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NM_000719.7(CACNA1C):c.5665C>T (p.Arg1889Cys) AND Timothy syndrome

Germline classification:
Benign (1 submission)
Last evaluated:
Jun 23, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002272059.9

Allele description [Variation Report for NM_000719.7(CACNA1C):c.5665C>T (p.Arg1889Cys)]

NM_000719.7(CACNA1C):c.5665C>T (p.Arg1889Cys)

Genes:
CACNA1C-AS1:CACNA1C antisense RNA 1 [Gene - HGNC]
CACNA1C:calcium voltage-gated channel subunit alpha1 C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p13.33
Genomic location:
Preferred name:
NM_000719.7(CACNA1C):c.5665C>T (p.Arg1889Cys)
Other names:
p.R1889C:CGC>TGC
HGVS:
  • NC_000012.12:g.2685827C>T
  • NG_008801.2:g.720042C>T
  • NM_000719.7:c.5665C>TMANE SELECT
  • NM_001129827.2:c.5809C>T
  • NM_001129829.2:c.5788C>T
  • NM_001129830.3:c.5770C>T
  • NM_001129831.2:c.5749C>T
  • NM_001129832.2:c.5725C>T
  • NM_001129833.2:c.5722C>T
  • NM_001129834.2:c.5722C>T
  • NM_001129835.2:c.5722C>T
  • NM_001129836.2:c.5716C>T
  • NM_001129837.2:c.5689C>T
  • NM_001129838.2:c.5689C>T
  • NM_001129839.2:c.5683C>T
  • NM_001129840.2:c.5665C>T
  • NM_001129841.2:c.5665C>T
  • NM_001129842.2:c.5665C>T
  • NM_001129843.2:c.5665C>T
  • NM_001129844.2:c.5656C>T
  • NM_001129846.2:c.5632C>T
  • NM_001167623.2:c.5665C>T
  • NM_001167624.3:c.5770C>T
  • NM_001167625.2:c.5845C>T
  • NM_199460.4:c.5914C>T
  • NP_000710.5:p.Arg1889Cys
  • NP_001123299.1:p.Arg1937Cys
  • NP_001123301.1:p.Arg1930Cys
  • NP_001123302.2:p.Arg1924Cys
  • NP_001123303.1:p.Arg1917Cys
  • NP_001123304.1:p.Arg1909Cys
  • NP_001123305.1:p.Arg1908Cys
  • NP_001123306.1:p.Arg1908Cys
  • NP_001123307.1:p.Arg1908Cys
  • NP_001123308.1:p.Arg1906Cys
  • NP_001123309.1:p.Arg1897Cys
  • NP_001123310.1:p.Arg1897Cys
  • NP_001123311.1:p.Arg1895Cys
  • NP_001123312.1:p.Arg1889Cys
  • NP_001123313.1:p.Arg1889Cys
  • NP_001123314.1:p.Arg1889Cys
  • NP_001123315.1:p.Arg1889Cys
  • NP_001123316.1:p.Arg1886Cys
  • NP_001123318.1:p.Arg1878Cys
  • NP_001161095.1:p.Arg1889Cys
  • NP_001161096.2:p.Arg1924Cys
  • NP_001161097.1:p.Arg1949Cys
  • NP_955630.3:p.Arg1972Cys
  • LRG_334t1:c.5665C>T
  • LRG_334:g.720042C>T
  • LRG_334p1:p.Arg1889Cys
  • NC_000012.11:g.2794993C>T
  • NM_000719.6:c.5665C>T
Protein change:
R1878C
Links:
dbSNP: rs185788586
NCBI 1000 Genomes Browser:
rs185788586
Molecular consequence:
  • NM_000719.7:c.5665C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129827.2:c.5809C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129829.2:c.5788C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129830.3:c.5770C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129831.2:c.5749C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129832.2:c.5725C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129833.2:c.5722C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129834.2:c.5722C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129835.2:c.5722C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129836.2:c.5716C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129837.2:c.5689C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129838.2:c.5689C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129839.2:c.5683C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129840.2:c.5665C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129841.2:c.5665C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129842.2:c.5665C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129843.2:c.5665C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129844.2:c.5656C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001129846.2:c.5632C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001167623.2:c.5665C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001167624.3:c.5770C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001167625.2:c.5845C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_199460.4:c.5914C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Timothy syndrome (TS)
Synonyms:
Long QT syndrome with syndactyly
Identifiers:
MONDO: MONDO:0010979; MeSH: C536962; MedGen: C1832916; OMIM: 601005

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002556950Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Jun 23, 2020) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetics and Molecular Pathology, SA Pathology, SCV002556950.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The CACNA1C c.5665C>T variant is classified as Benign (BA1, BP4) The frequency of this variant in population databases is higher than expected for this disorder indicating this variant is a benign polymorphism (BA1). Multiple lines of computational evidence suggest this variant has no impact on the gene or gene product (BP4). The variant has been reported in dbSNP (rs185788586) and in the HGMD database: CM1413436 - ?disease causing mutation. It has been reported as Benign/Likely benign by other diagnostic laboratories (ClinVar Variation ID: 93417).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024