Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Gene |
RCV000255984 | SCV000321491 | likely pathogenic | not provided | 2016-07-13 | criteria provided, single submitter | clinical testing | The R1193C variant in the C5orf42 gene has been reported previously in the presence of another C5orf42 variants in unrelated individuals with clinical diagnoses of OFD IV and Joubert syndrome (Lopez et al., 2014; Ohba et al., 2013). The R1193C variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R1193C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, we interpret R1193C as a likely pathogenic variant. |
| Broad Center for Mendelian Genomics, |
RCV001004928 | SCV001164445 | likely pathogenic | Joubert syndrome 17 | 2018-12-03 | criteria provided, single submitter | research | The heterozygous p.Arg1193Cys variant in C5orf42 was identified by our study in the compound heterozygous state, with a pathogenic variant, in one individual with Joubert syndrome. This variant has been identified in 0.005798% (1/17248) of East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs149170427). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools do not provide strong support for or against an impact to the protein. The p.Arg1193Cys variant in C5orf42 has been reported in 6 unrelated Japanese individuals with Joubert syndrome, including 2 individuals with the variant in the homozygous state and 4 individuals with the variant in the compound heterozygous state (PMID: 24091540, 24178751, 27434533, 28431631). The presence of this variant in combination with 4 unique variants (1 reported by our study, 1 reported pathogenic in ClinVar, 2 reported in the literature) and in an individual with Joubert syndrome increases the likelihood that the p.Arg1193Cys variant is pathogenic. In summary, although additional studies are required to fully establish its clinical significance, the p.Arg1193Cys variant is likely pathogenic. ACMG/AMP Criteria applied: PM2, PM3_Strong (Richards 2015). |
| Labcorp Genetics |
RCV000255984 | SCV001588174 | pathogenic | not provided | 2022-09-29 | criteria provided, single submitter | clinical testing | Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic. 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 expected to disrupt CPLANE1 protein function. ClinVar contains an entry for this variant (Variation ID: 265062). This missense change has been observed in individual(s) with clinical features of Joubert syndrome (PMID: 24091540, 24178751, 28431631). This variant is present in population databases (rs149170427, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1193 of the CPLANE1 protein (p.Arg1193Cys). |
| Department of Pediatrics, |
RCV004556055 | SCV005045311 | likely pathogenic | Orofaciodigital syndrome type 6 | 2024-02-01 | no assertion criteria provided | clinical testing |