GABRB2 p.Ser260=
c.780C>G · rs1160036447 · VCV1475239
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
intellectual disability
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 0.21 | GERP -1.4, phastCons 0.9 |
| Overall | ||
| CADD | 6.497 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GABRB2
- Protein
- p.Ser260=
- Coding
- c.780C>G
- MANE Select
- NM_001371727
- dbSNP
- rs1160036447
- Type
- single nucleotide variant
- Location
- chr5:161334804 (GRCh38)
- Gene constraint
- LOEUF 0.426 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.65 · 31 PDB
- Residue 260
- an α-helix
Similar variants
- GABRB2 p.Ala304Val Pathogenic/Likely pathogenic ★★ same condition
- GABRB2 p.Arg293Trp Pathogenic/Likely pathogenic ★★ same condition
- GABRB2 p.Asp125Asn Pathogenic ★★ same condition
- GABRB2 p.Ile288Thr Likely pathogenic ★★ same condition
- GABRB2 p.Phe245Leu Pathogenic/Likely pathogenic ★★ same condition
- GABRB2 p.Thr284Ile Pathogenic/Likely pathogenic ★★ same condition
- GABRB2 p.Tyr301Cys Pathogenic/Likely pathogenic ★★ same condition
- GABRB2 p.Tyr301Phe 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/gabrb2-p-ser260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown