NM_001040142.2(SCN2A):c.620T>G (p.Phe207Cys) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 5, 2019
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:: RCV000484447.4

Allele description [Variation Report for NM_001040142.2(SCN2A):c.620T>G (p.Phe207Cys)]

NM_001040142.2(SCN2A):c.620T>G (p.Phe207Cys)

Gene:

SCN2A:sodium voltage-gated channel alpha subunit 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_001040142.2(SCN2A):c.620T>G (p.Phe207Cys)

HGVS:

NC_000002.12:g.165309366T>G
NG_008143.1:g.74965T>G
NM_001040142.2:c.620T>GMANE SELECT
NM_001040143.2:c.697+110T>G
NM_001371246.1:c.697+110T>G
NM_001371247.1:c.620T>G
NM_021007.3:c.620T>G
NP_001035232.1:p.Phe207Cys
NP_001358176.1:p.Phe207Cys
NP_066287.2:p.Phe207Cys
NP_066287.2:p.Phe207Cys
NC_000002.11:g.166165876T>G
NM_021007.2:c.620T>G

Protein change:

F207C

Links:

dbSNP: rs1064796691

NCBI 1000 Genomes Browser:

rs1064796691

Molecular consequence:

NM_001040143.2:c.697+110T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001371246.1:c.697+110T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001040142.2:c.620T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001371247.1:c.620T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_021007.3:c.620T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000573661	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Sep 5, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000573661

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Sep 5, 2019)

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, SCV000573661.6

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

Description

Not observed in large population cohorts (Lek et al., 2016); 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; Predicted to be within the transmembrane segment S3 of the first homologous domain; Has not been previously published as pathogenic or benign to our knowledge

#	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: Mar 4, 2023

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