GNB2 p.Thr86=
c.258C>T · VCV4897127
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, 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 2.3 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 11.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,090 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00062%
10/1,613,906 alleles · very rare
exomes 10/1,461,520 · genomes 0/152,386 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,773 |
| European (non-Finnish) | 0.000509% | 196,654 |
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
- GNB2
- Protein
- p.Thr86=
- Coding
- c.258C>T
- MANE Select
- NM_005273
- Type
- single nucleotide variant
- Location
- chr7:100677406 (GRCh38)
- Gene constraint
- LOEUF 0.372 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 96.89 · 1 PDB
Similar variants
- GNB2 p.Ala73Thr Pathogenic/Likely pathogenic ★★ same type
- GNB2 p.Gly77Glu Pathogenic/Likely pathogenic ★★ same type
- GNB2 p.Thr198Lys Uncertain significance ★★ ⚠ same type
- GNB2 p.Thr50Ile Uncertain significance ★★ ⚠ same type
- GNB2 c.268-11C>G Likely benign ★★ same type
- GNB2 p.Arg129= Likely benign ★★ same type
- GNB2 p.Arg48Gln Likely pathogenic ★ same type
- GNB2 p.Asn119Lys 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/gnb2-p-thr86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown