Is TBX3 p.Pro437= (c.1311G>A) pathogenic?

TBX3 p.Pro437= (c.1311G>A) is classified Likely benign in TBX3 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-05-05). Very rare (popmax 0.00915%, amr); Associated with ulnar-mammary syndrome.

What condition is associated with TBX3 p.Pro437= (c.1311G>A)?

TBX3 p.Pro437= (c.1311G>A) is associated with ulnar-mammary syndrome (ClinVar).

How common is TBX3 p.Pro437= (c.1311G>A) in the general population?

TBX3 p.Pro437= (c.1311G>A) is very rare (popmax 0.00915%, amr) (gnomAD).

TBX3 p.Pro437=

c.1311G>A · rs759328763 · VCV1962948

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00915%, amr)

Conditions

ulnar-mammary syndrome

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 -3.4	GERP -3
Overall
CADD	6.578	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00915% Admixed American · 5/54,648 alleles

Filtering AF 0.00351% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00234%

Overall 0.000424% 6/1,416,632 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00915%	10,930
European (non-Finnish)	8.61e-05%	1,161,192

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: TBX3
Protein: p.Pro437=
Coding: c.1311G>A
MANE Select: NM_005996
dbSNP: rs759328763
Type: single nucleotide variant
Location: chr12:114674564 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 56.55 · 1 PDB
Residue 437: the 'disordered' region

Full TBX3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ulnar-mammary syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TBX3 p.Pro437Leu Uncertain significance ★ ⚠ same residue
TBX3 p.Pro437Arg Uncertain significance ⚠ same residue
TBX3 p.Gln475Ter Pathogenic ★★ same condition
TBX3 c.1710+3A>G Uncertain significance ★★ same condition
TBX3 p.Ala158Thr Uncertain significance ★★ ⚠ same condition
TBX3 p.Ala336Val Uncertain significance ★★ ⚠ same condition
TBX3 p.Ala357Pro Uncertain significance ★★ ⚠ same condition
TBX3 p.Ala391Gly 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/tbx3-p-pro437 (accessed [today's date]).

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