A wave of deep intronic mutations in X-linked Alport Syndrome

Alport syndrome: an update

PURPOSE OF REVIEW

The recent widespread availability of genetic testing has resulted in the diagnosis of many more people with Alport syndrome. This increased recognition has been paralleled by advances in understanding clinical consequences, genotype-phenotype correlations and in the development of new therapies.

RECENT FINDINGS

These include the international call for a change of name to 'Alport spectrum' which better reflects the diverse clinical features seen with autosomal dominant and X-linked Alport syndrome; the demonstration of how common Alport syndrome is in people with haematuria, proteinuria, or kidney failure; the inability of current genetic testing to detect all pathogenic variants in suspected Alport syndrome; the different genotype-phenotype correlations for autosomal dominant and X-linked disease; and the novel treatments that are available including SGLT2 inhibitors for persistent albuminuria despite renin-angiotensin-aldosterone blockade, as well as early studies of gene-modifying agents.

SUMMARY

Autosomal dominant Alport syndrome is the commonest genetic kidney disease and X-linked Alport syndrome is the second commonest genetic cause of kidney failure. Both these diseases are frequently seen in the renal clinic, and clinicians should be aware of their likelihood in a person with persistent glomerular haematuria, proteinuria or kidney failure. Autosomal dominant Alport syndrome is so common that it also occurs coincidentally in other kidney diseases especially IgA nephropathy.

Pathogenic variants in the Alport genes are prevalent in the Singapore multiethnic population with highest frequency in the Chinese

Alport syndrome is a common monogenic kidney disease resulting from pathogenic variants in COL4A3, COL4A4 or COL4A5 genes. The estimated global population prevalence is one in 106 individuals for autosomal dominant (AD) and one in 2,320 for sex-linked (XL) conditions. Here, we aimed to estimate the population prevalence of individuals carrying pathogenic variants that cause Alport syndrome in Singapore, and to stratify the prevalence by ancestry. We used population-scale genomic data of 9,051 unrelated subjects, comprising 5,443 (60.8%) Chinese, 1,922 (21.4%) Indian and 1,686 (17.8%) Malay individuals. The prevalence of individuals with pathogenic variants that cause AD and XL Alport syndrome are 1 in 165 and 1 in 2,262 respectively. Additionally, 0.8% of Chinese and 0.3% of Malay populations carry pathogenic Alport syndrome variants, with Chinese individuals being 2.7 times more affected than Malays (95% CI:1.147-6.437, P = 0.027). Interestingly, each pathogenic variant was associated with people of a single ancestry. The two most prevalent pathogenic variants, COL4A3: c.3856G > A (p.Gly1286Arg) (n = 8) and COL4A3: c.4793T > G (p.Leu1598Arg) (n = 4), were exclusively found in the Chinese population. In conclusion, AD Alport syndrome may be prevalent in Singapore, with higher frequencies among the Chinese. Furthermore, founder effects may exist within the ancestries.

A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing

BACKGROUND

Loss-of-function variants in MME (membrane metalloendopeptidase) are a known cause of recessive Charcot-Marie-Tooth Neuropathy (CMT). A deep intronic variant, MME c.1188+428A>G (NM_000902.5), was identified through whole genome sequencing (WGS) of two Australian families with recessive inheritance of axonal CMT using the seqr platform. MME c.1188+428A>G was detected in a homozygous state in Family 1, and in a compound heterozygous state with a known pathogenic MME variant (c.467del; p.Pro156Leufs*14) in Family 2.

AIMS

We aimed to determine the pathogenicity of the MME c.1188+428A>G variant through segregation and splicing analysis.

METHODS

The splicing impact of the deep intronic MME variant c.1188+428A>G was assessed using an in vitro exon-trapping assay.

RESULTS

The exon-trapping assay demonstrated that the MME c.1188+428A>G variant created a novel splice donor site resulting in the inclusion of an 83 bp pseudoexon between MME exons 12 and 13. The incorporation of the pseudoexon into MME transcript is predicted to lead to a coding frameshift and premature termination codon (PTC) in MME exon 14 (p.Ala397ProfsTer47). This PTC is likely to result in nonsense mediated decay (NMD) of MME transcript leading to a pathogenic loss-of-function.

INTERPRETATION

To our knowledge, this is the first report of a pathogenic deep intronic MME variant causing CMT. This is of significance as deep intronic variants are missed using whole exome sequencing screening methods. Individuals with CMT should be reassessed for deep intronic variants, with splicing impacts being considered in relation to the potential pathogenicity of variants.

Three exonic variants in the COL4A5 gene alter RNA splicing in a minigene assay

BACKGROUND

X-linked Alport syndrome (XLAS) is an inherited renal disease caused by rare variants of COL4A5 on chromosome Xq22. Many studies have indicated that single nucleotide variants (SNVs) in exons can disrupt normal splicing process of the pre-mRNA by altering various splicing regulatory signals. The male patients with XLAS have a strong genotype-phenotype correlation. Confirming the effect of variants on splicing can help to predict kidney prognosis. This study aimed to investigate whether single nucleotide substitutions, located within three bases at the 5' end of the exons or internal position of the exons in COL4A5 gene, cause aberrant splicing process.

METHODS

We analyzed 401 SNVs previously presumed missense and nonsense variants in COL4A5 gene by bioinformatics programs and identified candidate variants that may affect the splicing of pre-mRNA via minigene assays.

RESULTS

Our study indicated three of eight candidate variants induced complete or partial exon skipping. Variants c.2678G>C and c.2918G>A probably disturb classic splice sites leading to corresponding exon skipping. Variant c.3700C>T may disrupt splicing enhancer motifs accompanying with generation of splicing silencer sequences resulting in the skipping of exon 41.

CONCLUSION

Our study revealed that two missense variants positioned the first nucleotides of the 5' end of COL4A5 exons and one internal exonic nonsense variant caused aberrant splicing. Importantly, this study emphasized the necessity of assessing the effects of SNVs at the mRNA level.