ClinVar Miner

Submissions for variant NM_023073.3(CPLANE1):c.493del (p.Ile165fs) (rs606231259)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000521986 SCV000618307 pathogenic not provided 2019-01-14 criteria provided, single submitter clinical testing The c.493delA variant in the C5orf42 gene has been reported previously in multiple unrelated individuals with JSRD who also had a second C5orf42 variant identified (Lopez et al., 2014; Kroes et al., 2015). The c.493delA variant causes a frameshift starting with codon Isoleucine 165, changes this amino acid to a Tyrosine residue, and creates a premature Stop codon at position 17 of the new reading frame, denoted p.I165YfsX17. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Therefore, c.493delA is considered to be a pathogenic variant.
Genetic Services Laboratory, University of Chicago RCV000193986 SCV000246835 pathogenic Joubert syndrome 17 2015-06-12 criteria provided, single submitter clinical testing
Institute of Medical Genetics,University of Zurich RCV000193986 SCV000579463 pathogenic Joubert syndrome 17 2017-05-18 criteria provided, single submitter clinical testing
Invitae RCV000646709 SCV000768488 pathogenic Orofaciodigital syndrome 6; Joubert syndrome 17 2017-08-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ile165Tyrfs*17) in the C5orf42 gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been reported in individuals affected with Joubert syndrome (PMID: 25920555, 26092869, 28289185), as well as in individuals affected with Oral-Facial-Digital syndrome (PMID: 24178751). ClinVar contains an entry for this variant (Variation ID: 157513). Loss-of-function variants in C5orf42 are known to be pathogenic (PMID: 22425360). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000144858 SCV000191878 pathogenic Orofaciodigital syndrome 6 2014-03-01 no assertion criteria provided literature only
UW Hindbrain Malformation Research Program,University of Washington RCV000193986 SCV000256293 pathogenic Joubert syndrome 17 2015-02-23 criteria provided, single submitter research

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