GNB3 p.Asp153=
c.459T>C · rs200864177 · VCV1135293
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -4.9 |
| Overall | ||
| CADD | 3.702 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,086 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000929%
15/1,614,212 alleles · very rare
exomes 15/1,461,880 · genomes 0/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,362 |
| European (non-Finnish) | 0.00102% | 98,335 |
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
- GNB3
- Protein
- p.Asp153=
- Coding
- c.459T>C
- MANE Select
- NM_002075
- dbSNP
- rs200864177
- Type
- single nucleotide variant
- Location
- chr12:6843660 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.19 · 2 PDB
Similar variants
- GNB3 c.203+6G>A Uncertain significance ★★ same type
- GNB3 p.Ala106Ser Uncertain significance ★★ ⚠ same type
- GNB3 p.Ala231Thr Uncertain significance ★★ ⚠ same type
- GNB3 p.Ala64Thr Uncertain significance ★★ ⚠ same type
- GNB3 p.Arg129His Uncertain significance ★★ ⚠ same type
- GNB3 p.Arg137Gln Uncertain significance ★★ ⚠ same type
- GNB3 p.Arg150Cys Uncertain significance ★★ ⚠ same type
- GNB3 p.Arg42Gln 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/gnb3-p-asp153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown