NM_001040142.2(SCN2A):c.4683C>G (p.Asn1561Lys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 15, 2018
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:
RCV000658172.1

Allele description [Variation Report for NM_001040142.2(SCN2A):c.4683C>G (p.Asn1561Lys)]

NM_001040142.2(SCN2A):c.4683C>G (p.Asn1561Lys)

Gene:
SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001040142.2(SCN2A):c.4683C>G (p.Asn1561Lys)
HGVS:
  • NC_000002.12:g.165386877C>G
  • NG_008143.1:g.152476C>G
  • NM_001040142.2:c.4683C>GMANE SELECT
  • NM_001040143.2:c.4683C>G
  • NM_001371246.1:c.4683C>G
  • NM_001371247.1:c.4683C>G
  • NM_021007.3:c.4683C>G
  • NP_001035232.1:p.Asn1561Lys
  • NP_001035233.1:p.Asn1561Lys
  • NP_001358175.1:p.Asn1561Lys
  • NP_001358176.1:p.Asn1561Lys
  • NP_066287.2:p.Asn1561Lys
  • NP_066287.2:p.Asn1561Lys
  • NC_000002.11:g.166243387C>G
  • NM_021007.2:c.4683C>G
Protein change:
N1561K
Links:
dbSNP: rs1379550929
NCBI 1000 Genomes Browser:
rs1379550929
Molecular consequence:
  • NM_001040142.2:c.4683C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001040143.2:c.4683C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371246.1:c.4683C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371247.1:c.4683C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021007.3:c.4683C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000779943GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(May 15, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000779943.2

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

Description

The N1561K variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The N1561K variant is not observed in large population cohorts (Lek et al., 2016). The N1561K variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. This substitution is predicted to be within the extracellular loop between the S1and S2 transmembrane segments of the fourth homologous domain. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Sep 17, 2022