GABRB2 p.Pro16=
c.48C>T · rs1265831842 · VCV1160896
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00172%, amr)
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 2.2 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 11.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00172%
Admixed American · 1/58,158 alleles
Overall
0.000138%
2/1,448,862 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00172% | 58,158 |
| Finnishnot grpmax-eligible | 0.00158% | 63,226 |
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
- GABRB2
- Protein
- p.Pro16=
- Coding
- c.48C>T
- MANE Select
- NM_001371727
- dbSNP
- rs1265831842
- Type
- single nucleotide variant
- Location
- chr5:161546596 (GRCh38)
- Gene constraint
- LOEUF 0.426 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.65 · 31 PDB
Similar variants
- GABRB2 p.Pro16Ala Benign ★ same residue
- 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
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-pro16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown