ClinVar Miner

Submissions for variant NM_023073.3(CPLANE1):c.1819del (p.Tyr607fs) (rs777686211)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
UW Hindbrain Malformation Research Program,University of Washington RCV000201783 SCV000256325 pathogenic Joubert syndrome 17 2015-02-23 criteria provided, single submitter research
GeneDx RCV000313670 SCV000330222 pathogenic not provided 2017-07-03 criteria provided, single submitter clinical testing The c.1819delT pathogenic variant in the C5orf42 gene has been observed in an individual with Joubert syndrome and reported to be compound heterozygous with the L2606X nonsense variant; however, parental testing to confirm that the variants were in trans was not provided (Bachmann-Gagescu et al., 2015). Additionally, the c.1819delT variant has been observed with the Q142K variant in another individual with Joubert syndrome, although parental testing was not provided and this individual was reported to have two variants in the OFD1 gene (Bachmann-Gagescu et al., 2015). The c.1819delT variant was not observed with any significant frequency in approximately 2,300 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. This deletion causes a frameshift starting with codon Tyrosine 607, changes this amino acid to a Threonine residue and creates a premature Stop codon at position 6 of the new reading frame, denoted p.Y607TfsX6. The c.1819delT pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV000414845 SCV000492847 pathogenic Global developmental delay; Jaundice 2013-11-28 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000201783 SCV000593809 pathogenic Joubert syndrome 17 2015-08-26 criteria provided, single submitter clinical testing
Invitae RCV000627788 SCV000652564 pathogenic Orofaciodigital syndrome type 6; Joubert syndrome 17 2018-01-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr607Thrfs*6) in the C5orf42 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs777686211, ExAC 0.05%). This variant has been reported in the literature in individuals affected with Joubert syndrome (PMID: 26092869, 28125082). ClinVar contains an entry for this variant (Variation ID: 217590). Loss-of-function variants in C5orf42 are known to be pathogenic (PMID: 22425360). For these reasons, this variant has been classified as Pathogenic.
Mendelics RCV000201783 SCV001136827 pathogenic Joubert syndrome 17 2020-09-15 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000313670 SCV001247557 pathogenic not provided 2017-06-01 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV001198870 SCV001369865 pathogenic Orofaciodigital syndrome type 6 2019-04-18 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP5.
Institute of Human Genetics, University of Leipzig Medical Center RCV000201783 SCV001440004 likely pathogenic Joubert syndrome 17 2019-01-01 criteria provided, single submitter clinical testing This variant was identified as compound heterozygous.
Invitae RCV000313670 SCV001581112 pathogenic not provided 2020-06-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr607Thrfs*6) in the C5orf42 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs777686211, ExAC 0.05%). This variant has been reported in the literature in individuals affected with Joubert syndrome (PMID: 26092869, 28125082). ClinVar contains an entry for this variant (Variation ID: 217590). Loss-of-function variants in C5orf42 are known to be pathogenic (PMID: 22425360). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics,Fulgent Genetics RCV000627788 SCV001752717 pathogenic Orofaciodigital syndrome type 6; Joubert syndrome 17 2021-06-30 criteria provided, single submitter clinical testing
Sydney Genome Diagnostics,Children's Hospital Westmead RCV001328279 SCV001449200 likely pathogenic Nephronophthisis 2018-05-31 no assertion criteria provided clinical testing This patient is heterozygous for a likely pathogenic variant, c.1819del, in the C5orf42 gene. c.1819del (dbSNP: rs777686211) has been reported in the ExAC database (http://exac.broadinstitute.org/) with a low allele frequency of 0.024% (5/20526 alleles) and has also been reported as a compound heterozygous variant in a patient with Joubert syndrome (Bachmann-Gagescu et al. J.Med.Genet 2015; 52:514-522). This frameshifting variant is predicted to create a premature stop codon (p.Tyr607Thrfs*6) and may result in a null allele due to nonsense-mediated mRNA decay. This variant is considered to be a likely pathogenic according to the ACMG guidelines.
Human Genetics - Radboudumc,Radboudumc RCV000313670 SCV001956051 pathogenic not provided no assertion criteria provided clinical testing

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