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NM_001165963.4(SCN1A):c.5988A>C (p.Lys1996Asn) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Sep 30, 2019
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:
RCV000593278.7

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5988A>C (p.Lys1996Asn)]

NM_001165963.4(SCN1A):c.5988A>C (p.Lys1996Asn)

Genes:
SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.5988A>C (p.Lys1996Asn)
HGVS:
  • NC_000002.12:g.165991287T>G
  • NG_011906.1:g.87353A>C
  • NM_001165963.4:c.5988A>CMANE SELECT
  • NM_001165963.4:c.5988A>C
  • NM_001165964.3:c.5904A>C
  • NM_001202435.3:c.5988A>C
  • NM_001353948.2:c.5988A>C
  • NM_001353949.2:c.5955A>C
  • NM_001353950.2:c.5955A>C
  • NM_001353951.2:c.5955A>C
  • NM_001353952.2:c.5955A>C
  • NM_001353954.2:c.5952A>C
  • NM_001353955.2:c.5952A>C
  • NM_001353957.2:c.5904A>C
  • NM_001353958.2:c.5904A>C
  • NM_001353960.2:c.5901A>C
  • NM_001353961.2:c.3546A>C
  • NM_006920.6:c.5955A>C
  • NP_001159435.1:p.Lys1996Asn
  • NP_001159436.1:p.Lys1968Asn
  • NP_001189364.1:p.Lys1996Asn
  • NP_001340877.1:p.Lys1996Asn
  • NP_001340878.1:p.Lys1985Asn
  • NP_001340879.1:p.Lys1985Asn
  • NP_001340880.1:p.Lys1985Asn
  • NP_001340881.1:p.Lys1985Asn
  • NP_001340883.1:p.Lys1984Asn
  • NP_001340884.1:p.Lys1984Asn
  • NP_001340886.1:p.Lys1968Asn
  • NP_001340887.1:p.Lys1968Asn
  • NP_001340889.1:p.Lys1967Asn
  • NP_001340890.1:p.Lys1182Asn
  • NP_008851.3:p.Lys1985Asn
  • LRG_8:g.87353A>C
  • NC_000002.11:g.166847797T>G
  • NC_000002.11:g.166847797T>G
  • NM_001165963.1:c.5988A>C
  • NR_148667.2:n.6405A>C
Protein change:
K1182N
Links:
dbSNP: rs371243629
NCBI 1000 Genomes Browser:
rs371243629
Molecular consequence:
  • NM_001165963.4:c.5988A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5904A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5988A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5988A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5955A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5955A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5955A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5955A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5952A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5952A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5904A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5904A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5901A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3546A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5955A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.6405A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000703160Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Uncertain significance
(Dec 7, 2016) 		germlineclinical testing

Citation Link,

SCV001792583GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Sep 30, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown2not providednot providednot providednot providedclinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000703160.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV001792583.1

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge; This substitution is predicted to be within the C-terminal cytoplasmic domain.

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

Last Updated: Sep 29, 2024