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NM_001112741.2(KCNC1):c.1370del (p.Lys457fs) AND Progressive myoclonic epilepsy type 7

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 29, 2019
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:
RCV000853393.1

Allele description [Variation Report for NM_001112741.2(KCNC1):c.1370del (p.Lys457fs)]

NM_001112741.2(KCNC1):c.1370del (p.Lys457fs)

Gene:
KCNC1:potassium voltage-gated channel subfamily C member 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11p15.1
Genomic location:
Preferred name:
NM_001112741.2(KCNC1):c.1370del (p.Lys457fs)
HGVS:
  • NC_000011.10:g.17772464del
  • NG_041827.1:g.41517del
  • NM_001112741.2:c.1370delMANE SELECT
  • NM_004976.4:c.1370del
  • NP_001106212.1:p.Lys457fs
  • NP_001106212.1:p.Lys457fs
  • NP_004967.1:p.Lys457fs
  • NC_000011.9:g.17794011del
  • NM_001112741.1:c.1370del
Protein change:
K457fs
Links:
dbSNP: rs1590106815
NCBI 1000 Genomes Browser:
rs1590106815
Molecular consequence:
  • NM_001112741.2:c.1370del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004976.4:c.1370del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Progressive myoclonic epilepsy type 7
Identifiers:
MONDO: MONDO:0014521; MedGen: C4015420; Orphanet: 435438; OMIM: 616187

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000996271Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Mar 29, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not 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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV000996271.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

This frameshifting variant occurs in exon 2 of 4 in the ENST00000265969 transcript (known as Kv3.1B in the literature), and exon 2 of 2 in the ENST00000379472 transcript (known as Kv3.1A in the literature). The variant introduces a premature stop codon and is therefore predicted to result in loss of normal protein function. This variant has not been previously reported or functionally characterized in the literature to our knowledge. It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Based on the available evidence, the c.1370del, p.Lys457ArgfsTer20 variant is classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Nov 20, 2023