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NM_172107.4(KCNQ2):c.1617C>T (p.Ser539=) AND Seizure

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 1, 2021
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:
RCV001391281.2

Allele description [Variation Report for NM_172107.4(KCNQ2):c.1617C>T (p.Ser539=)]

NM_172107.4(KCNQ2):c.1617C>T (p.Ser539=)

Gene:
KCNQ2:potassium voltage-gated channel subfamily Q member 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.33
Genomic location:
Preferred name:
NM_172107.4(KCNQ2):c.1617C>T (p.Ser539=)
HGVS:
  • NC_000020.11:g.63414102G>A
  • NG_009004.2:g.63539C>T
  • NM_001382235.1:c.1563C>T
  • NM_004518.6:c.1533C>T
  • NM_172106.3:c.1563C>T
  • NM_172107.4:c.1617C>TMANE SELECT
  • NM_172108.5:c.1524C>T
  • NP_001369164.1:p.Ser521=
  • NP_004509.2:p.Ser511=
  • NP_742104.1:p.Ser521=
  • NP_742105.1:p.Ser539=
  • NP_742106.1:p.Ser508=
  • NC_000020.10:g.62045455G>A
  • NM_172107.3:c.1617C>T
Links:
dbSNP: rs2145547497
NCBI 1000 Genomes Browser:
rs2145547497
Molecular consequence:
  • NM_001382235.1:c.1563C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004518.6:c.1533C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_172106.3:c.1563C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_172107.4:c.1617C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_172108.5:c.1524C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Seizure
Synonyms:
Seizures
Identifiers:
MedGen: C0036572; Human Phenotype Ontology: HP:0001250

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001593162Cipher Gene Genetics Laboratory, Cipher Gene, Inc
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(May 1, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not 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 Cipher Gene Genetics Laboratory, Cipher Gene, Inc, SCV001593162.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

a synonymous variant Chr20(GRCh38): g.63414102G>A, NM_172107.3 (KCNQ2): c.1617C>T (p.Ser539=)) is absent from = population database (gnomAD, ExAC) , it segregates with disease in three affected relatives. Additionally, functional studies indicate the variant resulted in shorter transcripts with 20-nt deletion, owing to the activation of a novel cryptic 5’ donor splice site within exon14.

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

Last Updated: Jun 23, 2024