Phenotypic evolution of UNC80 loss of function

Abstract

Failure to thrive arises as a complication of a heterogeneous group of disorders. We describe two female siblings with spastic paraplegia and global developmental delay but also, atypically for the HSPs, poor weight gain classified as failure to thrive. After extensive clinical and biochemical investigations failed to identify the etiology, we used exome sequencing to identify biallelic UNC80 mutations (NM_032504.1:c.[3983-3_3994delinsA];[2431C>T]. The paternally inherited NM_032504.1:c.3983-3_3994delinsA is predicted to encode p.Ser1328Argfs*19 and the maternally inherited NM_032504.1:c.2431C>T is predicted to encode p.Arg811*. No UNC80 mRNA was detectable in patient cultured skin fibroblasts, suggesting UNC80 loss of function by nonsense mediated mRNA decay. Further supporting the UNC80 mutations as causative of these siblings' disorder, biallelic mutations in UNC80 have recently been described among individuals with an overlapping phenotype. This report expands the disease spectrum associated with UNC80 mutations. © 2016 Wiley Periodicals, Inc.

Keywords: emaciation; failure to thrive; growth restriction; intellectual disability; seizures.

FIG. 1

Clinical photographs of the proposita (arrow, II-1) and her affected sister (II-3). (A) Family pedigree. Affected individuals are shown by black symbols. (B–K) Photographs of the proposita at age 1 week (B), 4 months (C), 6 months (D), 17 months (E), 15 months (F), 19 months (G), 6 years and 11 months (H, I), and 12 years and 10 months (J, K). (L–Q) Photographs of the affected sister (II-3) of the proposita as a newborn (L) and at ages 2 years (M), 5 years (N), 6 years (O, P) and 7 years (Q).

FIG. 2

Identification and characterization of biallelic UNC80 mutations. (A) IGV views of aligned exome sequencing short reads showing paternally inherited NM_032504.1:c.3983-3_3994delinsA. (B) IGV views of aligned exome sequencing short reads showing maternally inherited NM_032504.1:c.2431C>T. Neither mutation has been previously published. (C) Sanger traces for PCR amplification products of NM_032504.1:c.3983-3_3994delinsA. (D) Sanger traces for PCR amplification products of NM_032504.1:c.2431C>T. (E) UNC80 qRT-PCR amplification showing the absence of detectable UNC80 mRNA in cultured skin fibroblasts derived from patient II-3. Target amplification was normalized to that of GAPDH and shown as expression relative to control.

FIG 3

STRING diagram referenced by Exomiser and showing the proximity of UNC80 in the interactome to NALCN. The edges of this diagram indicate predicted functional links and are colored to indicate supporting evidence for that link (green indicates proteins in the same neighborhood; pink indicates a connection made through experimentation; yellow connections established via text mining for co-occurrence of gene or protein names in abstracts; and light blue indicates relationships supported in databases Biocarta, BioCyc, GO, KEGG, and Reactome). Applying Exomiser to each variant that passed the frequency and segregation filters, we were able to compare the patient’s HPO terms to all human diseases associated with the gene containing the variant in OMIM or Orphanet, to phenotypes associated with orthologs mutated in mice or zebrafish, and lastly to phenotypes associated with nearby genes in the protein-protein association network. For the propositae, Exomiser calculated the phenotype score by considering the similarity of their phenotype to mutation of NACLN (Table I) and the proximity of NACLN to UNC80. The Exomiser variant score is a measure of the predicted pathogenicity and allele frequency of a variant. Exomiser also generated a general score that was calculated from the phenotype and variant scores.