Alport syndrome caused by inversion of a 21 Mb fragment of the long arm of the X-chromosome comprising exon 9 through 51 of the COL4A5 gene

Familial hemophagocytic lymphohistiocytosis type 3 (FHL3) caused by deep intronic mutation and inversion in UNC13D

Familial hemophagocytic lymphohistiocytosis (FHL) is an autosomal recessive, often-fatal hyperinflammatory disorder. Mutations in PRF1, UNC13D, STX11, and STXBP2 are causative of FHL2, 3, 4, and 5, respectively. In a majority of suspected FHL patients from Northern Europe, sequencing of exons and splice sites of such genes required for lymphocyte cytotoxicity revealed no or only monoallelic UNC13D mutations. Here, in 21 patients, we describe 2 pathogenic, noncoding aberrations of UNC13D. The first is a point mutation localized in an evolutionarily conserved region of intron 1. This mutation selectively impairs UNC13D transcription in lymphocytes, abolishing Munc13-4 expression. The second is a 253-kb inversion straddling UNC13D, affecting the 3′-end of the transcript and likewise abolishing Munc13-4 expression. Carriership of the intron 1 mutation was found in patients across Europe, whereas carriership of the inversion was limited to Northern Europe. Notably, the latter aberration represents the first description of an autosomal recessive human disease caused by an inversion. These findings implicate an intronic sequence in cell-type specific expression of Munc13-4 and signify variations outside exons and splice sites as a common cause of FHL3. Based on these data, we propose a strategy for targeted sequencing of evolutionary conserved noncoding regions for the diagnosis of primary immunodeficiencies.

MLPA and cDNA analysis improves COL4A5 mutation detection in X-linked Alport syndrome

The X-linked form of Alport syndrome (AS) is caused by mutations in the COL4A5 gene encoding the alpha5 chain of type IV collagen. Most COL4A5 mutations are individual, and mutation analysis is complicated by the size of the gene and the number of exons. Larger structural rearrangements account for 10-15% of mutations. We have established a method for mutation analysis of COL4A5 based on reverse transcriptase-polymerase chain reaction analysis of mRNA from cultured skin fibroblasts and multiplex ligation-dependent probe amplification (MLPA) on genomic DNA. One advantage of using skin biopsies for the mRNA analysis is the possibility of immunohistochemical staining for the alpha5(IV) chain on skin sections to support a diagnosis of X-linked AS. A mutation was detected in all five cases included. One patient presenting with AS and diffuse leiomyomatosis was found to have a COL4A5 deletion extending into and comprising COL4A6 exons 1, 1', and 2. We have evaluated the MLPA assay on samples from 67 previously tested AS patients (45 males and 22 females) and 20 controls. We found that the combination of cDNA and MLPA analysis improves the mutation detection rate in COL4A5 and that MLPA should be the first step in genetic testing for X-linked AS.