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NM_001165963.4(SCN1A):c.5639G>A (p.Gly1880Glu) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 27, 2017
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]


Generalized epilepsy with febrile seizures plus, type 2 (GEFSP2)
MONDO: MONDO:0011461; MedGen: C1858673; Orphanet: 36387; OMIM: 604403

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001296301Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001296301.1

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


This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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

Last Updated: May 12, 2024