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NM_001165963.4(SCN1A):c.5639G>A (p.Gly1880Glu) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Jun 1, 2022
Review status:
criteria provided, conflicting classifications
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:
RCV000488340.28

Allele description

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

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.5639G>A (p.Gly1880Glu)
Other names:
p.G1880E:GGA>GAA
HGVS:
  • 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:
G1066E
Links:
UniProtKB: P35498#VAR_073654; dbSNP: rs201905405
NCBI 1000 Genomes Browser:
rs201905405
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]
Observations:
6

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000242644GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Mar 10, 2020)
germlineclinical testing

Citation Link,

SCV000341238Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Uncertain significance
(Apr 21, 2016)
germlineclinical testing

Citation Link,

SCV000575245CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Jun 1, 2022)
germlineclinical testing

Citation Link,

SCV001475473Athena Diagnostics Inc
criteria provided, single submitter

(Athena Diagnostics Criteria)
Likely benign
(Dec 30, 2019)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes4not providednot providednot providednot providedclinical testing
not providedgermlineunknown2not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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]
PMID:
21248271

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]
PMID:
21719429
PMCID:
PMC3187538
See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000242644.13

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

Description

This variant is associated with the following publications: (PMID: 32090326, 23884151, 26501104, 21248271, 27231140, 21719429)

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

From Eurofins Ntd Llc (ga), SCV000341238.4

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

From CeGaT Center for Human Genetics Tuebingen, SCV000575245.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testingnot provided

Description

SCN1A: PP2, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided4not providednot providednot provided

From Athena Diagnostics Inc, SCV001475473.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024