COL4A5-p.Gly624Asp is the Predominant Variant in Europe Associated With a Mild Alport Syndrome Phenotype

Abstract

Introduction: Pathogenic variants in COL4A3-5 are common causes of inherited kidney disease. The clinical presentation extends from classical Alport syndrome (AS) to focal segmental glomerulosclerosis (FSGS) without extrarenal manifestation. In this study, we aimed to assess the genetic and phenotypic spectrum, along with the associated natural histories, in a cohort of patients with AS from 3 tertiary centers in Central Europe.

Methods: A total of 210 patients with disease causing variants in one of the COL4A3-5 genes were characterized and evaluated for genotype-phenotype correlations. In addition, 48 COL4A5-p.Gly624Asp carriers were analyzed for replication and pooled analysis.

Results: COL4A5-p.Gly624Asp was by far the most common variant, accounting for 16% of all genetic diagnoses. These patients presented with overall milder renal phenotypes than patients with other COL4A5 missense variants and COL4A5 glycine-missense variants after age- and sex-matching. In patients lacking a wild-type allele (X-Linked AS [XLAS] males and autosomal recessive AS [ARAS]), histological AS was most frequently observed in kidney biopsies, and truncating variants were associated with increased disease severity. Conversely, in patients with a wild-type allele present (XLAS females and autosomal dominant AS [ADAS]), FSGS was more frequently observed. Predicted protein truncation was not inferior to missense alterations in terms of renal survival.

Conclusion: The predominance of the European COL4A5 founder variant p.Gly624Asp allowed for the creation of the largest cohort of patients with an identical Alport variant to date, confirming the more favorable renal prognosis specific to this amino acid change. Allelic and gene dosage effects drive phenotypic differences and should be incorporated into future risk models.

Keywords: COL4A3; COL4A4; COL4A5; alport syndrome; chronic kidney disease; collagen type IV.

Graphical abstract

Figure 1

Overview of study design. In the first step, 210 patients from 2 tertiary centers (Charité Berlin and Leipzig University) with variants in one of the Alport genes were characterized clinically and genetically (discovery cohort). As a result, COL4A5-p.Gly624Asp (n = 34) turned out to be the predominant variant. In the second step, we sought for independent replication by collaboration with another tertiary center (TUM Munich), which yielded confirmatory results regarding predominance of the founder variant. Lastly, patients with the COL4A5-p.Gly624Asp variant were combined (n = 82) for joint comparison to an age-matched and sex-matched cohort with patients harboring other COL4A5 glycine missense variants (replication cohort).

Figure 2

Genetic characteristics of all disease-causing variants found (n = 238) in the combined discovery cohort. (a) Frequency of different variants in the genes COL4A5, COL4A4 and COL4A3, respectively. The length of a bar symbolizes the frequency of individual variants. (b) Type of disease-causing variant. (c) Frequency of pathogenic (P), likely pathogenic (LP) and clinically suspicious (“hot”) variants of uncertain significance (VUS) according to the American College of Medical Genetics and Genomics/Association for Clinical Genomic Science classifications. (d) Frequency distribution of truncating versus nontruncating variants. (e) Frequency distribution of glycine missense changes versus nonglycine missense changes.

Figure 3

Histological findings on native kidney biopsies in the combined discovery cohort. (a)Top left: light microscopy of a glomerulus afflicted with FSGS from a patient harboring the variant c.1030-1G>C in the COL4A4 gene; top right: electron microscopy, × 20,000, from the same patient revealing primary FSGS; bottom left: COL4A5 immunohistochemistry of a patient harboring the compound heterozygous variants p.Gly637Arg and p.Leu1474Pro in the gene COL4A3 shows marked deficiency of staining. Bottom right: electron microscopy, × 20,000, of the same patient shows capillary with thickening and lamellation of glomerular basement membrane. (b) Histological entities according to inheritance. Other includes interstitial nephritis, thrombotic microangiopathy, normal and unspecified findings. (c) Renal survival showed no significant discrimination when comparing patients with histological Alport syndrome to those with FSGS and (d) neither to those with FSGS or TBMN. ADAS, autosomal dominant Alport syndrome; ARAS, autosomal recessive Alport syndrome; AS, Alport syndrome; FSGS, focal segmental glomerulosclerosis; GN, immune-mediated glomerular disease (including minimal change disease, membranous nephropathy, and IgA nephropathy); TBMN, thin basement membrane nephropathy; XLAS, X-linked Alport syndrome.

Figure 4

Comparative renal survival analyses of truncation versus nontruncation in the combined discovery cohort. (a) Renal survival showed significant discrimination when comparing truncating versus nontruncating variants in patients lacking the wild-type allele (XLAS males and ARAS). (b) This discrimination was not observed in patients harboring the wild-type allele, as in XLAS females and ADAS. ADAS, autosomal dominant Alport syndrome; ARAS, autosomal recessive Alport syndrome; XLAS, X-linked Alport syndrome.

Figure 5

(a) Comparative renal survival analyses of carriers with COL4A5-p.Gly624Asp versus other COL4A5 missense variants in the combined discovery cohort. (b and c) This difference was found in male as well as female individuals. (d) Mean proteinuria and mean albuminuria did not differ between patients carrying COL4A5-p.Gly624Asp and patients carrying other COL4A5-missense variants.

Figure 6

Comparative renal survival analyses of carriers with COL4A5-p.Gly624Asp versus matched carriers with other COL4A5 Gly-missense variants in the combined replication cohort. (a) Renal survival showed significant discrimination when comparing male individuals with the missense variant COL4A5-p.Gly624Asp with individuals with other COL4A5 glycine missense variants. (b) This difference was not found in female individuals. (c) Age at onset of hematuria was reported similar in both groups. (d) Onset of proteinuria was reported later in patients with COL4A5-p.Gly624Asp.