NM_000719.7(CACNA1C):c.5619GGA[1] (p.Glu1874del) AND Long QT syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 26, 2023
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:: RCV000462994.11

Allele description [Variation Report for NM_000719.7(CACNA1C):c.5619GGA[1] (p.Glu1874del)]

NM_000719.7(CACNA1C):c.5619GGA[1] (p.Glu1874del)

Genes:

CACNA1C-AS1:CACNA1C antisense RNA 1 [Gene - HGNC]
CACNA1C:calcium voltage-gated channel subunit alpha1 C [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

12p13.33

Genomic location:

Preferred name:

NM_000719.7(CACNA1C):c.5619GGA[1] (p.Glu1874del)

HGVS:

NC_000012.12:g.2685781GGA[1]
NG_008801.2:g.719996GGA[1]
NM_000719.7:c.5619GGA[1]MANE SELECT
NM_001129827.2:c.5763GGA[1]
NM_001129829.2:c.5742GGA[1]
NM_001129830.3:c.5724GGA[1]
NM_001129831.2:c.5703GGA[1]
NM_001129832.2:c.5679GGA[1]
NM_001129833.2:c.5676GGA[1]
NM_001129834.2:c.5676GGA[1]
NM_001129835.2:c.5676GGA[1]
NM_001129836.2:c.5670GGA[1]
NM_001129837.2:c.5643GGA[1]
NM_001129838.2:c.5643GGA[1]
NM_001129839.2:c.5637GGA[1]
NM_001129840.2:c.5619GGA[1]
NM_001129841.2:c.5619GGA[1]
NM_001129842.2:c.5619GGA[1]
NM_001129843.2:c.5619GGA[1]
NM_001129844.2:c.5610GGA[1]
NM_001129846.2:c.5586GGA[1]
NM_001167623.2:c.5619GGA[1]
NM_001167624.3:c.5724GGA[1]
NM_001167625.2:c.5799GGA[1]
NM_199460.4:c.5868GGA[1]
NP_000710.5:p.Glu1874del
NP_001123299.1:p.Glu1922del
NP_001123301.1:p.Glu1915del
NP_001123302.2:p.Glu1909del
NP_001123303.1:p.Glu1902del
NP_001123304.1:p.Glu1894del
NP_001123305.1:p.Glu1893del
NP_001123306.1:p.Glu1893del
NP_001123307.1:p.Glu1893del
NP_001123308.1:p.Glu1891del
NP_001123309.1:p.Glu1882del
NP_001123310.1:p.Glu1882del
NP_001123311.1:p.Glu1880del
NP_001123312.1:p.Glu1874del
NP_001123313.1:p.Glu1874del
NP_001123314.1:p.Glu1874del
NP_001123315.1:p.Glu1874del
NP_001123316.1:p.Glu1871del
NP_001123318.1:p.Glu1863del
NP_001161095.1:p.Glu1874del
NP_001161096.2:p.Glu1909del
NP_001161097.1:p.Glu1934del
NP_955630.3:p.Glu1957del
LRG_334t1:c.5622_5624del
LRG_334:g.719996GGA[1]
NC_000012.11:g.2794945_2794947del
NC_000012.11:g.2794947GGA[1]
NM_000719.6:c.5622_5624del
NM_000719.6:c.5622_5624delGGA

Protein change:

E1863del

Links:

dbSNP: rs757172314

NCBI 1000 Genomes Browser:

rs757172314

Molecular consequence:

NM_000719.7:c.5619GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129827.2:c.5763GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129829.2:c.5742GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129830.3:c.5724GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129831.2:c.5703GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129832.2:c.5679GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129833.2:c.5676GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129834.2:c.5676GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129835.2:c.5676GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129836.2:c.5670GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129837.2:c.5643GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129838.2:c.5643GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129839.2:c.5637GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129840.2:c.5619GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129841.2:c.5619GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129842.2:c.5619GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129843.2:c.5619GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129844.2:c.5610GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001129846.2:c.5586GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001167623.2:c.5619GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001167624.3:c.5724GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001167625.2:c.5799GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_199460.4:c.5868GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Long QT syndrome (LQTS)
Identifiers:: MONDO: MONDO:0002442; MeSH: D008133; MedGen: C0023976

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000553025	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 26, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000553025

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 26, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000553025.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant, c.5622_5624del, results in the deletion of 1 amino acid(s) of the CACNA1C protein (p.Glu1874del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs757172314, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CACNA1C-related conditions. ClinVar contains an entry for this variant (Variation ID: 411730). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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