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

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: May 5, 2021)
Last evaluated:
Sep 29, 2017
Accession:
VCV000392297.5
Variation ID:
392297
Description:
single nucleotide variant
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NM_001384732.1(CPLANE1):c.1270C>T (p.Arg424Ter)

Allele ID
368487
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5p13.2
Genomic location
5: 37227669 (GRCh38) GRCh38 UCSC
5: 37227771 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.9:g.37227771G>A
NC_000005.10:g.37227669G>A
NG_032772.2:g.26760C>T
... more HGVS
Protein change
R424*
Other names
-
Canonical SPDI
NC_000005.10:37227668:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00004
Links
ClinGen: CA3239117
dbSNP: rs755097302
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Sep 15, 2017 RCV000438829.2
Pathogenic 1 criteria provided, single submitter Sep 29, 2017 RCV000694430.1
Pathogenic 1 no assertion criteria provided Jan 2, 2021 RCV001729596.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CPLANE1 - - GRCh38
GRCh37
715 824

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 29, 2017)
criteria provided, single submitter
Method: clinical testing
Orofaciodigital syndrome 6
Joubert syndrome 17
Allele origin: germline
Invitae
Accession: SCV000822876.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (1)
Comment:
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 … (more)
Pathogenic
(Jan 16, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000535549.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
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 … (more)
Pathogenic
(Sep 15, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001584116.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
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 … (more)
Pathogenic
(Jan 02, 2021)
no assertion criteria provided
Method: research
Joubert syndrome 1
(Autosomal recessive inheritance)
Allele origin: inherited
Department of Neurology, Linyi People’s Hospital,The Eleventh Clinical Medical College of Qingdao University
Accession: SCV001571327.1
Submitted: (May 05, 2021)
Evidence details
Comment:
The nonsense variant c.1270C>T (p.Arg424*) in exon 10 resulted in the 2120th base with the change from C to T in the coding region of … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Mutations in C5ORF42 cause Joubert syndrome in the French Canadian population. Srour M American journal of human genetics 2012 PMID: 22425360

Text-mined citations for rs755097302...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021