A role for VAX2 in correct retinal function revealed by a novel genomic deletion at 2p13.3 causing distal Renal Tubular Acidosis: case report

Abstract

Background: Distal Renal Tubular Acidosis is a disorder of acid-base regulation caused by functional failure of α-intercalated cells in the distal nephron. The recessive form of the disease (which is usually associated with sensorineural deafness) is attributable to mutations in ATP6V1B1 or ATP6V0A4, which encode the tissue-restricted B1 and a4 subunits of the renal apical H(+)-ATPase. ATP6V1B1 lies adjacent to the gene encoding the homeobox domain protein VAX2, at 2p13.3. To date, no human phenotype has been associated with VAX2 mutations.

Case presentation: The male Caucasian proband, born of a first cousin marriage, presented at 2 months with failure to thrive, vomiting and poor urine output. No anatomical problems were identified, but investigation revealed hyperchloremic metabolic acidosis with inappropriately alkaline urine and bilateral nephrocalcinosis. Distal Renal Tubular Acidosis was diagnosed and audiometry confirmed hearing loss at 2 years. ATP6V0A4 was excluded from genetic causation by intragenic SNP linkage analysis, but ATP6V1B1 completely failed to PCR-amplify in the patient, suggesting a genomic deletion. Successful amplification of DNA flanking ATP6V1B1 facilitated systematic chromosome walking to ascertain that the proband harbored a homozygous deletion at 2p13.3 encompassing all of ATP6V1B1 and part of VAX2; gene dosage was halved in the parents. This results in the complete deletion of ATP6V1B1 and disruption of the VAX2 open reading frame. Later ocular examinations revealed bilateral rod / cone photoreceptor dystrophy and mild optic atrophy. Similar changes were not detected in an adult harbouring a disruptive mutation in ATP6V1B1.

Conclusions: The genomic deletion reported here is firstly, the only reported example of a whole gene deletion to underlie Distal Renal Tubular Acidosis, where the clinical phenotype is indistinguishable from that of other patients with ATP6V1B1 mutations; secondly, this is the first reported example of a human VAX2 mutation and associated ocular phenotype, supporting speculation in the literature that VAX2 is important for correct retinal functioning.

Fig. 1

Evidence that the deletion of ATP6V1B1 underlies dRTA in this family (a) ATP6V0A4 was excluded by heterozygosity of SNPs in the patient in exons 4, 17 and 18. b Failure of PCR to amplify exons 3–4 and 13–14 of ATP6V1B1 in the patient (P) suggested a large deletion compared to positive control (+). c Successful PCR amplification in the patient for exon 1 of VAX2 () and exon 1 of ANKRD53 (), but not exon 2 of VAX2 () and exon 21 of ATP6V1B1 () define regions on either side of ATP6V1B1 for the deletion breakpoints on chromosome 2. L = 100bp ladder

Fig. 2

Characterization and gene dosage of the genomic deletion at 2p13.3 (a) Successful PCR amplification across the junction breakpoint in the patient (P) and his parents (F, M) but not in a control individual with normal genomic DNA (C). b Sequencing revealed the insertion of 2 nucleotides (GG) at the site of the deletion. c Semi-quantitative PCR confirmed that gene dosage of ATP6V1B1 and exons 2 and 3 of VAX2 is reduced in the parents (F, M) compared to the control (C)

Fig. 3

Fundus photographs of the right eye (left image) and left eye (right image). Abnormal pigmentation around the macula and mild bilateral optic atrophy can be seen.