Is TAB2 p.His158= (c.474C>T) pathogenic?

TAB2 p.His158= (c.474C>T) is classified Likely benign in TAB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-28). Absent from gnomAD v4.1.

How common is TAB2 p.His158= (c.474C>T) in the general population?

TAB2 p.His158= (c.474C>T) is absent from gnomAD v4.1 (gnomAD).

TAB2 p.His158=

c.474C>T · rs2483386125 · VCV2957187

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 4.2	GERP 1.8, phastCons 1
Overall
CADD	5.793	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TAB2
Protein: p.His158=
Coding: c.474C>T
MANE Select: NM_001292034
dbSNP: rs2483386125
Type: single nucleotide variant
Location: chr6:149378389 (GRCh38)
Gene constraint: LOEUF 0.117 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 53.24 · 6 PDB

Full TAB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TAB2 p.His158Arg Uncertain significance ★ ⚠ same residue
TAB2 p.His158Tyr Conflicting classifications of pathogenicity ★ ⚠ same residue
TAB2 p.His158fs Pathogenic ★ 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

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-his158 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown