Mutations in the COL4A5 gene in Alport syndrome: a possible mutation in primordial germ cells

Expert consensus guidelines for the genetic diagnosis of Alport syndrome

Recent expert guidelines recommend genetic testing for the diagnosis of Alport syndrome. Here, we describe current best practice and likely future developments. In individuals with suspected Alport syndrome, all three COL4A5, COL4A3 and COL4A4 genes should be examined for pathogenic variants, probably by high throughput-targeted next generation sequencing (NGS) technologies, with a customised panel for simultaneous testing of the three Alport genes. These techniques identify up to 95% of pathogenic COL4A variants. Where causative pathogenic variants cannot be demonstrated, the DNA should be examined for deletions or insertions by re-examining the NGS sequencing data or with multiplex ligation-dependent probe amplification (MLPA). These techniques identify a further 5% of variants, and the remaining few changes include deep intronic splicing variants or cases of somatic mosaicism. Where no pathogenic variants are found, the basis for the clinical diagnosis should be reviewed. Genes in which mutations produce similar clinical features to Alport syndrome (resulting in focal and segmental glomerulosclerosis, complement pathway disorders, MYH9-related disorders, etc.) should be examined. NGS approaches have identified novel combinations of pathogenic variants in Alport syndrome. Two variants, with one in COL4A3 and another in COL4A4, produce a more severe phenotype than an uncomplicated heterozygous change. NGS may also identify further coincidental pathogenic variants in genes for podocyte-expressed proteins that also modify the phenotype. Our understanding of the genetics of Alport syndrome is evolving rapidly, and both genetic and non-genetic factors are likely to contribute to the observed phenotypic variability.

Mutational analysis of type IV collagen alpha5 chain, with respect to heterotrimer formation

Alport syndrome (AS) is caused by mutations in type IV collagen alpha3, alpha4, and alpha5 chains. The three chains form a heterotrimer. In this study, we introduced 12 kinds of missense and three kinds of nonsense mutations, corresponding to AS mutations, into the NC1 domain of alpha5(IV) and characterized the mutant chains. Nine alpha5(IV) chains with amino acid substitutions and all three truncated alpha5(IV) chains did not form a heterotrimer and were not secreted from cells. Three alpha5(IV) chains with amino acid substitutions did, however, form heterotrimers in cells, but these were not secreted from cells. These findings indicate that a defect in heterotrimer formation is the main molecular mechanism underlying the pathogenesis of AS caused by mutation in the NC1 domain. We also showed that even a single amino acid deletion in the carboxyl-terminal region markedly affected the heterotrimerization, indicating that the carboxyl-terminal end is indispensable for heterotrimer formation.

The clinical spectrum of type IV collagen mutations

Clinical manifestations of type IV collagen mutations can vary from the severe, clinically and genetically heterogeneous renal disorder, Alport syndrome, to autosomal dominant familial benign hematuria. The predominant form of Alport syndrome is X-linked; more than 160 different mutations have yet been identified in the type IV collagen alpha 5 chain (COL4A5) gene, located at Xq22-24 head to head to the COL4A6 gene. The autosomal recessive form of Alport syndrome is caused by mutations in the COL4A3 and COL4A4 genes, located at 2q35-37. Recently, the first mutation in the COL4A4 gene was identified in familial benign hematuria. This paper presents an overview of type IV collagen mutations, including eight novel COL4A5 mutations from our own group in patients with Alport syndrome. The spectrum of mutations is broad and provides insight into the clinical heterogeneity of Alport syndrome with respect to age at renal failure and accompanying features such as deafness, leiomyomatosis, and anti-GBM nephritis.

Detection of mutations in the COL4A5 gene in over 90% of male patients with X-linked Alport's syndrome by RT-PCR and direct sequencing

X-linked Alport's syndrome is caused by mutations in the COL4A5 gene encoding the type IV collagen alpha5 chain (alpha5[IV]). Polymerase chain reaction-single-str and conformation polymorphism (PCR-SSCP) on genomic DNA has previously been used to screen for mutations in the COL4A5 gene, but this method was relatively insensitive, with mutations detected in less than 50% of patients. Here, we report a systematic analysis of the entire coding region of the COL4A5 gene, using nested reverse-transcription-polymerase chain reaction (RT-PCR) and the direct sequence method using leukocytes. This study examines twenty-two unrelated Japanese patients with X-linked Alport's syndrome showing abnormal expression of alpha5(IV) in the glomerular or epidermal basement membranes. Mutations that were predicted to be pathogenic were identified in 12 of the 13 male patients (92%) and five of the nine female patients (56%). Six patients had missense mutations, four had out-of-frame deletion mutations, three had nonsense mutations, and three had mutations causing exon loss of the transcript. The current study shows that nested RT-PCR and the direct sequence method using leukocytes are highly sensitive and offer a useful approach for systematic gene analysis in patients with X-linked Alport's syndrome.

Splicing mutations in the COL4A5 gene in Alport's syndrome: different mRNA expression between leukocytes and fibroblasts

The COL4A5 gene from 40 patients with Alport's syndrome was examined using single-strand conformation substitution at the acceptor site (-2) of intron 50 and a G-to-C substitution at the donor site (+1) of intron 47, respectively. The transcript in peripheral leukocytes from the former had a 10-nucleotide deletion. This shortened transcript was derived from abnormal splicing in a cryptic acceptor site within exon 51. This could be translated into a protein with an alteration of three amino acids followed by premature termination, which eliminated 23 amino acids from the carboxyl end. Gene tracking revealed that the mother and a brother carried the mutant allele. In the latter, the transcript in leukocytes was normal, but that in cultured skin fibroblasts showed skipping of exon 47, the result being that 71 amino acids were absent. Glomerular basement membrane from the patient did not react with the anti-alpha 5(IV) antibody. His maternal grandmother, mother, and a sister, all with abnormal urinalysis, carried the mutant allele. Thus, the appearance of exons of the COL4A5 gene in leukocytes may differ from that in fibroblasts. If kidney mRNA is not available, mRNAs from cultured skin fibroblasts, in addition to leukocytes, can be used for gene analysis in subjects with Alport's syndrome.