We identified seven different likely mutations in six IRD families; of these, six had not been reported previously (
Table 2;
Fig. 1). Four of the variants are missense, one is predicted to affect splicing, and two are predicted to result in frameshift and protein truncation. None of the variants has been reported in the whole-genome sequence data of 100 Zulu, 100 Bagandan, or 120 Ethiopian individuals in the AGVP study.
33 Additionally, these variants are not detected in 97 Luyha or 88 Yoruba individuals in the 1000 Genomes data.
30 Therefore, the seven variants identified in IRD families are not present in 505 control African individuals (1010 chromosomes), providing additional evidence in support of their pathogenicity. The previously reported autosomal recessive RP (arRP) mutation p.(His620GlnfsTer23) in
PDE6B was present only once in 4266 alleles in the NHLBI WES dataset (ESP) of African Americans (rs769671323, as of 27 October 2015); this frameshift mutation is predicted to generate a truncated protein lacking over 200 C-terminal amino acids.
34 The second frameshift mutation identified in
ABCA4 is predicted to truncate the protein by 612 C-terminal amino acids. The c.698-1G>A variant in the acceptor splice site of exon 8 of
PRPF31, interrogated by Human Splicing Finder 3.0,
35 is predicted to activate an intronic cryptic acceptor site while simultaneously disrupting an exon splicing silencer site and creating an exon splicing enhancer site. Therefore, all seven variants were computationally predicted to be pathogenic, cosegregated with disease in the respective families, verified by Sanger sequencing, and exhibited conservation across vertebrates (
Fig. 2). According to ACMG guidelines for the interpretation of sequence variants,
36 the frameshift truncations identified in this study have sufficient evidence to classify them as “pathogenic,” while each of the splice site or missense variants meets the criteria of “likely pathogenic” variants in the absence of functional studies.