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NM_001165963.4(SCN1A):c.5639G>A (p.Gly1880Glu) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 25, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5639G>A (p.Gly1880Glu)]

NM_001165963.4(SCN1A):c.5639G>A (p.Gly1880Glu)

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]
LOC102724058:uncharacterized LOC102724058 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001165963.4(SCN1A):c.5639G>A (p.Gly1880Glu)
Other names:
  • NC_000002.12:g.165991636C>T
  • NG_011906.1:g.87004G>A
  • NM_001165963.4:c.5639G>AMANE SELECT
  • NM_001165963.4:c.5639G>A
  • NM_001165964.3:c.5555G>A
  • NM_001202435.3:c.5639G>A
  • NM_001353948.2:c.5639G>A
  • NM_001353949.2:c.5606G>A
  • NM_001353950.2:c.5606G>A
  • NM_001353951.2:c.5606G>A
  • NM_001353952.2:c.5606G>A
  • NM_001353954.2:c.5603G>A
  • NM_001353955.2:c.5603G>A
  • NM_001353957.2:c.5555G>A
  • NM_001353958.2:c.5555G>A
  • NM_001353960.2:c.5552G>A
  • NM_001353961.2:c.3197G>A
  • NM_006920.6:c.5606G>A
  • NP_001159435.1:p.Gly1880Glu
  • NP_001159436.1:p.Gly1852Glu
  • NP_001189364.1:p.Gly1880Glu
  • NP_001340877.1:p.Gly1880Glu
  • NP_001340878.1:p.Gly1869Glu
  • NP_001340879.1:p.Gly1869Glu
  • NP_001340880.1:p.Gly1869Glu
  • NP_001340881.1:p.Gly1869Glu
  • NP_001340883.1:p.Gly1868Glu
  • NP_001340884.1:p.Gly1868Glu
  • NP_001340886.1:p.Gly1852Glu
  • NP_001340887.1:p.Gly1852Glu
  • NP_001340889.1:p.Gly1851Glu
  • NP_001340890.1:p.Gly1066Glu
  • NP_008851.3:p.Gly1869Glu
  • LRG_8:g.87004G>A
  • NC_000002.11:g.166848146C>T
  • NC_000002.11:g.166848146C>T
  • NM_001165963.1:c.5639G>A
  • NM_001202435.1:c.5639G>A
  • NR_148667.2:n.6056G>A
  • P35498:p.Gly1880Glu
Protein change:
UniProtKB: P35498#VAR_073654; dbSNP: rs201905405
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001165963.4:c.5639G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5555G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5639G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5639G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5603G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5603G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5555G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5555G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5552G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3197G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.6056G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]


Inborn genetic diseases
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV002650327Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Mar 25, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

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



Genotype-phenotype associations in SCN1A-related epilepsies.

Zuberi SM, Brunklaus A, Birch R, Reavey E, Duncan J, Forbes GH.

Neurology. 2011 Feb 15;76(7):594-600. doi: 10.1212/WNL.0b013e31820c309b. Epub 2011 Jan 19.

PubMed [citation]

Dravet syndrome as epileptic encephalopathy: evidence from long-term course and neuropathology.

Catarino CB, Liu JY, Liagkouras I, Gibbons VS, Labrum RW, Ellis R, Woodward C, Davis MB, Smith SJ, Cross JH, Appleton RE, Yendle SC, McMahon JM, Bellows ST, Jacques TS, Zuberi SM, Koepp MJ, Martinian L, Scheffer IE, Thom M, Sisodiya SM.

Brain. 2011 Oct;134(Pt 10):2982-3010. doi: 10.1093/brain/awr129. Epub 2011 Jun 29.

PubMed [citation]
See all PubMed Citations (5)

Details of each submission

From Ambry Genetics, SCV002650327.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)


This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024