Identification of novel tumor protein 63 variant associated with split-hand/foot malformation and tooth agenesis

Split-hand/foot malformation (SHFM) is a serious congenital anomaly. A multitude of pathogenic genes associated with SHFM have been identified; TP63, DLX5, FGFR1, and WNT10B are currently recognized. As a transcription factor, TP63 plays an important role in the development of the ectoderm.

We identified a pathogenic variant by extracting DNA from the peripheral blood of a patient with SHFM and performing whole-exome sequencing (WES). After verifying the variant through Sanger sequencing, a series of analytical procedures were conducted to determine its pathogenicity. These included conservative analysis, tolerance analysis of the mutant region, and three-dimensional molecular modeling of the protein.

A TP63 frameshift mutation (NM_003722; c.2009_2010insA; p.N670Kfs^*) associated with SHFM was identified by WES and is predicted to cause a segmental deletion within the transactivation inhibitory domain (TID) of TP63. Bioinformatic analyses revealed that this locus is highly evolutionarily conserved and poorly tolerant of variation.

We identified a TP63 shift mutation in a patient with SHFM. This research contributes to the expansion of the spectrum of TP63 variants and disease phenotypes, and is expected to provide valuable information for genetic counseling and prenatal diagnosis in families affected by similar congenital anomalies.