Is TAB2 p.Asp40Val (c.119A>T) pathogenic?

TAB2 p.Asp40Val (c.119A>T) is classified Uncertain significance in TAB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-28). AlphaMissense: likely pathogenic (0.7149); Very rare (popmax 0.00133%, afr); Associated with Inborn genetic diseases.

What condition is associated with TAB2 p.Asp40Val (c.119A>T)?

TAB2 p.Asp40Val (c.119A>T) is associated with Inborn genetic diseases (ClinVar).

How common is TAB2 p.Asp40Val (c.119A>T) in the general population?

TAB2 p.Asp40Val (c.119A>T) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about TAB2 p.Asp40Val (c.119A>T)?

AlphaMissense predicts likely pathogenic (score 0.7149) — an in-silico prediction, not a clinical call.

TAB2 p.Asp40Val

c.119A>T · rs1781462536 · VCV3173208

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7149 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.7149	likely pathogenic
REVEL	0.66	pathogenic-leaning
SaProt	LLR -8.77	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	Δ0.33	acceptor gain · deltas
Pangolin	Δ0.24	gain · loss 0.14 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 20 kb · p 7.3e-06 · regional, not allelic
Overall
CADD	26.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,930 alleles

Overall 0.000124% 2/1,613,842 alleles · very rare exomes 1/1,461,628 · genomes 1/152,214 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	74,930
European (non-Finnish)	8.48e-05%	1,179,871

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.Asp40Val
Coding: c.119A>T
MANE Select: NM_001292034
dbSNP: rs1781462536
Type: single nucleotide variant
Location: chr6:149378034 (GRCh38)
Gene constraint: LOEUF 0.117 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 53.24 · 6 PDB
Residue 40: the cue domain; an α-helix

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TAB2 p.Ala618Val Uncertain significance ★★ ⚠ same condition
TAB2 p.Arg72His Uncertain significance ★★ ⚠ same condition
TAB2 p.Arg96Ser Uncertain significance ★★ same condition
TAB2 p.Asn118Tyr Uncertain significance ★★ ⚠ same condition
TAB2 p.Asn669Thr Uncertain significance ★★ ⚠ same condition
TAB2 p.Gln209Lys Uncertain significance ★★ ⚠ same condition
TAB2 p.Glu49Lys Uncertain significance ★★ ⚠ same condition
TAB2 p.Glu93Lys Uncertain significance ★★ ⚠ same condition

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-asp40val (accessed [today's date]).

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