NM_001165963.4(SCN1A):c.5870A>G (p.Glu1957Gly) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Feb 14, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000416094.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5870A>G (p.Glu1957Gly)]

NM_001165963.4(SCN1A):c.5870A>G (p.Glu1957Gly)

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.5870A>G (p.Glu1957Gly)
Other names:
p.E1957G:GAA>GGA
HGVS:
  • NC_000002.12:g.165991405T>C
  • NG_011906.1:g.87235A>G
  • NM_001165963.4:c.5870A>GMANE SELECT
  • NM_001165963.4:c.5870A>G
  • NM_001165964.3:c.5786A>G
  • NM_001202435.3:c.5870A>G
  • NM_001353948.2:c.5870A>G
  • NM_001353949.2:c.5837A>G
  • NM_001353950.2:c.5837A>G
  • NM_001353951.2:c.5837A>G
  • NM_001353952.2:c.5837A>G
  • NM_001353954.2:c.5834A>G
  • NM_001353955.2:c.5834A>G
  • NM_001353957.2:c.5786A>G
  • NM_001353958.2:c.5786A>G
  • NM_001353960.2:c.5783A>G
  • NM_001353961.2:c.3428A>G
  • NM_006920.6:c.5837A>G
  • NP_001159435.1:p.Glu1957Gly
  • NP_001159436.1:p.Glu1929Gly
  • NP_001189364.1:p.Glu1957Gly
  • NP_001340877.1:p.Glu1957Gly
  • NP_001340878.1:p.Glu1946Gly
  • NP_001340879.1:p.Glu1946Gly
  • NP_001340880.1:p.Glu1946Gly
  • NP_001340881.1:p.Glu1946Gly
  • NP_001340883.1:p.Glu1945Gly
  • NP_001340884.1:p.Glu1945Gly
  • NP_001340886.1:p.Glu1929Gly
  • NP_001340887.1:p.Glu1929Gly
  • NP_001340889.1:p.Glu1928Gly
  • NP_001340890.1:p.Glu1143Gly
  • NP_008851.3:p.Glu1946Gly
  • LRG_8t1:c.5837A>G
  • LRG_8:g.87235A>G
  • NC_000002.11:g.166847915T>C
  • NM_001165963.1:c.5870A>G
  • NM_006920.4:c.5837A>G
  • NR_148667.2:n.6287A>G
Protein change:
E1143G
Links:
UniProtKB/Swiss-Prot: VAR_029731; dbSNP: rs121918802
NCBI 1000 Genomes Browser:
rs121918802
Molecular consequence:
  • NM_001165963.4:c.5870A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001165964.3:c.5786A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001202435.3:c.5870A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353948.2:c.5870A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353949.2:c.5837A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353950.2:c.5837A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353951.2:c.5837A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353952.2:c.5837A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353954.2:c.5834A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353955.2:c.5834A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353957.2:c.5786A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353958.2:c.5786A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353960.2:c.5783A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353961.2:c.3428A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006920.6:c.5837A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148667.2:n.6287A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000242655GeneDxcriteria provided, single submitter
Benign
(Feb 14, 2020)
germlineclinical testing

Citation Link,

SCV000493672CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Jul 31, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000242655.12

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

Description

Reported previously an individual with infantile spasms and mild intellectual disability; however, family studies were not performed (Wallace et al., 2003); This substitution is within the C-terminal cytoplasmic domain of the protein (Escayg et al., 2010); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 23527921, 14504318)

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000493672.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 27, 2021

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