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

Abstract

The X-linked form of Alport syndrome (AS) is caused by mutation in the COL4A5 gene located at Xq22.3 and encoding the alpha5-chain of type IV-collagen. More than 400 different mutations have so far been detected in the COL4A5 gene. Not all mutations, however, will be detected using an exon-by-exon mutation detection strategy such as SSCP analysis or direct sequencing. We have previously reported the results of SSCP analysis of 81 patients suspected of X-linked AS. Genomic DNA from these 81 patients was also analyzed for larger genomic rearrangements, using Southern blotting analysis. Abnormal band patterns were found in three patients, two of which were caused by single base substitutions in the coding region, also detected by the SSCP analysis. Here we report the results of the analysis of a larger structural COL4A5 rearrangement that escaped the SSCP analysis. The rearrangement was found to be an inversion of a 21 Mb fragment of the COL4A5 gene comprising exon 9 through 51 with proximal breakpoint within intron 8 at Xq22.3 and a distal breakpoint 56 kb upstream to the initiation codon in the RAB33A gene at Xq25. The inversion of exon 9 through 51 is expected to result in a truncated or absent alpha5(IV)-chain and has not previously been associated with AS. These findings emphasize the need for a supplement to mutation detection strategies such as SSCP analysis and direct sequencing, in order to detect more complicated structural COL4A5 rearrangements. Larger structural rearrangements constitute 2.3% (1/43) of the mutations in the present material.

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

“…However, some mutations will remain undetected even using MLPA, cDNA analysis, direct sequencing of genomic DNA, or an exon‐by‐exon screening strategy (SSCP, denaturing gradient gel electrophoresis, and dHPLC). Some larger structural rearrangements like inversion of a part of COL4A5 will only be detected using other techniques such as Southern blot analysis (29).…”

“…like inversion of a part of COL4A5 will only be detected using other techniques such as Southern blot analysis (29).…”

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

“…Most likely, the genomic rearrangement occurred by pairing of the inverted Alu repeats, as described in the X-linked recessive hemophilia A and Alport syndrome. 46,47 To our knowledge, this is the first paracentric inversion alone that causes an autosomal recessive disease in humans. Functionally, IL-2 stimulation slightly increased degranulation by NK cells carrying the UNC13D inversion relative to NK cells from patients with other UNC13D mutations.…”