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NM_172107.4(KCNQ2):c.430C>T (p.Arg144Trp) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
May 15, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000521018.25

Allele description [Variation Report for NM_172107.4(KCNQ2):c.430C>T (p.Arg144Trp)]

NM_172107.4(KCNQ2):c.430C>T (p.Arg144Trp)

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.430C>T (p.Arg144Trp)
Other names:
KCNQ2
HGVS:
  • NC_000020.11:g.63445322G>A
  • NG_009004.2:g.32319C>T
  • NM_004518.6:c.430C>T
  • NM_172106.3:c.430C>T
  • NM_172107.4:c.430C>TMANE SELECT
  • NM_172108.5:c.430C>T
  • NM_172109.3:c.430C>T
  • NP_004509.2:p.Arg144Trp
  • NP_742104.1:p.Arg144Trp
  • NP_742105.1:p.Arg144Trp
  • NP_742106.1:p.Arg144Trp
  • NP_742107.1:p.Arg144Trp
  • NC_000020.10:g.62076675G>A
  • NM_172107.2:c.430C>T
  • NM_172107.3:c.430C>T
Protein change:
R144W
Links:
Molecular consequence:
  • NM_004518.6:c.430C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172106.3:c.430C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172107.4:c.430C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172108.5:c.430C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172109.3:c.430C>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
  • Moderate decrease in peak current [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0086]
  • Severe hyperpolarizing shift of voltage dependence of activation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0031]
  • Severe slowing of activation [Functional Epilepsy Nomenclature for Ion Channels: FENICS-0015]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000621298GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(May 15, 2023)
germlineclinical testing

Citation Link,

SCV001502408CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely pathogenic
(Oct 1, 2020)
germlineclinical testing

Citation Link,

SCV001927054Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001953679Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000621298.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); This substitution is predicted to be in the Intracellular loop between the S2 and S3 transmembrane segments; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 28628100, 28867141, 27479843, 28135719, 33754465, 31785789, 35599849, 35780567)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001502408.20

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001927054.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001953679.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024