GABRA2 p.Arg147=
c.441A>C · VCV3708913
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
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 -0.097 | GERP -0.53, phastCons 0.8 |
| Overall | ||
| CADD | 9.763 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,054 alleles
Filtering AF
0.00583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00118%
19/1,607,280 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,027 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,719 |
| South Asian | 0.00223% | 44,808 |
| African / African-American | 0.00134% | 74,592 |
| European (non-Finnish) | 0.000934% | 107,048 |
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.Arg147=
- Coding
- c.441A>C
- MANE Select
- NM_000807
- Type
- single nucleotide variant
- Location
- chr4:46312531 (GRCh38)
- Gene constraint
- LOEUF 0.49 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 83.71 · 15 PDB
- Residue 147
- a β-strand
Similar variants
- GABRA2 p.Arg147fs Uncertain significance ★★ same residue
- 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
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-arg147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown