Is TAB2 p.Gln7= (c.21A>G) pathogenic?

TAB2 p.Gln7= (c.21A>G) is classified Benign/Likely benign in TAB2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-01). Low-frequency (popmax 1.34%, sas); Associated with congenital heart defects, multiple types, 2.

What condition is associated with TAB2 p.Gln7= (c.21A>G)?

TAB2 p.Gln7= (c.21A>G) is associated with congenital heart defects, multiple types, 2 (ClinVar).

How common is TAB2 p.Gln7= (c.21A>G) in the general population?

TAB2 p.Gln7= (c.21A>G) is low-frequency (popmax 1.34%, sas) (gnomAD).

TAB2 p.Gln7=

c.21A>G · rs553008331 · VCV1540615

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.34%, sas)

Conditions

congenital heart defects, multiple types, 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Overall
CADD	12.17	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.34% South Asian · 1,222/91,084 alleles

Filtering AF 1.28% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.25%

Overall 0.0823% 1,328/1,614,096 alleles · low-frequency exomes 1,254/1,461,786 · genomes 74/152,310 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	1.34%	75
Remaining individualsnot grpmax-eligible	0.088%	1,136
Middle Eastern	0.0495%	2,019
Admixed American	0.005%	20,001
East Asian	0.00446%	22,437
African / African-American	0.004%	25,014
European (non-Finnish)	0.00339%	29,500

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.Gln7=
Coding: c.21A>G
MANE Select: NM_001292034
dbSNP: rs553008331
Type: single nucleotide variant
Location: chr6:149370018 (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

Disease context

congenital heart defects, multiple types, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TAB2 c.1764+1G>A Pathogenic/Likely pathogenic ★★ same condition
TAB2 p.Arg574Ter Likely pathogenic ★★ same condition
TAB2 p.Arg96Lys Uncertain significance ★★ ⚠ same condition
TAB2 p.His6Arg Uncertain significance ★★ ⚠ same condition
TAB2 p.Ile68Thr Uncertain significance ★★ same condition
TAB2 p.Ser50Asn Uncertain significance ★★ ⚠ same condition
TAB2 p.Gln127Ter Pathogenic ★ same condition
TAB2 p.Pro183Leu Likely pathogenic ★ 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-gln7 (accessed [today's date]).

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