TAB2 p.Phe140=
c.420T>C · VCV4797898
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00246%, nfe)
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 2.8 | GERP 0.58, phastCons 1 |
| Overall | ||
| CADD | 9.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00246%
European (non-Finnish) · 29/1,180,048 alleles
Filtering AF
0.00172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00149%
Overall
0.00192%
31/1,614,120 alleles · very rare
exomes 30/1,461,888 · genomes 1/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00246% | 40,691 |
| East Asian | 0.00223% | 44,900 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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.Phe140=
- Coding
- c.420T>C
- MANE Select
- NM_001292034
- Type
- single nucleotide variant
- Location
- chr6:149378335 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.24 · 6 PDB
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-phe140 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown