NM_001165963.4(SCN1A):c.302G>A (p.Arg101Gln) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 17, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000188829.31

Allele description [Variation Report for NM_001165963.4(SCN1A):c.302G>A (p.Arg101Gln)]

NM_001165963.4(SCN1A):c.302G>A (p.Arg101Gln)

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.302G>A (p.Arg101Gln)

Other names:

p.R101Q:CGG>CAG

HGVS:

NC_000002.12:g.166058651C>T
NG_011906.1:g.19989G>A
NM_001165963.4:c.302G>AMANE SELECT
NM_001165963.4:c.302G>A
NM_001165964.3:c.302G>A
NM_001202435.3:c.302G>A
NM_001353948.2:c.302G>A
NM_001353949.2:c.302G>A
NM_001353950.2:c.302G>A
NM_001353951.2:c.302G>A
NM_001353952.2:c.302G>A
NM_001353954.2:c.302G>A
NM_001353955.2:c.302G>A
NM_001353957.2:c.302G>A
NM_001353958.2:c.302G>A
NM_001353960.2:c.302G>A
NM_001353961.2:c.-2124G>A
NM_006920.6:c.302G>A
NP_001159435.1:p.Arg101Gln
NP_001159436.1:p.Arg101Gln
NP_001189364.1:p.Arg101Gln
NP_001340877.1:p.Arg101Gln
NP_001340878.1:p.Arg101Gln
NP_001340879.1:p.Arg101Gln
NP_001340880.1:p.Arg101Gln
NP_001340881.1:p.Arg101Gln
NP_001340883.1:p.Arg101Gln
NP_001340884.1:p.Arg101Gln
NP_001340886.1:p.Arg101Gln
NP_001340887.1:p.Arg101Gln
NP_001340889.1:p.Arg101Gln
NP_008851.3:p.Arg101Gln
LRG_8t1:c.302G>A
LRG_8:g.19989G>A
NC_000002.11:g.166915161C>T
NC_000002.11:g.166915161C>T
NM_001165963.1:c.302G>A
NM_001165963.2:c.302G>A
NM_006920.4:c.302G>A
NR_148667.2:n.688G>A
P35498:p.Arg101Gln

Protein change:

R101Q

Links:

UniProtKB: P35498#VAR_029661; UniProtKB/Swiss-Prot: VAR_029661; dbSNP: rs121917918

NCBI 1000 Genomes Browser:

rs121917918

Molecular consequence:

NM_001353961.2:c.-2124G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001165963.4:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.302G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.688G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV000111453	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Sep 11, 2015)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 14738421, 19589774, 20431604, 24328833 Citation Link,
SCV000242458	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 17, 2021)	germline	clinical testing	Citation Link,
SCV001249711	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jun 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000111453

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Sep 11, 2015)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV000242458

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 17, 2021)

germline

clinical testing

Citation Link,

SCV001249711

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jun 1, 2017)

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	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations of neuronal voltage-gated Na+ channel alpha 1 subunit gene SCN1A in core severe myoclonic epilepsy in infancy (SMEI) and in borderline SMEI (SMEB).

Fukuma G, Oguni H, Shirasaka Y, Watanabe K, Miyajima T, Yasumoto S, Ohfu M, Inoue T, Watanachai A, Kira R, Matsuo M, Muranaka H, Sofue F, Zhang B, Kaneko S, Mitsudome A, Hirose S.

Epilepsia. 2004 Feb;45(2):140-8.

PubMed [citation]

PMID:: 14738421

De novo SCN1A mutations in Dravet syndrome and related epileptic encephalopathies are largely of paternal origin.

Heron SE, Scheffer IE, Iona X, Zuberi SM, Birch R, McMahon JM, Bruce CM, Berkovic SF, Mulley JC.

J Med Genet. 2010 Feb;47(2):137-41. doi: 10.1136/jmg.2008.065912. Epub 2009 Jul 8.

PubMed [citation]

PMID:: 19589774

See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000111453.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From GeneDx, SCV000242458.11

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

Description

Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); This substitution is predicted to be within the N-terminal cytoplasmic domain.; Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27465585, 25885068, 24328833, 23195492, 23808377, 23158734, 14738421, 15508916, 15277629, 17347258, 17561957, 18930999, 29056246, 30945278, 32090326)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001249711.21

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

#	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		1	not provided	not provided	not provided

Last Updated: Jun 2, 2024

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