Genome‐wide linkage and sequence analysis challenge CCDC66 as a human retinal dystrophy candidate gene and support a distinct NMNAT1‐related fundus phenotype

Abstract

Funding informationStiftung Auge (Deutsche Ophthalmologische Gesellschaft, DOG.To uncover the genotype underlying early-onset cone-rod dystrophy and central nummular macular atrophic lesion in 2 siblings from an endogamous Arab family, we performed targeted next-generation sequencing (NGS) of 44 retinal dystrophy genes, whole-exome sequencing (WES) and genome-wide linkage analysis. Targeted NGS and WES in the index patient highlighted 2 homozygous variants, a CCDC66 frameshift deletion and a novel missense NMNAT1 variant, c.500G>A (p.Asn167Ser). Linkage and segregation analysis excluded the CCDC66 variant and confirmed the NMNAT1 mutation. Biallelic NMNAT1 mutations cause Leber congenital amaurosis with a central nummular macular atrophic lesion (LCA9). The NMNAT1 mutation reported here underlied cone-rod dystrophy rather than LCA but the fundus lesion was compatible with that of LCA9 patients, highlighting that such a fundus appearance should raise suspicion for biallelic mutations in NMNAT1 when in the context of any retinal dystrophy.Although Ccdc66 mutations have been proposed to cause retinal disease in dogs, our results and public databases challenge CCDC66 as a candidate gene for human retinal dystrophy. | METHODS Institutional board approval (Ethics Committee of the University ofCologne) and signed informed consent were obtained for this report.Methodology of NGS of known retinal dystrophy genes, genome-wide linkage analysis, and whole-exome sequencing (WES) are provided in Appendix S1, Methodology.3 | RESULTS | Clinical investigationsA 13-year-old index patient (Figure 1A,B; II:1, Figure 2B), the first of 4 siblings, had worsening visual acuity since early childhood.Her parents were from the same tribe, and a younger brother, the third sibling (Figure 1C,D; II:3, Figure 2B), was similarly affected. Development was considered normal until II:1 was 3 years old, when the parents noted difficulty with navigating stairs. Soon thereafter, poor vision, particularly in daylight, and eye shaking were noted. When seen at 13 years of age, she had 4/200 vision in either eye, eccentric fixation, moderate exotropia, and pendular nystagmus with small amplitude and high frequency.

NMNAT1 variants cause cone and cone-rod dystrophy

“…Our findings indicate that the homozygous variant in Case 1, initially reported as "inconclusive", is significant and should not be ignored, and that the NMNAT1 variants in Case 2 are causative of the disease phenotype. This is further supported by the recent report of two siblings with a homozygous NMNAT1 variant c.[500A > G] p.(Asn167Ser) who had a clinical diagnosis of CRD with atrophic macular changes [21]. This affects clinical management, especially for adult cases where there may be a consanguineous union, heralding the need for investigation for the variant in the partner, since presence would indicate a 50% recurrence risk.…”

SARM1 depletion rescues NMNAT1-dependent photoreceptor cell death and retinal degeneration

“…NMNAT1 is a nuclear enzyme that synthesizes NAD + , an essential metabolite that is central to all aspects of cellular metabolism. NMNAT1 is indispensable for mouse development ( Conforti et al, 2011 ) and recent studies identified causative mutations in NMNAT1 in patients with Leber congenital amaurosis type 9 (LCA9), a disorder associated with severe, early-onset retinal degeneration and vision loss ( Falk et al, 2012 ; Perrault et al, 2012 ; Koenekoop et al, 2012 ; Chiang et al, 2012 ; Coppieters et al, 2015 ; Khan et al, 2018 ). Patients with LCA9 have no systemic involvement outside the eye, suggesting that certain cells within the retina are particularly vulnerable to the loss of NMNAT1 function.…”

“…LCA is the most common cause of blindness in children and about 70% of LCA cases are associated with mutations in genes related to the visual cycle, cGMP production, ciliogenesis, or transcription. Recently, more than thirty mutations in the nuclear NAD + biosynthetic enzyme NMNAT1 were identified in patients with autosomal recessive LCA type 9 (LCA9) ( Falk et al, 2012 ; Perrault et al, 2012 ; Koenekoop et al, 2012 ; Chiang et al, 2012 ; Coppieters et al, 2015 ; Khan et al, 2018 ). Despite the ubiquitous expression of this key NAD + biosynthesis enzyme, LCA9 patients have no other systemic deficits outside the retina.…”

Neurodegeneration in the olfactory bulb and olfactory deficits in the Ccdc66 -/- mouse model for retinal degeneration

“…In a cohort of 80 RP and 20 Leber congenital amaurosis patients no pathogenic variant has been found ( Gerding et al, 2011 ). In addition, a homozygous missense mutation in the CCDC66 gene was recently excluded by linkage and segregation analysis to be disease causing in two Arabian siblings with retinal dystrophy, or in this particular type of retinal degeneration ( Khan et al, 2018 ). The more precise description of the Ccdc66 -/- mouse may allow to predict defined groups of patients with retinal degeneration of unknown cause (besides RP) that might be promising candidates to be tested for CCDC66 mutation in order to identify disease-causing mutations in humans.…”