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NM_001128840.3(CACNA1D):c.1998G>A (p.Leu666=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 18, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000504766.5
Variation ID:
504766
Description:
single nucleotide variant
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NM_001128840.3(CACNA1D):c.1998G>A (p.Leu666=)

Allele ID
496365
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p21.1
Genomic location
3: 53723897 (GRCh38) GRCh38 UCSC
3: 53757924 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.53757924G>A
NC_000003.12:g.53723897G>A
NG_032999.1:g.233849G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:53723896:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00111
1000 Genomes Project 0.00120
The Genome Aggregation Database (gnomAD) 0.00271
Exome Aggregation Consortium (ExAC) 0.00189
The Genome Aggregation Database (gnomAD), exomes 0.00196
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00146
Links
ClinGen: CA2454110
dbSNP: rs146747080
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jun 5, 2016 RCV000613860.1
Likely benign 1 criteria provided, single submitter Jun 28, 2017 RCV000625436.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 31, 2019 RCV000729981.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CACNA1D - - GRCh38
GRCh37
388 399

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 10, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000857685.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jun 05, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000711486.1
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Leu686Leu in exon 15 of CACNA1D: This variant is not expected to have clinical significance because it does not alter an amino acid residue and … (more)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001032122.2
Submitted: (Jan 29, 2020)
Evidence details
Benign
(Nov 06, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001891335.1
Submitted: (Sep 18, 2021)
Evidence details
Likely benign
(Jun 28, 2017)
criteria provided, single submitter
Method: clinical testing
Sinoatrial node dysfunction and deafness
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745352.1
Submitted: (Apr 09, 2018)
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CACNA1D - - - -

Text-mined citations for rs146747080...

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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 Sep 18, 2021