NM_000218.3(KCNQ1):c.713_719del (p.Met238fs) AND Cardiovascular phenotype

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 10, 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:: RCV003311290.2

Allele description [Variation Report for NM_000218.3(KCNQ1):c.713_719del (p.Met238fs)]

NM_000218.3(KCNQ1):c.713_719del (p.Met238fs)

Gene:

KCNQ1:potassium voltage-gated channel subfamily Q member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p15.5

Genomic location:

Preferred name:

NM_000218.3(KCNQ1):c.713_719del (p.Met238fs)

HGVS:

NC_000011.10:g.2572042_2572048del
NG_008935.1:g.132052_132058del
NM_000218.3:c.713_719delMANE SELECT
NM_001406836.1:c.713_719del
NM_001406837.1:c.443_449del
NM_001406838.1:c.478-11393_478-11387del
NM_181798.2:c.332_338del
NP_000209.2:p.Met238Thrfs
NP_000209.2:p.Met238fs
NP_001393765.1:p.Met238fs
NP_001393766.1:p.Met148fs
NP_861463.1:p.Met111Thrfs
NP_861463.1:p.Met111fs
LRG_287t1:c.713_719del
LRG_287t2:c.332_338del
LRG_287:g.132052_132058del
LRG_287p1:p.Met238Thrfs
LRG_287p2:p.Met111Thrfs
NC_000011.9:g.2593272_2593278del
NM_000218.2:c.713_719delTGCTACA
NM_181798.1:c.332_338delTGCTACA
NR_040711.2:n.606_612delTGCTACA

Protein change:

M111fs

Molecular consequence:

NM_000218.3:c.713_719del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406836.1:c.713_719del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406837.1:c.443_449del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181798.2:c.332_338del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406838.1:c.478-11393_478-11387del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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BioSample links for Nucleotide (Select 6099033) (1)
BioSample
NIH_BMAP_M_S3.1
NIH_BMAP_M_S3.1

biosample
interleukin-31 receptor subunit alpha isoform 1 [Homo sapiens]
interleukin-31 receptor subunit alpha isoform 1 [Homo sapiens]
gi|115430248|ref|NP_620586.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004007864	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Apr 10, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004007864

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Apr 10, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV004007864.2

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

Description

The c.713_719delTGCTACA pathogenic mutation, located in coding exon 5 of the KCNQ1 gene, results from a deletion of 7 nucleotides at nucleotide positions 713 to 719, causing a translational frameshift with a predicted alternate stop codon (p.M238Tfs*23). This alteration has been observed in at least one individual with a personal and/or family history that is consistent with long QT syndrome (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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: May 1, 2024

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