NM_001384732.1(CPLANE1):c.1270C>T (p.Arg424Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Sep 15, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000438829.2

Allele description [Variation Report for NM_001384732.1(CPLANE1):c.1270C>T (p.Arg424Ter)]

NM_001384732.1(CPLANE1):c.1270C>T (p.Arg424Ter)

Gene:
CPLANE1:ciliogenesis and planar polarity effector 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p13.2
Genomic location:
Preferred name:
NM_001384732.1(CPLANE1):c.1270C>T (p.Arg424Ter)
HGVS:
  • NC_000005.10:g.37227669G>A
  • NG_032772.2:g.26760C>T
  • NM_001384732.1:c.1270C>TMANE SELECT
  • NM_023073.3:c.1270C>T
  • NM_023073.4:c.1270C>T
  • NP_001371661.1:p.Arg424Ter
  • NP_075561.3:p.Arg424Ter
  • NP_075561.3:p.Arg424Ter
  • NC_000005.9:g.37227771G>A
Protein change:
R424*
Links:
dbSNP: rs755097302
NCBI 1000 Genomes Browser:
rs755097302
Molecular consequence:
  • NM_001384732.1:c.1270C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_023073.3:c.1270C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_023073.4:c.1270C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000535549GeneDxcriteria provided, single submitter
Pathogenic
(Jan 16, 2017)
germlineclinical testing

Citation Link,

SCV001584116Invitaecriteria provided, single submitter
Pathogenic
(Sep 15, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in C5ORF42 cause Joubert syndrome in the French Canadian population.

Srour M, Schwartzentruber J, Hamdan FF, Ospina LH, Patry L, Labuda D, Massicotte C, Dobrzeniecka S, Capo-Chichi JM, Papillon-Cavanagh S, Samuels ME, Boycott KM, Shevell MI, Laframboise R, D├ęsilets V; FORGE Canada Consortium., Maranda B, Rouleau GA, Majewski J, Michaud JL.

Am J Hum Genet. 2012 Apr 6;90(4):693-700. doi: 10.1016/j.ajhg.2012.02.011. Epub 2012 Mar 15.

PubMed [citation]
PMID:
22425360
PMCID:
PMC3322222

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From GeneDx, SCV000535549.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The R424X variant in the C5orf42 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R424X variant was not observed in approximately 2300 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret R424X as a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001584116.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Arg424*) in the C5orf42 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs755097302, ExAC 0.03%). This variant has not been reported in the literature in individuals with C5orf42-related disease. ClinVar contains an entry for this variant (Variation ID: 392297). Loss-of-function variants in C5orf42 are known to be pathogenic (PMID: 22425360). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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