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NM_000069.3(CACNA1S):c.5049-2A>G

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 8, 2020
Accession:
VCV000541072.4
Variation ID:
541072
Description:
single nucleotide variant
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NM_000069.3(CACNA1S):c.5049-2A>G

Allele ID
515444
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q32.1
Genomic location
1: 201041591 (GRCh38) GRCh38 UCSC
1: 201010719 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.201010719T>C
NC_000001.11:g.201041591T>C
NG_009816.1:g.75976A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:201041590:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00009
Exome Aggregation Consortium (ExAC) 0.00010
The Genome Aggregation Database (gnomAD) 0.00045
1000 Genomes Project 0.00020
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
Trans-Omics for Precision Medicine (TOPMed) 0.00051
Links
ClinGen: CA083706
dbSNP: rs148989517
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Oct 8, 2020 RCV000651268.3
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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
Likely pathogenic
(Oct 08, 2020)
criteria provided, single submitter
Method: clinical testing
Hypokalemic periodic paralysis 1
Malignant hyperthermia, susceptibility to, 5
Allele origin: germline
Invitae
Accession: SCV000773119.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change affects an acceptor splice site in intron 40 of the CACNA1S gene. It is expected to disrupt RNA splicing and likely results … (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
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 rs148989517...

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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 Oct 08, 2021