Exome sequencing reveals cubilin mutation as a single-gene cause of proteinuria

Abstract

In two siblings of consanguineous parents with intermittent nephrotic-range proteinuria, we identified a homozygous deleterious frameshift mutation in the gene CUBN, which encodes cubulin, using exome capture and massively parallel re-sequencing. The mutation segregated with affected members of this family and was absent from 92 healthy individuals, thereby identifying a recessive mutation in CUBN as the single-gene cause of proteinuria in this sibship. Cubulin mutations cause a hereditary form of megaloblastic anemia secondary to vitamin B(12) deficiency, and proteinuria occurs in 50% of cases since cubilin is coreceptor for both the intestinal vitamin B(12)-intrinsic factor complex and the tubular reabsorption of protein in the proximal tubule. In summary, we report successful use of exome capture and massively parallel re-sequencing to identify a rare, single-gene cause of nephropathy.

Figure 1.

Nonparametric lod (NPL) scores across the human genome in two siblings with intermittent gross proteinuria of consanguinous family A2410 reveal four regions of homozygosity by descent. The x-axis shows Affymetrix 250K SNP StyI array SNP positions on human chromosomes concatenated from p-ter (left) to q-ter (right). Genetic distance is given in centimorgan (cM). Seven maximum NPL peaks (red circles) indicate candidate regions of homozygosity by descent. The arrow shows the region of homozygosity in chromosome 10, which includes CUBN.

Figure 2.

The novel single-base homozygous deletion (c.8355delA) in exon 53 of the cubilin (CUBN) gene that causes nephrotic syndrome in family A2410. Note that the sequence shown depicts the plus strand of chromosome 10 and that CUBN is encoded on the reverse strand, therefore showing a deletion of a T (thymine) rather than A (adenine).

Figure 3.

Novel homozygous mutation in CUBN. A novel homozygous of a single-bp deletion is shown that leads to a frameshift mutation in exon 53 of CUBN (c.8355delA; p.S2785fsX19) in patient A2410-22 who has intermittent nephrotic range proteinuria. Nucleotide sequence traces and deduced amino acid sequence are shown for mutated (top) and wild-type (bottom) sequences. Adenine deleted in A2410-22 is marked with an asterisk in the wild-type sequence. Mutation numbering is based on CUBN human reference sequence NM_001081.3, where +1 corresponds to the A of the ATG translation start codon.