VCV001805737.1 - ClinVar

NM_172107.4(KCNQ2):c.856C>G (p.Gln286Glu)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_172107.4(KCNQ2):c.856C>G (p.Gln286Glu)

Variation ID: 1805737 Accession: VCV001805737.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 20q13.33 20: 63439669 (GRCh38) [ NCBI UCSC ] 20: 62071022 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 24, 2022	Dec 24, 2022	May 21, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NM_172107.4:c.856C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_742105.1:p.Gln286Glu	missense
NM_001382235.1:c.856C>G	NP_001369164.1:p.Gln286Glu	missense
NM_004518.6:c.856C>G	NP_004509.2:p.Gln286Glu	missense
NM_172106.3:c.856C>G	NP_742104.1:p.Gln286Glu	missense
NM_172108.5:c.856C>G	NP_742106.1:p.Gln286Glu	missense
NM_172109.3:c.856C>G	NP_742107.1:p.Gln286Glu	missense
NC_000020.11:g.63439669G>C
NC_000020.10:g.62071022G>C
NG_009004.2:g.37972C>G

... more HGVS ... less HGVS

Protein change

Q286E

Other names

Canonical SPDI

NC_000020.11:63439668:G:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
KCNQ2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh38 GRCh37	2152	2283

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Developmental and epileptic encephalopathy, 7	Uncertain significance (1)	criteria provided, single submitter	May 21, 2020	RCV002472155.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (May 21, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Developmental and epileptic encephalopathy, 7 (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute Additional submitter: Shariant Australia, Australian Genomics Accession: SCV002768613.1 First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022	Publications: PubMed (2) PubMed: 24318194‚ 27781029 Comment: Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as a 3A-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of … (more) Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as a 3A-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. Multiple NMD-predicted variants have previously been reported in this gene (ClinVar). (N) 0104 - Dominant Negative is a mechanism of disease for this gene (PMID: 24318194) (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0112 - Variants in this gene associated with benign neonatal seizures are known to have reduced penetrance (PMID: 27781029). (N) 0200 - Variant is predicted to result in a missense amino acid change from a glutamine to a glutamic acid (exon 6). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0502 - Missense variant with conflicting in silico predictions and moderate conservation with a minor amino acid change. (N) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (ion transport domain). (P) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region). (P) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1205 - Variant is maternally inherited. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign (less)

Comment:

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as a 3A-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. Multiple NMD-predicted variants have previously been reported in this gene (ClinVar). (N) 0104 - Dominant Negative is a mechanism of disease for this gene (PMID: 24318194) (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0112 - Variants in this gene associated with benign neonatal seizures are known to have reduced penetrance (PMID: 27781029). (N) 0200 - Variant is predicted to result in a missense amino acid change from a glutamine to a glutamic acid (exon 6). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0502 - Missense variant with conflicting in silico predictions and moderate conservation with a minor amino acid change. (N) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (ion transport domain). (P) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region). (P) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1205 - Variant is maternally inherited. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Novel KCNQ3 Mutation in a Large Family with Benign Familial Neonatal Epilepsy: A Rare Cause of Neonatal Seizures.	Maljevic S	Molecular syndromology	2016	PMID: 27781029
Dominant-negative effects of KCNQ2 mutations are associated with epileptic encephalopathy.	Orhan G	Annals of neurology	2014	PMID: 24318194

Text-mined citations for this variant ...

Record last updated Aug 06, 2023

ClinVar Genomic variation as it relates to human health

NM_172107.4(KCNQ2):c.856C>G (p.Gln286Glu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...