Mutations in SLC38A8 and FOXD1 in patients with nystagmus and foveal hypoplasia.

Abstract

Purpose : Foveal hypoplasia with optic nerve decussation defects in the absence of pigmentation deficits (FHONDA) is a rare recessive disorder which presents with congenital nystagmus. To date, SLC38A8 is the only gene known to be mutated in this disease. However, many patients with the FHONDA phenotype do not have detectable mutations in SLC38A8, suggesting that this disorder is either genetically heterogeneous or that a proportion of mutations in SLC38A8 are not identified by Sanger screening. The aim of this study was to genetically analyse a cohort of FHONDA patients to expand the mutation spectrum of SLC38A8, investigate if mutations in new genes cause this disorder, or if SLC38A8 mutations are being missed.

Methods : Exons of SLC38A8 were screened by Sanger sequencing. Whole exome sequencing (WES) was performed on the Illumina HiSeq3000 using the Agilent SureSelect capture reagent. Whole genome sequencing (WGS) was performed by Edinburgh Genomics using an Illumina HiSeqX. Data was aligned using BWA and variants were processed using Picard and GATK. ExomeDepth and BreakDancer were used to look for copy number/structural rearrangements.

Results : Two novel mutations were identified in SLC38A8. In one patient, a homozygous missense mutation was identified (c.848A>C, p.(D283A)). In a second patient, a single missense mutation was identified (c.2T>C, p.?(M1?)), but a second mutation was not detected. WGS was performed on this patient, along with a third case with a large region of autozygosity spanning SLC38A8, but no identifiable mutation. A homozygous structural rearrangement within SLC38A8 was detected in the third patient and analysis is still ongoing in the other. WES in SLC38A8-negative cases identified a homozygous missense variant in FOXD1 (c.581G>A, p.(G194D)). This variant is rare and predicted to be damaging. Transcriptional luciferase assays are currently underway to investigate this variant’s effect on FOXD1 function.

Conclusions : Three novel SLC38A8 mutations were identified. One of the mutations was missed by traditional sequencing, thus raising the possibility of additional “missing” mutations in SLC38A8. A potential mutation in FOXD1 was detected indicating that this may be a new FHONDA disease gene. FOXD1 is required for the specification of the temporal retina in mammals and animal mutant models have aberrant axonal projections making it an excellent candidate gene for this disorder.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.