COL4A5 and LAMA5 variants co-inherited in familial hematuria: digenic inheritance or genetic modifier effect?

Abstract

Background: About 40-50% of patients with familial microscopic hematuria (FMH) caused by thin basement membrane nephropathy (TBMN) inherit heterozygous mutations in collagen IV genes (COL4A3, COL4A4). On long follow-up, the full phenotypic spectrum of these patients varies a lot, ranging from isolated MH or MH plus low-grade proteinuria to chronic renal failure of variable degree, including end-stage renal disease (ESRD).

Methods: Here, we performed Whole Exome Sequencing (WES) in patients of six families, presenting with autosomal dominant FMH, with or without progression to proteinuria and loss of renal function, all previously found negative for severe collagen IV mutations. Hierarchical filtering of the WES data was performed, followed by mutation prediction analysis, Sanger sequencing and genetic segregation analysis.

Results: In one family with four patients, we found evidence for the contribution of two co-inherited variants in two crucial genes expressed in the glomerular basement membrane (GBM); LAMA5-p.Pro1243Leu and COL4A5-p.Asp654Tyr. Mutations in COL4A5 cause classical X-linked Alport Syndrome, while rare mutations in the LAMA5 have been reported in patients with focal segmental glomerulosclerosis. The phenotypic spectrum of the patients includes hematuria, proteinuria, focal segmental glomerulosclerosis, loss of kidney function and renal cortical cysts.

Conclusions: A modifier role of LAMA5 on the background of a hypomorphic Alport syndrome causing mutation is a possible explanation of our findings. Digenic inheritance is another scenario, following the concept that mutations at both loci more accurately explain the spectrum of symptoms, but further investigation is needed under this concept. This is the third report linking a LAMA5 variant with human renal disease and expanding the spectrum of genes involved in glomerular pathologies accompanied by familial hematurias. The cystic phenotype overlaps with that of a mouse model, which carried a Lama5 hypomorphic mutation that caused severely reduced Lama5 protein levels and produced kidney cysts.

Keywords: Alport syndrome; Collagen IV; Digenic inheritance; FSGS; Familial hematuria; Kidney disease; Laminin alpha 5; Metalloproteinase; Modifier gene; Renal cysts; Synaptopodin; Thin Basement Membrane Nephropathy (TBMN).

Fig. 1

Hierarchical filtering that we followed for mining the Whole Exome Sequencing data

Fig. 2

Pedigree of family CY5500. For family members with a UCY code, there is available a DNA sample. Four patients of the family carry both variants (patients UCY2075 and UCY2069 are actually hemizygous for the COL4A5 variant). Family member UCY2067 carries only the LAMA5 variant in heterozygosity, having normal kidney function and being negative for microscopic hematuria, aged 27

Fig. 3

Ultra-sound of the kidneys of patient CA (UCY2069 on Fig. 1), aged 57-yrs, presently on ESRD. Both Kidneys are smaller than normal, measuring Rt kidney 8.88 cm in long diameter and the Lt kidney 9.51 cm, with increased echogenicity and cortical thinning, cortex measuring about 0.88 cm. There is no polycystic kidney disease (pelvocalyceal dilatation). Multiple cortical cysts are noted in both kidneys, about 6–8 cysts in each kidney, the bigger to the Rt about 4.5 cm and to the Lt about 3.6 cm. The cysts however have been present at least since 4-yrs, according to the patient’s medical record, at the time his renal function was much better (MDRD 50 ml/min)