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NM_006888.6(CALM1):c.293A>G (p.Asn98Ser) AND Catecholaminergic polymorphic ventricular tachycardia

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 10, 2017
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:
RCV000714909.11

Allele description [Variation Report for NM_006888.6(CALM1):c.293A>G (p.Asn98Ser)]

NM_006888.6(CALM1):c.293A>G (p.Asn98Ser)

Gene:
CALM1:calmodulin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q32.11
Genomic location:
Preferred name:
NM_006888.6(CALM1):c.293A>G (p.Asn98Ser)
Other names:
N97S
HGVS:
  • NC_000014.9:g.90404386A>G
  • NG_013338.1:g.12404A>G
  • NM_001363669.2:c.185A>G
  • NM_001363670.2:c.296A>G
  • NM_006888.6:c.293A>GMANE SELECT
  • NP_001350598.1:p.Asn62Ser
  • NP_001350599.1:p.Asn99Ser
  • NP_008819.1:p.Asn98Ser
  • NC_000014.8:g.90870730A>G
  • NM_006888.4:c.293A>G
  • NM_006888.5:c.293A>G
  • NP_008819.1:p.Asn98Ser(Asn97Ser)
  • P62158:p.Asn98Ser
Note:
NCBI staff reviewed the sequence information reported in PubMed 23040497 to determine the location of this allele on the current reference sequence. Their numbering of Asn97Ser, when begun at Met1, will be Asn98Ser.
Protein change:
N62S; ASN97SER
Links:
UniProtKB: P62158#VAR_069223; OMIM: 114180.0002; dbSNP: rs267607277
NCBI 1000 Genomes Browser:
rs267607277
Molecular consequence:
  • NM_001363669.2:c.185A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363670.2:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006888.6:c.293A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Catecholaminergic polymorphic ventricular tachycardia (CVPT)
Synonyms:
Familial polymorphic ventricular tachycardia; Catecholamine-induced polymorphic ventricular tachycardia; Polymorphic catecholergic ventricular tachycardia
Identifiers:
MONDO: MONDO:0017990; MedGen: C5574922; Orphanet: 3286; OMIM: PS604772

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000845664Royal Brompton Clinical Genetics And Genomics Laboratory, NHS South East Genomic Laboratory Hub
criteria provided, single submitter

(RBHT-CGGL ClinVar Assertion Criteria)		Likely pathogenic
(Aug 10, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Royal Brompton Clinical Genetics And Genomics Laboratory, NHS South East Genomic Laboratory Hub, SCV000845664.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

To the best of our knowledge the CALM1 c.293A>G variant has not been reported in any other patients, nor detected in approximately 120,000 individuals in control populations. Functional studies have demonstrated the variant has an impact on protein structure/function (Hwang et al. Circ Res. 2014 Mar 28;114(7):1114-24; Søndergaard et al. FEBS J. 2015 Feb;282(4):803-16; Søndergaard et al. J Biol Chem. 2015 Oct 23;290(43):26151-62; Vassilakopoulou et al. Biochim Biophys Acta. 2015 Nov;1850(11):2168-76). Evidence for pathogenicity: - Population Controls alleles / total (frequency): Exome Agregation Consortium (ExAC) - 0/121412 (0.0), RBH healthy cohort - 0/2144 (0.0) - Missense Effect Predictions - 42.86% (3/7) of algorithms have predicted that this variant will adversely affect protein function

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 9, 2024