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NM_001165963.4(SCN1A):c.5434T>G (p.Trp1812Gly) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Mar 2, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000478850.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5434T>G (p.Trp1812Gly)]

NM_001165963.4(SCN1A):c.5434T>G (p.Trp1812Gly)

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.5434T>G (p.Trp1812Gly)
HGVS:
  • NC_000002.12:g.165991841A>C
  • NG_011906.1:g.86799T>G
  • NM_001165963.4:c.5434T>GMANE SELECT
  • NM_001165964.3:c.5350T>G
  • NM_001202435.3:c.5434T>G
  • NM_001353948.2:c.5434T>G
  • NM_001353949.2:c.5401T>G
  • NM_001353950.2:c.5401T>G
  • NM_001353951.2:c.5401T>G
  • NM_001353952.2:c.5401T>G
  • NM_001353954.2:c.5398T>G
  • NM_001353955.2:c.5398T>G
  • NM_001353957.2:c.5350T>G
  • NM_001353958.2:c.5350T>G
  • NM_001353960.2:c.5347T>G
  • NM_001353961.2:c.2992T>G
  • NM_006920.6:c.5401T>G
  • NP_001159435.1:p.Trp1812Gly
  • NP_001159436.1:p.Trp1784Gly
  • NP_001189364.1:p.Trp1812Gly
  • NP_001340877.1:p.Trp1812Gly
  • NP_001340878.1:p.Trp1801Gly
  • NP_001340879.1:p.Trp1801Gly
  • NP_001340880.1:p.Trp1801Gly
  • NP_001340881.1:p.Trp1801Gly
  • NP_001340883.1:p.Trp1800Gly
  • NP_001340884.1:p.Trp1800Gly
  • NP_001340886.1:p.Trp1784Gly
  • NP_001340887.1:p.Trp1784Gly
  • NP_001340889.1:p.Trp1783Gly
  • NP_001340890.1:p.Trp998Gly
  • NP_008851.3:p.Trp1801Gly
  • LRG_8t1:c.5401T>G
  • LRG_8:g.86799T>G
  • NC_000002.11:g.166848351A>C
  • NM_001165963.1:c.5434T>G
  • NM_006920.4:c.5401T>G
  • NR_148667.2:n.5851T>G
Protein change:
W1783G
Links:
UniProtKB/Swiss-Prot: VAR_029724; dbSNP: rs121918751
NCBI 1000 Genomes Browser:
rs121918751
Molecular consequence:
  • NM_001165963.4:c.5434T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5350T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5434T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5434T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5401T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5401T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5401T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5401T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5398T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5398T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5350T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5350T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5347T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.2992T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5401T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.5851T>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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000567067GeneDxcriteria provided, single submitter
Likely pathogenic
(Mar 2, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000567067.4

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

Description

The W1812G missense variant in the SCN1A gene has been reported previously as a denovo variant in an individual with severe myoclonic epilepsy in infancy (SMEI) (Fujiwaraet al., 2003). It was not observed in approximately 6,500 individuals of European andAfrican American ancestry in the NHLBI Exome Sequencing Project, indicating it is not acommon benign variant in these populations. The W1812G variant is a semi-conservativeamino acid substitution, which may impact secondary protein structure as these residuesdiffer in some properties. This substitution occurs at a position that is conserved acrossspecies, and different missense variants in the same residue (W1812S, W1812R) havebeen reported previously as de novo in association with SCN1A-related disorders(SCN1A Variant Database). In silico analysis predicts this variant is probably damaging tothe protein structure/function. Therefore, we consider the W1812G variant to be pathogenic.

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

Last Updated: Jun 24, 2022

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