Genotype-phenotype associations in a large PRPH2-related retinopathy cohort

Abstract

Molecular variant interpretation lacks disease gene-specific cohorts for determining variant enrichment in disease versus healthy populations. To address the molecular etiology of retinal degeneration, specifically the PRPH2-related retinopathies, we reviewed genotype and phenotype information obtained from 187 eyeGENE® participants from 161 families. Clinical details were provided by referring clinicians participating in the eyeGENE® Network. The cohort was sequenced for variants in PRPH2. Variant complementary DNA clusters and cohort frequency were compared to variants in public databases to help us to determine pathogenicity by current American College of Medical Genetics and Genomics/Association for Molecular Pathology interpretation criteria. The most frequent variant was c.828+3A>T, which affected 28 families (17.4%), and 25 of 79 (31.64%) variants were novel. The majority of missense variants clustered in the D2 intracellular loop of the peripherin-2 protein, constituting a hotspot. Disease enrichment was noted for 23 (29.1%) of the variants. Hotspot and disease-enrichment evidence modified variant classification for 16.5% of variants. The missense allele p.Arg172Trp was associated with a younger age of onset. To the best of our knowledge, this is the largest patient cohort review of PRPH2-related retinopathy. Large disease gene-specific cohorts permit gene modeling for hotspot and disease-enrichment analysis, providing novel variant classification evidence, including for novel missense variants.

Keywords: PRPH2; clinical variant interpretation; eyeGENE; genotype; phenotype; retinopathy.

Figure 1. Variable Expressions within eyeGENE^® Family 4 and Participant Diagnoses:

A: Participant 4.1 was enrolled under the preliminary diagnosis of Choroideremia at age 62 years. Age of onset was at 52 years. The participant’s visual acuity was 20/20 OU, with an abnormal, but recordable full-field ERG. B: Participant 4.2 was enrolled under the preliminary diagnosis of Stargardt disease at age 39 years. Age of onset was at 38 years. The participant’s visual acuity was 20/20 OD and 20/40 OS. An ERG was not performed. C: Pedigree of Family 4. Participant 4.3 was enrolled under the preliminary diagnosis of Stargardt disease but did not carry the familial PRPH2 variant c.828+3A>T. D: Percentage of participants by diagnosis category and variant exon location.

Figure 2. Age of Disease Onset of eyeGENE^® PRPH2 Variants:

A: Age of onsets were plotted against variant types. Median, 10%, 25%, 75%, 90% of quartiles were displayed in the box plots. The individual data points were also plotted. B: Age of onset for seven of the most recurrent eyeGENE^® variants with cohort AF > 0.01. The lowest median age of onset was for the p.Arg172Trp variant at 26 years of age. The p.Arg142Trp variant had the highest median age of onset at 57 years of age.

Figure 3. Schematic Representations of Peripherin-2 Protein and cDNA Positions of Variants and Allele Frequencies in eyeGENE^® Probands and gnomAD:

A: Top, PRPH2 gnomAD allele frequencies by cDNA position and variant type, only variants with gnomAD allele frequencies less than 0.5 are shown. Middle, cDNA variant location and allele frequencies in eyeGENE^® probands. Bottom, cDNA variant location and number of submitters in ClinVar. B: Schematic representation of Peripherin-2 protein with the distribution of variants found in eyeGENE^® participants by color. D1 and D2 represent the two intradiskal loops. The N and C termini are located in the space between the disk membrane and the rod outer segment plasma membrane, with the fusion peptide region from a.a. 312 to 326. Missense variants are indicated in red, truncating variants in blue, in-frame deletions in orange, and sites with both missense and truncating variants in pink. Figure created and modified from Protter (Omasits, Ahrens, Muller, & Wollscheid, 2014).

Figure 4. ACMG Classification of Variants, ClinVar Concordance, Fisher’s Exact Test of gnomAD Allele Frequency versus Proband Allele Frequency, and eyeGENE^® Proband Allele Frequencies versus gnomAD Allele Frequencies:

A: gnomAD allele frequency of ClinVar variants according to ClinVar classification. There were 29 variants classified as pathogenic in ClinVar, of which 2 were also found in gnomAD: c.425G>A p.Arg142Gln and c.623G>A p.Gly208Asp. B: eyeGENE^® proband allele frequency and gnomAD allele frequency for the common variants between these two datasets. The variants with p value < 0.00063 in the Fisher’s Exact test were annotated. C: PM1 and PS4 help determination of pathogenicity by ACMG classification criteria. D: Concordance of classifications between ClinVar and this study.