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NM_000069.3(CACNA1S):c.1948+1G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 14, 2019
Accession:
VCV000402472.4
Variation ID:
402472
Description:
single nucleotide variant
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NM_000069.3(CACNA1S):c.1948+1G>A

Allele ID
389357
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q32.1
Genomic location
1: 201075494 (GRCh38) GRCh38 UCSC
1: 201044622 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.201044622C>T
NC_000001.11:g.201075494C>T
NM_000069.3:c.1948+1G>A MANE Select splice donor
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:201075493:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
Links
ClinGen: CA078688
dbSNP: rs745712829
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 20, 2016 RCV000455181.1
Likely pathogenic 1 criteria provided, single submitter Jun 14, 2019 RCV001218682.2
Uncertain significance 1 no assertion criteria provided Sep 16, 2018 RCV000782247.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CACNA1S No evidence available No evidence available GRCh38
GRCh37
1121 1136

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 20, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000538560.1
Submitted: (Apr 03, 2017)
Evidence details
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Likely pathogenic
(Jun 14, 2019)
criteria provided, single submitter
Method: clinical testing
Hypokalemic periodic paralysis 1
Malignant hyperthermia, susceptibility to, 5
Allele origin: germline
Invitae
Accession: SCV001390577.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects a donor splice site in intron 13 of the CACNA1S gene. It is expected to disrupt RNA splicing and likely results … (more)
Uncertain significance
(Sep 16, 2018)
no assertion criteria provided
Method: research
not provided
Allele origin: germline
Gharavi Laboratory,Columbia University
Accession: SCV000920737.1
Submitted: (Mar 05, 2019)
Evidence details

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
Dihydropyridine receptor (DHPR, CACNA1S) congenital myopathy. Schartner V Acta neuropathologica 2017 PMID: 28012042
Novel pathogenic variants and genes for myopathies identified by whole exome sequencing. Hunter JM Molecular genetics & genomic medicine 2015 PMID: 26247046
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs745712829...

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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 Jul 07, 2021