Next-generation Sequencing Identified a Novel EDA Mutation in a Chinese Pedigree of Hypohidrotic Ectodermal Dysplasia with Hyperplasia of the Sebaceous Glands

Compound heterozygous WNT10A missense variations exacerbated the tooth agenesis caused by hypohidrotic ectodermal dysplasia

BACKGROUND

The aim of this study was to analyse the differences in the phenotypes of missing teeth between a pair of brothers with hypohidrotic ectodermal dysplasia (HED) and to investigate the underlying mechanism by comparing the mutated gene loci between the brothers with whole-exome sequencing.

METHODS

The clinical data of the patients and their mother were collected, and genomic DNA was extracted from peripheral blood samples. By Whole-exome sequencing filtered for a minor allele frequency (MAF) ≤0.05 non-synonymous single-nucleotide variations and insertions/deletions variations in genes previously associated with tooth agenesis, and variations considered as potentially pathogenic were assessed by SIFT, Polyphen-2, CADD and ACMG. Sanger sequencing was performed to detect gene variations. The secondary and tertiary structures of the mutated proteins were predicted by PsiPred 4.0 and AlphaFold 2.

RESULTS

Both brothers were clinically diagnosed with HED, but the younger brother had more teeth than the elder brother. An EDA variation (c.878 T > G) was identified in both brothers. Additionally, compound heterozygous variations of WNT10A (c.511C > T and c.637G > A) were identified in the elder brother. Digenic variations in EDA (c.878 T > G) and WNT10A (c.511C > T and c.637G > A) in the same patient have not been reported previously. The secondary structure of the variant WNT10A protein showed changes in the number and position of α-helices and β-folds compared to the wild-type protein. The tertiary structure of the WNT10A variant and molecular simulation docking showed that the site and direction where WNT10A binds to FZD5 was changed.

CONCLUSIONS

Compound heterozygous WNT10A missense variations may exacerbate the number of missing teeth in HED caused by EDA variation.

Pathogenic EDA Mutations in Chinese Han Families With Hypohidrotic Ectodermal Dysplasia and Genotype-Phenotype: A Correlation Analysis

Background

This study aimed to investigate the genetic causes of hypohidrotic ectodermal dysplasia (HED) in two families and elucidate the molecular pathogenesis of HED in Chinese Han patients.

Methods

Whole-exome sequencing (WES) was used to screen HED-related genes in two family members, followed by confirmatory Sanger sequencing. Bioinformatics analysis was performed for the mutations. We reviewed HED-related articles in PubMed. χ²- and Fisher's tests were used to analyze the genotype–phenotype correlations.

Results

(1) WES identified EDA missense mutations [c.1127 C > T (p.T376M; NM_001005609)] in family 1 and an EDA nonframeshift deletion mutation [c.648_683delACCTGGTCCTCCAGGTCCTCCTGGTCCTCAAGGACC (p.216_228delPPGPPGPPGPQGP; NM_001005609)] in family 2. Sanger sequencing validated the results. ANNOVAR (ANNOtate VARiation) annotation indicated that c.1127 c > T was a deleterious mutation. (2) The review of published papers revealed 68 novel mutations related to HED: 57 (83.8%) were EDA mutations, 8 (11.8%) were EDAR mutations, 2 (2.9%) were EDARADD mutations, 1 (1.5%) was a WNT10A mutation, 31 (45.6%) were missense mutations, 23 (33.8%) were deletion mutations, and 1 (1.5%) was an indel. Genotype–phenotype correlation analysis revealed that patients with EDA missense mutations had a higher frequency of hypohidrosis (P = 0.021).

Conclusions

This study identified two EDA gene mutations in two Chinese Han HED families and provides a foundation for genetic diagnosis and counseling.

Genetic diagnosis for X-linked hypohidrotic ectodermal dysplasia family with a novel Ectodysplasin A gene mutation

AIM

To make a gene diagnosis for a family with Ectodysplasin A (EDA) gene mutation as well as prenatal diagnosis, and report a novel EDA gene mutation.

METHODS

All coding sequences and flanking sequences of EDA gene were analyzed by Sanger sequencing in the proband, and then, according to EDA gene mutation in the proband, the EDA gene sequencing was performed on the family members. Based on the results above, the pathogenic mutation in EDA gene was finally identified, which was used for making prenatal diagnosis.

RESULTS

Sanger sequencing revealed c.302_303delCC [p.Pro101HisfsX11] mutation in EDA gene of the proband. This mutation induced EDA gene frame shift mutation which led to early termination of EDA gene translation because there was a termination codon TAA at the 11th codon behind the mutational site. Heterozygous deletion mutation (CC/--) at this locus was observed in the proband's mother and proband's grandmother, but the proband's aunt had no mutation at this locus. The analyses of amniotic fluid samples indicated negative sex-determining region on Y (SRY), and c.302_303delCC heterozygous deletion mutation.

CONCLUSION

We identified a pathogenetic mutation in EDA gene for the X-linked hypohidrotic ectodermal dysplasia family, made a prenatal diagnosis for the female carrier, and reported a novel EDA gene mutation.