Novel missense alteration in LRP4 gene underlies Cenani–Lenz syndactyly syndrome in a consanguineous family

• Published in: The journal of gene medicine 2020-01, Vol.22 (1), p.e3143-n/a
• Main Authors: Alrayes, Nuha, Aziz, Abdul, Ullah, Farman, Ishfaq, Muhammad, Jelani, Musharraf, Wali, Abdul
• Format: Article
• Language: English
• Subjects: Aplasia; Bioinformatics; Cenani–Lenz syndactyly syndrome; Dentition; Dysplasia; Finger; Gene therapy; Genetic analysis; Genomes; Hypoplasia; LRP4; missense variant; Nails (Anatomy); Phenotypes; Syndactyly; Teeth; WES analysis
• ISSN: 1099-498X; 1521-2254
• DOI: 10.1002/jgm.3143

Background Syndactyly is a clinical feature of split‐hand foot malformation (SHFM), ectodermal‐dysplasia‐syndactyly (EDSS1) and Cenani–Lenz syndactyly syndromes (CLSS). In EDSS1, only cutaneous syndactyly is observed, with sparse hair, abnormal nails and dentition. In SHFM, bony syndactyly may vary from hypoplasia of one phalanx to aplasia of central digits, extending to complete fusion of all fingers and toes in CLSS. Several genes have been assigned to these syndromes. Performing a single step molecular diagnostics becomes a challenge when a phenotype has overlaps with several syndromes or when some of the clinical features are not fully expressed in patients. Methods Whole exome sequencing (WES) analysis on one sample derived from a consanguineous family was performed. A causative variant in WES data was prioritized via standard bioinformatics tools. The selected variant was Sanger sequenced in all the available family members for autosomal recessive segregation. Results A novel missense variant (c.1151A>G; p.Tyr384Cys) was identified in the LRP4 gene. Sanger validation confirmed that all affected individuals were homozygous and the obligate carriers were heterozygous for this variant. The variant is neither reported in 1000 human genomes, nor in 60 706 exomes databases, and is predicted as “pathogenic” by SIFT, Polyphen‐2 and MutationTaster software. Conclusions The present study broadens the pathogenic spectrum of the LRP4 gene in syndactyly syndromes. WES is a powerful tool for genetic analysis in research and can be readily used as a first‐line diagnostic test in syndactyly and related phenotypes.