Mutations in TULP1, NR2E3, and MFRP genes in Indian families with autosomal recessive retinitis pigmentosa

Abstract

Purpose: To identify genes underlying autosomal recessive retinitis pigmentosa (ARRP) by homozygosity mapping.

Methods: Families with ARRP were recruited after complete ophthalmic evaluation of all members and diagnosis of RP by predefined criteria. Genomic DNA from affected members of 26 families was genotyped on Illumina single nucleotide polymorphism (SNP) 6.0 K arrays with standard procedures. Genotypes were evaluated for homozygous regions that were common and concordant between affected members of each family. The genes mapping to homozygous intervals within these families were screened for pathogenic changes with PCR amplification and sequencing of coding regions. Co-segegration of sequence changes with disease was determined within each pedigree, and each variation was tested for presence in 100 unrelated normal controls.

Results: A genome-wide scan for homozygosity showed homozygous regions harboring the tubby like protein 1 gene (TULP1; chromosome 6) in one family, the nuclear receptor subfamily 2, group E, member 3 gene (NR2E3; chromosome 15) in three families, and the membrane frizzled-related protein gene (MFRP; chromosome 11) in one family. Screening of the three genes in the respective families revealed homozygous disease-causing mutations in three families. These included a missense mutation in TULP1, a deletion-cum-insertion in NR2E3, and a single base deletion in MFRP. Patients from all three families had a rod-cone type of dystrophy with night blindness initially. The NR2E3 and MFRP genes were associated with fundus features atypical of RP.

Conclusions: This study shows involvement of the TULP1, NR2E3, and MFRP genes in ARRP in Indian cases. Genome-wide screening with SNP arrays followed by a prioritized candidate gene evaluation is useful in identifying genes in these patients.

Figure 1

Details of ARRP patient from Family A with a mutation in the TULP1 gene. A: Pedigree shows affected (dark symbols) and unaffected (open) symbols, with squares representing men and circles representing women. A double line connecting spouses denotes consanguinity. B: Sequence chromatogram of the TULP1 gene in normal control (top) and in patient A-1 (bottom) with homozygous mutation T>G (arrows), resulting in a codon change AAT (Asn) to AAG (Lys). The protein sequence alignment of TULP1 from different species (C) shows conservation of the Asn349 residue. Fundus photograph of right (D) and left (E) eyes of patient A-1 taken at age nine years shows greyish discoloration of the retina due to widespread RPE atrophy, severe arterial narrowing, disc pallor, and cellophane retinopathy due to a thin epiretinal membrane.

Figure 2

Molecular and clinical details of a patient from Family B with a mutation in the NR2E3 gene. A: Pedigree is shown (explanation of symbols as in Figure 1). B: Sequence of the NR2E3 gene in normal control (top) and patient B2 with homozygous deletion+insertion (bottom). The dinucleotide undergoing deletion is boxed in top panel. The arrows in the bottom panel mark the inserted sequence. C: Fundus montage of right eye of patient B-2 (aged 10 years) with NR2E3 mutation showing peripheral graying of retina with white flecks due to RPE atrophy with macular sparing with hardly any disc or arterial changes. The right temporal retina had unexplained sub-retinal scarring/gliosis and no obvious bone corpuscular pigment migration at this age.

Figure 3

Molecular and clinical details of patient from Family C with a mutation in the MFRP gene. A: The family pedigree is shown. B: Sequence of MFRP gene in normal control (top panel) and in patient C-1 (bottom panel). The arrows in the top and bottom panels respectively, mark the SNP c.492C>T (rs36015759) and the position of the single base deletion in patient C-1. C: Fundus montage of the right eye of patient C-1 (aged 21 years) from Family C with an MFRP gene mutation showing perifoveal pigment deposits, relative parafoveal sparing, diffuse extensive graying of retina with white flecks extending from arcades to the peripheral retina, and the presence of a peripheral reticular, bone corpuscular type of pigmentary retinopathy. There is not much disc pallor or arterial narrowing.