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NM_172107.4(KCNQ2):c.1763+1576T>G AND Developmental and epileptic encephalopathy, 7

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 12, 2020
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:
RCV001420585.1

Allele description [Variation Report for NM_172107.4(KCNQ2):c.1763+1576T>G]

NM_172107.4(KCNQ2):c.1763+1576T>G

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.1763+1576T>G
HGVS:
  • NC_000020.11:g.63411874A>C
  • NG_009004.2:g.65767T>G
  • NM_001382235.1:c.1718T>G
  • NM_004518.6:c.1679+1576T>G
  • NM_172106.3:c.1709+1576T>G
  • NM_172107.4:c.1763+1576T>GMANE SELECT
  • NM_172108.5:c.1670+1576T>G
  • NP_001369164.1:p.Met573Arg
  • NC_000020.10:g.62043227A>C
Protein change:
M573R
Links:
dbSNP: rs62208003
NCBI 1000 Genomes Browser:
rs62208003
Molecular consequence:
  • NM_004518.6:c.1679+1576T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_172106.3:c.1709+1576T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_172107.4:c.1763+1576T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_172108.5:c.1670+1576T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001382235.1:c.1718T>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Developmental and epileptic encephalopathy, 7 (DEE7)
Synonyms:
Early infantile epileptic encephalopathy 7; KCNQ2-Related Neonatal Epileptic Encephalopathy
Identifiers:
MONDO: MONDO:0013387; MedGen: C3150986; Orphanet: 439218; OMIM: 613720

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001622900New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(May 12, 2020) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV001622900.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The deep intronic c.1763+1576T>G variant identified in the KCNQ2 gene is a single nucleotide variant which substitutes a very well conserved Adenine for Cytosine at the nucleotide level, within intron 15/16. This variant is found with low frequency in gnomAD (6 heterozygotes, 0 homozygotes; allele frequency: 4.19e-5) suggesting it is not a common benign variant in the populations represented in that database. The Transcript inferred Pathogenicity Score (TraP; v3) for this variant is 0.412, which is >99th score-percentile, suggesting it is probably damaging to the canonical transcript. Human Splicing Finder suggests this variant activates an intronic cryptic splice acceptor site, and potentially alters splicing. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. Given the lack of compelling evidence for its pathogenicity, the deep intronic c.1763+1576T>G variant identified in the KCNQ2gene is reported here as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023