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NM_001127222.2(CACNA1A):c.5897G>A (p.Arg1966Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 29, 2021)
Last evaluated:
Aug 30, 2020
Accession:
VCV000381583.9
Variation ID:
381583
Description:
single nucleotide variant
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NM_001127222.2(CACNA1A):c.5897G>A (p.Arg1966Gln)

Allele ID
377235
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 13214276 (GRCh38) GRCh38 UCSC
19: 13325090 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.13325090C>T
NC_000019.10:g.13214276C>T
NG_011569.1:g.297185G>A
... more HGVS
Protein change
R1967Q, R1972Q, R1969Q, R1966Q
Other names
-
Canonical SPDI
NC_000019.10:13214275:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
Trans-Omics for Precision Medicine (TOPMed) 0.00039
The Genome Aggregation Database (gnomAD), exomes 0.00059
Trans-Omics for Precision Medicine (TOPMed) 0.00044
The Genome Aggregation Database (gnomAD) 0.00013
Exome Aggregation Consortium (ExAC) 0.00036
The Genome Aggregation Database (gnomAD) 0.00039
Links
ClinGen: CA9239549
dbSNP: rs199886234
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Jun 17, 2019 RCV000653359.5
Likely benign 1 criteria provided, single submitter Mar 21, 2017 RCV000719656.1
Uncertain significance 1 criteria provided, single submitter May 28, 2019 RCV000990165.1
Benign 1 criteria provided, single submitter Aug 30, 2020 RCV001083556.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 23, 2017 RCV000439336.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CACNA1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2001 2040

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000538549.1
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)
Benign
(May 23, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000708577.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Mar 21, 2017)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000850526.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Does not segregate with disease in family study (genes with incomplete penetrance);Subpopulation frequency in support of benign classification
Benign
(Aug 30, 2020)
criteria provided, single submitter
Method: clinical testing
Developmental and epileptic encephalopathy, 42
Episodic ataxia type 2
Allele origin: germline
Invitae
Accession: SCV000775238.4
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jun 03, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000521005.5
Submitted: (Sep 29, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 23869231, 21703448, 28488083)
Uncertain significance
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Episodic ataxia type 2
Allele origin: unknown
Mendelics
Accession: SCV001141008.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Jun 17, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143338.1
Submitted: (Sep 25, 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
Whole genome SNP genotyping and exome sequencing reveal novel genetic variants and putative causative genes in congenital hyperinsulinism. Proverbio MC PloS one 2013 PMID: 23869231
Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Klassen T Cell 2011 PMID: 21703448
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CACNA1A - - - -

Text-mined citations for rs199886234...

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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