GNB1 p.Asp290=
c.870C>T · VCV3675309
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.351 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -5 |
| Overall | ||
| CADD | 5.884 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,090 alleles
Overall
6.2e-05%
1/1,614,158 alleles · very rare
exomes 1/1,461,850 · genomes 0/152,308 · 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
- GNB1
- Protein
- p.Asp290=
- Coding
- c.870C>T
- MANE Select
- NM_002074
- Type
- single nucleotide variant
- Location
- chr1:1789099 (GRCh38)
- Gene constraint
- LOEUF 0.222 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 97.04 · 1043 PDB
Similar variants
- GNB1 c.498-2A>G Likely pathogenic ★★ same type
- GNB1 p.Ala73Ser Pathogenic/Likely pathogenic ★★ same type
- GNB1 p.Ala73Thr Pathogenic/Likely pathogenic ★★ same type
- GNB1 p.Ala92Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- GNB1 p.Asp118Gly Pathogenic ★★ same type
- GNB1 p.Asp118His Likely pathogenic ★★ same type
- GNB1 p.Asp118Tyr Pathogenic ★★ same type
- GNB1 p.Asp76Asn Pathogenic/Likely pathogenic ★★ 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/gnb1-p-asp290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown