NM_001165963.4(SCN1A):c.1604G>A (p.Arg535His) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 15, 2020
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:: RCV000188874.4

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1604G>A (p.Arg535His)]

NM_001165963.4(SCN1A):c.1604G>A (p.Arg535His)

Gene:

SCN1A:sodium voltage-gated channel alpha subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001165963.4(SCN1A):c.1604G>A (p.Arg535His)

Other names:

p.R535H:CGC>CAC

HGVS:

NC_000002.12:g.166045101C>T
NG_011906.1:g.33539G>A
NM_001165963.4:c.1604G>AMANE SELECT
NM_001165964.3:c.1604G>A
NM_001202435.3:c.1604G>A
NM_001353948.2:c.1604G>A
NM_001353949.2:c.1604G>A
NM_001353950.2:c.1604G>A
NM_001353951.2:c.1604G>A
NM_001353952.2:c.1604G>A
NM_001353954.2:c.1601G>A
NM_001353955.2:c.1601G>A
NM_001353957.2:c.1604G>A
NM_001353958.2:c.1604G>A
NM_001353960.2:c.1601G>A
NM_001353961.2:c.-822G>A
NM_006920.6:c.1604G>A
NP_001159435.1:p.Arg535His
NP_001159436.1:p.Arg535His
NP_001189364.1:p.Arg535His
NP_001340877.1:p.Arg535His
NP_001340878.1:p.Arg535His
NP_001340879.1:p.Arg535His
NP_001340880.1:p.Arg535His
NP_001340881.1:p.Arg535His
NP_001340883.1:p.Arg534His
NP_001340884.1:p.Arg534His
NP_001340886.1:p.Arg535His
NP_001340887.1:p.Arg535His
NP_001340889.1:p.Arg534His
NP_008851.3:p.Arg535His
LRG_8:g.33539G>A
NC_000002.11:g.166901611C>T
NM_001165963.1:c.1604G>A
NM_006920.5:c.1604G>A
NR_148667.2:n.1990G>A

Protein change:

R534H

Links:

dbSNP: rs184524479

NCBI 1000 Genomes Browser:

rs184524479

Molecular consequence:

NM_001353961.2:c.-822G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001165963.4:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.1601G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.1601G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.1601G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.1604G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.1990G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000242504	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jan 15, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000242504

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jan 15, 2020)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000242504.11

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Substitution is predicted to be in the cytoplasmic loop between the first and second homologous domains; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31780880)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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