GABRB3 p.Pro440=
c.1320T>C · rs1209124720 · VCV1998960
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
Conditions
2
epilepsy, childhood absence, susceptibility to, 1
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 0.018 | GERP -5.1, phastCons 0.049 |
| Overall | ||
| CADD | 4.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,944 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000186%
3/1,614,094 alleles · very rare
exomes 0/1,461,872 · genomes 3/152,222 · joint denominator
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
- GABRB3
- Protein
- p.Pro440=
- Coding
- c.1320T>C
- MANE Select
- NM_000814
- dbSNP
- rs1209124720
- Type
- single nucleotide variant
- Location
- chr15:26547895 (GRCh38)
- Gene constraint
- LOEUF 0.439 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.64 · 109 PDB
Similar variants
- GABRB3 p.Arg111Ter Pathogenic ★★ same condition
- GABRB3 p.Arg194Ter Pathogenic ★★ same condition
- GABRB3 p.Arg232Gln Pathogenic/Likely pathogenic ★★ same condition
- GABRB3 p.Arg96Ser Pathogenic/Likely pathogenic ★★ same condition
- GABRB3 p.Asp120Asn Pathogenic/Likely pathogenic ★★ same condition
- GABRB3 p.Glu77Gln Likely pathogenic ★★ ⚠ same condition
- GABRB3 p.Ile280Phe Likely pathogenic ★★ same condition
- GABRB3 p.Leu124Phe Pathogenic/Likely pathogenic ★★ same condition
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/gabrb3-p-pro440 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown