LADD syndrome with glaucoma is caused by a novel gene

Abstract

Purpose: Lacrimo-auriculo-dento-digital (LADD) syndrome is an autosomal dominant disorder displaying variable expression of multiple congenital anomalies including hypoplasia or aplasia of the lacrimal and salivary systems causing abnormal tearing and dry mouth. Mutations in the FGF10, FGFR2, and FGFR3 genes were found to cause some cases of LADD syndrome in prior genetic studies. The goal of this study is to identify the genetic basis of a case of LADD syndrome with glaucoma and thin central corneal thickness (CCT).

Methods: Whole exome sequencing was performed, and previously described disease-causing genes (FGF10, FGFR2, and FGFR3) were first evaluated for mutations. Fifty-eight additional prioritized candidate genes were identified by searching gene annotations for features of LADD syndrome. The potential pathogenicity of the identified mutations was assessed by determining their frequency in large public exome databases; through sequence analysis using the Blosum62 matrix, PolyPhen2, and SIFT algorithms; and through homology analyses. A structural analysis of the effects of the top candidate mutation in tumor protein 63 (TP63) was also conducted by superimposing the mutation over the solved crystal structure.

Results: No mutations were detected in FGF10, FGFR2, or FGFR3. The LADD syndrome patient's exome data was searched for mutations in the 58 candidate genes and only one mutation was detected, an Arg343Trp mutation in the tumor protein 63 (TP63) gene. This TP63 mutation is absent from the gnomAD sequence database. Analysis of the Arg343Trp mutation with Blosum62, PolyPhen2, and SIFT all suggest it is pathogenic. This arginine residue is highly conserved in orthologous genes. Finally, crystal structure analysis showed that the Arg343Trp mutation causes a significant alteration in the structure of TP63's DNA binding domain.

Conclusions: We report a patient with no mutations in known LADD syndrome genes (FGF10, FGFR2, and FGFR3). Our analysis provides strong evidence that the Arg343Trp mutation in TP63 caused LADD syndrome in our patient and that TP63 is a fourth gene contributing to this condition. TP63 encodes a transcription factor involved in the development and differentiation of tissues affected by LADD syndrome. These data suggest that TP63 is a novel LADD syndrome gene and may also influence corneal thickness and risk for open-angle glaucoma.

Figure 1

TP63 amino acid sequence conservation. The arginine amino acid that is altered by the Arg343Trp mutation (indicated with a bold “R”) is highly conserved in the TP63 transcription factor across many species (indicated by the gray shading), which suggests that it may have a conserved role in the protein’s function.

Figure 2

Modeling of the effects of the Arg343Trp mutation on TP63 structure. Beginning from a TP63 crystal structure, mutation of residue 343 from Arg to Trp followed by side-chain repacking demonstrates a loss of favorable electrostatic contacts between wild-type Arg and negatively charged phosphates of the accompanying double stranded DNA. This suggests that the functional consequence of Trp is diminished binding affinity and thereby a change (i.e., a reduction) in transcriptional control. The wild-type structure of TP63 (with an Arg residue at position 343) is shown in blue, the mutant structure with a Trp residue at position 343 is shown in yellow, and a DNA helix is shown in brown and green.