Genotype–phenotype correlations for COL4A3–COL4A5 variants resulting in Gly substitutions in Alport syndrome

Abstract

Alport syndrome is the commonest inherited kidney disease and nearly half the pathogenic variants in the COL4A3–COL4A5 genes that cause Alport syndrome result in Gly substitutions. This study examined the molecular characteristics of Gly substitutions that determine the severity of clinical features. Pathogenic COL4A5 variants affecting Gly in the Leiden Open Variation Database in males with X-linked Alport syndrome were correlated with age at kidney failure (n = 157) and hearing loss diagnosis (n = 80). Heterozygous pathogenic COL4A3 and COL4A4 variants affecting Gly (n = 304) in autosomal dominant Alport syndrome were correlated with the risk of haematuria in the UK 100,000 Genomes Project. Gly substitutions were stratified by exon location (1 to 20 or 21 to carboxyl terminus), being adjacent to a non-collagenous region (interruption or terminus), and the degree of instability caused by the replacement residue. Pathogenic COL4A5 variants that resulted in a Gly substitution with a highly destabilising residue reduced the median age at kidney failure by 7 years (p = 0.002), and age at hearing loss diagnosis by 21 years (p = 0.004). Substitutions adjacent to a non-collagenous region delayed kidney failure by 19 years (p = 0.014). Heterozygous pathogenic COL4A3 and COL4A4 variants that resulted in a Gly substitution with a highly destabilising residue (Arg, Val, Glu, Asp, Trp) were associated with an increased risk of haematuria (p = 0.018), and those adjacent to a non-collagenous region were associated with a reduced risk (p = 0.046). Exon location had no effect. In addition, COL4A5 variants adjacent to non-collagenous regions were over-represented in the normal population in gnomAD (p < 0.001). The nature of the substitution and of nearby residues determine the risk of haematuria, early onset kidney failure and hearing loss for Gly substitutions in X-linked and autosomal dominant Alport syndrome.

A Systematic Review of Pathogenic COL4A5 Variants and Proteinuria in Women and Girls With X-linked Alport Syndrome

“…The intermediate collagenous domain of the collagen IV α5 chain is 'interrupted' by twenty-two short non-collagenous sequences. Gly substitutions directly adjacent to the interruptions are associated with later onset kidney failure 11 because the interruptions allow more space for differently-sized amino acids than the relatively inflexible collagen helix. Gly substitutions with mildly destabilising residues such as Ala, Ser and Cys also result in a later age at kidney failure than substitutions with highly destabilising residues such as Arg, Val, Glu, Asp and Trp.…”

Pathogenicity of missense variants affecting the collagen IV α5 carboxy non-collagenous domain in X-linked Alport syndrome

“…In the collagen IV α5 chain, substitutions have been reported for all 12 NC1 Cys residues and were associated with all the typical clinical features of Alport syndrome. The median age at kidney failure for males was more than 30 years, but not different from that for other NC1 substitutions, nor for collagenous domain Gly substitutions 27 . However, the median age at kidney failure for both NC1 groups suggest that variants in this region cause later-onset disease, and the lack of a difference with the Gly substitutions may have been due to the small cohort.…”

“…a Comparison with Cys missense (NC1 domain). b Data previously reported 27 .

Figure 1 Proportion of cases without kidney failure for males with collagen IV α5 missense variants reported in LOVD.

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“…Clinical data were extracted for all affected males, and survival analysis performed to determine the median age at kidney failure. This was compared with the median age at kidney failure in males with non-Cys substitutions in the NC1 domain identified in LOVD, and with previously-published data for males with collagen IV α5 Gly substitutions in the collagenous domain 27 .…”

“…This study determined the clinical and molecular implications of missense variants affecting the NC1 domain of the collagen IV α5 chain. Firstly, the expected phenotype for Cys substitutions was established and compared with previously-published data for collagenous Gly substitutions in the same molecule 27 . A structural modelling tool was then used to identify additional variants that resulted in further damaging change.…”