM_007325
- Type
- single nucleotide variant
- Location
- chrX:123417776 (GRCh38)
- Structure
- AlphaFold pLDDT 83.98
Similar variants
- GRIA3 p.Ala650Val Pathogenic/Likely pathogenic ★★ same type
- GRIA3 p.Arg216Ter Pathogenic/Likely pathogenic ★★ same type
- GRIA3 p.Arg394Ter Pathogenic/Likely pathogenic ★★ same type
- GRIA3 c.1878-3T>C Uncertain significance ★★ same type
- GRIA3 c.696+5G>A Uncertain significance ★★ same type
- GRIA3 p.Ala148Thr Uncertain significance ★★ ⚠ same type
- GRIA3 p.Ala14Thr Uncertain significance ★★ ⚠ same type
- GRIA3 p.Ala176Glu 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/gria3-p-pro625 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown