NM_001165963.4(SCN1A):c.3650A>G (p.His1217Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 6, 2014
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:
RCV000188922.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.3650A>G (p.His1217Arg)]

NM_001165963.4(SCN1A):c.3650A>G (p.His1217Arg)

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.3650A>G (p.His1217Arg)
Other names:
p.H1217R:CAT>CGT
HGVS:
  • NC_000002.12:g.166013799T>C
  • NG_011906.1:g.64841A>G
  • NM_001165963.4:c.3650A>GMANE SELECT
  • NM_001165964.3:c.3566A>G
  • NM_001202435.3:c.3650A>G
  • NM_001353948.2:c.3650A>G
  • NM_001353949.2:c.3617A>G
  • NM_001353950.2:c.3617A>G
  • NM_001353951.2:c.3617A>G
  • NM_001353952.2:c.3617A>G
  • NM_001353954.2:c.3614A>G
  • NM_001353955.2:c.3614A>G
  • NM_001353957.2:c.3566A>G
  • NM_001353958.2:c.3566A>G
  • NM_001353960.2:c.3563A>G
  • NM_001353961.2:c.1208A>G
  • NM_006920.6:c.3617A>G
  • NP_001159435.1:p.His1217Arg
  • NP_001159436.1:p.His1189Arg
  • NP_001189364.1:p.His1217Arg
  • NP_001340877.1:p.His1217Arg
  • NP_001340878.1:p.His1206Arg
  • NP_001340879.1:p.His1206Arg
  • NP_001340880.1:p.His1206Arg
  • NP_001340881.1:p.His1206Arg
  • NP_001340883.1:p.His1205Arg
  • NP_001340884.1:p.His1205Arg
  • NP_001340886.1:p.His1189Arg
  • NP_001340887.1:p.His1189Arg
  • NP_001340889.1:p.His1188Arg
  • NP_001340890.1:p.His403Arg
  • NP_008851.3:p.His1206Arg
  • LRG_8:g.64841A>G
  • NC_000002.11:g.166870309T>C
  • NM_001165963.1:c.3650A>G
  • NR_148667.2:n.4003A>G
Protein change:
H1188R
Links:
dbSNP: rs796052996
NCBI 1000 Genomes Browser:
rs796052996
Molecular consequence:
  • NM_001165963.4:c.3650A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.3566A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.3650A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.3650A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.3617A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.3617A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.3617A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.3617A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.3614A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.3614A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.3566A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.3566A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.3563A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.1208A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.3617A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.4003A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000242552GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jun 6, 2014) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000242552.11

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

Description

p.His1217Arg (CAT>CGT): c.3650 A>G in exon 18 of the SCN1A gene (NM_001165963.1) The H1217R variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution alters a conserved position in transmembrane segment S1 in the third homologous domain of the SCN1A protein and other missense mutations in this region have been reported in association with SCN1A-related disorders in an external mutation database, supporting the functional importance of this region of the protein . In silico analysis predicts this variant is probably damaging to the protein structure/function. However, the H1217R variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant.The variant is found in EPILEPSY panel(s).

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

Last Updated: Apr 23, 2022