TBX15

Chr 1AR

T-box transcription factor 15

Also known as: TBX14

TBX15 encodes a transcriptional regulator that controls mesenchymal precursor cells and chondrocytes during development of the limb skeleton, vertebral column, and head. Biallelic mutations cause Cousin syndrome, an autosomal recessive disorder characterized by skeletal abnormalities. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.437), consistent with its developmental importance.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.441 OMIM phenotype
Clinical SummaryTBX15
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.66) — some intolerance to loss-of-function variants.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.44LOEUF
pLI 0.658
Z-score 3.43
OE 0.19 (0.090.44)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.99Z-score
OE missense 0.83 (0.740.93)
218 obs / 263.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.19 (0.090.44)
00.351.4
Missense OE0.83 (0.740.93)
00.61.4
Synonymous OE0.87
01.21.6
LoF obs/exp: 4 / 20.9Missense obs/exp: 218 / 263.3Syn Z: 1.04
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveTBX15-related craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature (Cousin syndrome)LOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.5280th %ile
GOF
0.3491th %ile
LOF
0.73top 10%

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

TBX15 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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