GABRA2 p.Pro382=
c.1146A>G · rs753313894 · VCV1615168
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0447%, 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 -3.6 | GERP -2.4 |
| Overall | ||
| CADD | 5.001 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0447%
East Asian · 20/44,784 alleles
Filtering AF
0.0295%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0247%
Overall
0.00186%
30/1,611,780 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0447% | 2,239 |
| Admixed American | 0.00837% | 11,950 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,184 |
| South Asian | 0.0022% | 45,521 |
| African / African-American | 0.00134% | 74,716 |
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
- GABRA2
- Protein
- p.Pro382=
- Coding
- c.1146A>G
- MANE Select
- NM_000807
- dbSNP
- rs753313894
- Type
- single nucleotide variant
- Location
- chr4:46250518 (GRCh38)
- Gene constraint
- LOEUF 0.49 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 83.71 · 15 PDB
Similar variants
- GABRA2 p.Ala332Val Pathogenic/Likely pathogenic ★★ same type
- GABRA2 p.Pro280Leu Pathogenic/Likely pathogenic ★★ same type
- GABRA2 p.Thr294Ile Pathogenic/Likely pathogenic ★★ same type
- GABRA2 c.1059+1G>A Uncertain significance ★★ same type
- GABRA2 c.1060-5643C>T Uncertain significance ★★ same type
- GABRA2 c.1060-5644A>G Uncertain significance ★★ same type
- GABRA2 p.Arg301Trp Uncertain significance ★★ ⚠ same type
- GABRA2 p.Arg56Trp 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/gabra2-p-pro382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown