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NM_001165963.4(SCN1A):c.1662+2T>C AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 20, 2016
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:
RCV000492939.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1662+2T>C]

NM_001165963.4(SCN1A):c.1662+2T>C

Gene:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.1662+2T>C
HGVS:
  • NC_000002.12:g.166045041A>G
  • NG_011906.1:g.33599T>C
  • NM_001165963.4:c.1662+2T>CMANE SELECT
  • NM_001165964.3:c.1662+2T>C
  • NM_001202435.3:c.1662+2T>C
  • NM_001353948.2:c.1662+2T>C
  • NM_001353949.2:c.1662+2T>C
  • NM_001353950.2:c.1662+2T>C
  • NM_001353951.2:c.1662+2T>C
  • NM_001353952.2:c.1662+2T>C
  • NM_001353954.2:c.1659+2T>C
  • NM_001353955.2:c.1659+2T>C
  • NM_001353957.2:c.1662+2T>C
  • NM_001353958.2:c.1662+2T>C
  • NM_001353960.2:c.1659+2T>C
  • NM_001353961.2:c.-764+2T>C
  • NM_006920.6:c.1662+2T>C
  • LRG_8:g.33599T>C
  • NC_000002.11:g.166901551A>G
  • NM_001165963.1:c.1662+2T>C
Links:
dbSNP: rs1131691545
NCBI 1000 Genomes Browser:
rs1131691545
Molecular consequence:
  • NM_001165963.4:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001165964.3:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001202435.3:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353948.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353949.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353950.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353951.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353952.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353954.2:c.1659+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353955.2:c.1659+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353957.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353958.2:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353960.2:c.1659+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353961.2:c.-764+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_006920.6:c.1662+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000582345GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(May 20, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000582345.3

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

Description

The c.1662+2 T>C splice site variant in the SCN1A gene has been previously reported as a de novo pathogenic variant in an individual with severe myoclonic epilepsy of infancy (Harkin et al., 2007). This variantdestroys the canonical splice donor site in intron 10, and is expected to cause abnormal gene splicing. Therefore, c.1662+2 T>C in SCN1A is interpreted as a pathogenic variant.

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

Last Updated: Jun 10, 2023