TAB2 p.Glu125=
c.375G>A · rs116851068 · VCV1554981
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.533%, eas)
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 5.3 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 5.884 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.533%
East Asian · 239/44,880 alleles
Filtering AF
0.477%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.456%
Overall
0.0193%
311/1,614,218 alleles · rare
exomes 271/1,461,888 · genomes 40/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.533% | 188 |
| Ashkenazi Jewishnot grpmax-eligible | 0.145% | 688 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,907 |
| African / African-American | 0.00133% | 75,050 |
| European (non-Finnish) | 0.00102% | 98,337 |
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.Glu125=
- Coding
- c.375G>A
- MANE Select
- NM_001292034
- dbSNP
- rs116851068
- Type
- single nucleotide variant
- Location
- chr6:149378290 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.24 · 6 PDB
- Residue 125
- the 'disordered' region
Similar variants
- 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
- TAB2 p.Arg17Gln Uncertain significance ★★ ⚠ same type
- TAB2 p.Arg576Cys 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-glu125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown