ClinVar Genomic variation as it relates to human health

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PP3,PP5.

The CNGA1 c.1166C>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PM2, PP1, PS3, PM3. Based on this evidence we have classified this variant as Likely Pathogenic.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22995991, 24265693, 7479749, 31054281, 28981474, 31456290, 34426522, 31429209, 32531858, 35456422, 36460718, 25326637, 34906470)

The CNGA1 c.959C>T (p.Ser320Phe) missense variant, also referred to as c.1166C>T (p.Ser389Phe) and p.Ser316Phe, was found in a compound heterozygous state in six probands, including two sibling pairs, with autosomal recessive retinintis pigmentosa (Dryja et al. 1995; Eisenberger et al. 2013; Comander et al. 2017). Control data is unavailable for this variant, which is reported at a frequency of 0.001914 in the European (non-Finnish) population of the Genome Aggregation Database. Dryja et al. (1995) investigated channel function and found the p.Ser389Phe variant was similar to wild type for channel current and open times of the channel, however, the location was found to be intracellular, whereas wild type CNGA1 protein was located at the cell membrane. Based on the evidence, this variant is classified as likely pathogenic for autosomal recessive retinitis pigmentosa. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The p.Ser320Phe variant in CNGA1 (also described as p.Ser316Phe and p.Ser389Phe in the literature) has been reported in compound heterozygous state in 4 individ uals with autosomal recessive retinitis pigmentosa (RP), and segregated with dis ease in 2 affected relatives from 2 families (Dryja 1995, Eisenberger 2013, Coma nder 2017). In vitro functional studies provide some evidence that the p.Ser320P he variant may impact protein function (Dryja 1995). This variant has been repor ted in ClinVar (Variation ID: 424770) and has been identified in 0.19% (242/1264 08) Of European chromosomes by the Genome Aggregation Database (gnomAD, http://g nomad.broadinstitute.org; dbSNP rs62625014). Please note that this frequency is low enough to be consistent with the frequency of RP in the general population. In summary, although additional studies are required to fully establish its clin ical significance, the p.Ser320Phe variant is likely pathogenic for RP in an aut osomal recessive manner. ACMG/AMP Criteria applied: PM3_Strong; PP1; PS3_Support ing.

Variant summary: CNGA1 c.947C>T (p.Ser316Phe) results in a non-conservative amino acid change located in the Ion transport domain (IPR005821) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0011 in 249220 control chromosomes, predominantly at a frequency of 0.0019 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 2-fold of the estimated maximal expected allele frequency for a pathogenic variant in CNGA1 causing Retinitis Pigmentosa phenotype (0.00088), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.947C>T has been reported in the literature in multiple individuals affected with Retinitis Pigmentosa, either at a compound heterozygous with second pathogenic variants or at a homozygous state (examples, Dryja_1995, Lee_CNGA1_2014, Weisschuh_2020). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of frequencies of detecting functional cGMP-activated channel in HEK293 cells and the variant CNGA1 was predominantly retained inside the cell instead of being targeted to the plasma membrane (Dryja_1995). The following publications have been ascertained in the context of this evaluation (PMID: 7479749, 25326637, 32531858). 12 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 320 of the CNGA1 protein (p.Ser320Phe). This variant is present in population databases (rs62625014, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of retinitis pigmentosa (PMID: 7479749, 24265693, 25326637, 28981474; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is also known as Ser316Phe and p.Ser389Phe. ClinVar contains an entry for this variant (Variation ID: 16932). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CNGA1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects CNGA1 function (PMID: 7479749). For these reasons, this variant has been classified as Pathogenic.

CNGA1: PM3:Very Strong, PP1:Strong, PM2:Supporting

The CNGA1 c.959C>T variant is predicted to result in the amino acid substitution p.Ser320Phe. This variant has been reported in compound heterozygous state in several individuals with retinal disorders (reported as p.Ser316Phe or p.Ser389Phe in Dryja et al. 1995. PubMed ID: 7479749; Eisenberger et al. 2013. PubMed ID: 24265693; Comander et al. 2017. PubMed ID: 28981474; Table S1, Weisschuh et al. 2020. PubMed ID: 32531858). Functional studies using protein expression in cell culture found that the p.Ser320Phe substitution causes the protein to mislocalize within the cell (Dryja et al. 1995. PubMed ID: 7479749). This variant is reported in 0.19% of alleles in individuals of European (Non-Finnish) descent in gnomAD, indicating it is relatively common in this population. This variant is interpreted as pathogenic.