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NM_001165963.4(SCN1A):c.5582G>A (p.Arg1861Gln) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 12, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000481884.5

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5582G>A (p.Arg1861Gln)]

NM_001165963.4(SCN1A):c.5582G>A (p.Arg1861Gln)

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.5582G>A (p.Arg1861Gln)
HGVS:
  • NC_000002.12:g.165991693C>T
  • NG_011906.1:g.86947G>A
  • NM_001165963.4:c.5582G>AMANE SELECT
  • NM_001165963.4:c.5582G>A
  • NM_001165964.3:c.5498G>A
  • NM_001202435.3:c.5582G>A
  • NM_001353948.2:c.5582G>A
  • NM_001353949.2:c.5549G>A
  • NM_001353950.2:c.5549G>A
  • NM_001353951.2:c.5549G>A
  • NM_001353952.2:c.5549G>A
  • NM_001353954.2:c.5546G>A
  • NM_001353955.2:c.5546G>A
  • NM_001353957.2:c.5498G>A
  • NM_001353958.2:c.5498G>A
  • NM_001353960.2:c.5495G>A
  • NM_001353961.2:c.3140G>A
  • NM_006920.6:c.5549G>A
  • NP_001159435.1:p.Arg1861Gln
  • NP_001159436.1:p.Arg1833Gln
  • NP_001189364.1:p.Arg1861Gln
  • NP_001340877.1:p.Arg1861Gln
  • NP_001340878.1:p.Arg1850Gln
  • NP_001340879.1:p.Arg1850Gln
  • NP_001340880.1:p.Arg1850Gln
  • NP_001340881.1:p.Arg1850Gln
  • NP_001340883.1:p.Arg1849Gln
  • NP_001340884.1:p.Arg1849Gln
  • NP_001340886.1:p.Arg1833Gln
  • NP_001340887.1:p.Arg1833Gln
  • NP_001340889.1:p.Arg1832Gln
  • NP_001340890.1:p.Arg1047Gln
  • NP_008851.3:p.Arg1850Gln
  • LRG_8:g.86947G>A
  • NC_000002.11:g.166848203C>T
  • NM_001165963.1:c.5582G>A
  • NR_148667.2:n.5999G>A
Protein change:
R1047Q
Links:
dbSNP: rs796053042
NCBI 1000 Genomes Browser:
rs796053042
Molecular consequence:
  • NM_001165963.4:c.5582G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5498G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5582G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5582G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5549G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5549G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5549G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5549G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5546G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5546G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5498G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5498G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5495G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3140G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5549G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.5999G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000570875GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Oct 12, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000570875.5

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This substitution is predicted to be within the C-terminal cytoplasmic domain.; This variant is associated with the following publications: (PMID: 23195492)

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

Last Updated: May 1, 2024