GABRB3 p.Phe56=
c.168C>T · rs2504095027 · VCV3049363
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000173%, nfe)
Conditions
1
GABRB3-related disorder
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 5.1 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 15.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000173%
European (non-Finnish) · 2/1,158,008 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000127%
2/1,569,294 alleles · very rare
exomes 2/1,417,486 · genomes 0/151,808 · 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.Phe56=
- Coding
- c.168C>T
- MANE Select
- NM_000814
- dbSNP
- rs2504095027
- Type
- single nucleotide variant
- Location
- chr15:26772685 (GRCh38)
- Gene constraint
- LOEUF 0.439 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.64 · 109 PDB
- Residue 56
- a turn
Disease context
GABRB3-related disorder
Similar variants
- GABRB3 p.Phe56Ser Uncertain significance ★ ⚠ same residue
- GABRB3 p.Arg96Ser Pathogenic/Likely pathogenic ★★ same condition
- GABRB3 p.Tyr302Cys Pathogenic/Likely pathogenic ★★ same condition
- GABRB3 p.Ala305Thr Likely pathogenic ★ same condition
- GABRB3 p.Ile255Val Likely pathogenic ★ ⚠ same condition
- GABRB3 p.Ile306Ser Likely pathogenic ★ same condition
- GABRB3 p.Met80Arg Conflicting classifications of pathogenicity ★ ⚠ same condition
- GABRB3 p.Asp126Val Uncertain significance ⚠ 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-phe56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown