TAB2 p.Gln169=
c.507A>G · rs962520265 · VCV1666818
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
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 0.79 | GERP -2.9, phastCons 0.98 |
| Overall | ||
| CADD | 4.724 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/60,006 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.00136%
22/1,614,088 alleles · ultra-rare
exomes 13/1,461,886 · genomes 9/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 5,001 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| South Asian | 0.0011% | 91,094 |
| European (non-Finnish) | 0.000508% | 196,674 |
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
- TAB2
- Protein
- p.Gln169=
- Coding
- c.507A>G
- MANE Select
- NM_001292034
- dbSNP
- rs962520265
- Type
- single nucleotide variant
- Location
- chr6:149378422 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.24 · 6 PDB
Similar variants
- TAB2 p.Gln169Ter Pathogenic ★ same residue
- TAB2 p.Gln169His Uncertain significance ★ ⚠ same residue
- TAB2 c.1604-2A>G Pathogenic/Likely pathogenic ★★ same type
- TAB2 c.1764+1G>A Pathogenic/Likely pathogenic ★★ same type
- TAB2 p.Arg546Ter Pathogenic/Likely pathogenic ★★ same type
- TAB2 p.Arg574Ter Likely pathogenic ★★ same type
- TAB2 p.Ala618Val Uncertain significance ★★ ⚠ same type
- TAB2 p.Arg173Lys 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/tab2-p-gln169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown