ClinVar Miner

Submissions for variant NM_023073.3(CPLANE1):c.8710C>T (p.Arg2904Ter) (rs141507441)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
UW Hindbrain Malformation Research Program,University of Washington RCV000201591 SCV000256303 pathogenic Joubert syndrome 17 2015-02-23 criteria provided, single submitter research
GeneDx RCV000523918 SCV000619642 pathogenic not provided 2017-10-25 criteria provided, single submitter clinical testing The R2904X variant in the C5orf42 gene has been reported previously in the homozygous state, and in the compound heterozygous state with a C5orf42 missense variant, in association with Joubert syndrome (Kroes et al., 2015). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R2904X variant is observed in 5/126498 (0.004%) alleles from individuals of non-Finnish European background in large population cohorts, but is not observed in the homozygous state (Lek et al., 2016). We interpret R2904X as a pathogenic variant.
Invitae RCV000523918 SCV000961477 pathogenic not provided 2020-01-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2904*) in the CPLANE1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs141507441, ExAC 0.009%). This variant has been observed in individual(s) with Joubert syndrome (PMID: 26092869, 25920555). This gene is also known as C5orf42 in the literature. ClinVar contains an entry for this variant (Variation ID: 217571). Loss-of-function variants in CPLANE1 are known to be pathogenic (PMID: 22425360, 24178751). For these reasons, this variant has been classified as Pathogenic.

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