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:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000703160	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Dec 7, 2016)	germline	clinical testing	Citation Link,
SCV001792583	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 30, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000703160

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Dec 7, 2016)

germline

clinical testing

Citation Link,

SCV001792583

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 30, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000703160.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From GeneDx, SCV001792583.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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