NM_006922.4(SCN3A):c.4114A>G (p.Met1372Val) AND Epilepsy, familial focal, with variable foci 4

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 2020
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000625710.5

Allele description [Variation Report for NM_006922.4(SCN3A):c.4114A>G (p.Met1372Val)]

NM_006922.4(SCN3A):c.4114A>G (p.Met1372Val)

Gene:

SCN3A:sodium voltage-gated channel alpha subunit 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_006922.4(SCN3A):c.4114A>G (p.Met1372Val)

HGVS:

NC_000002.12:g.165097377T>C
NG_042289.1:g.111712A>G
NM_001081676.2:c.3967A>G
NM_001081677.2:c.3967A>G
NM_006922.4:c.4114A>GMANE SELECT
NP_001075145.1:p.Met1323Val
NP_001075146.1:p.Met1323Val
NP_008853.3:p.Met1372Val
NC_000002.11:g.165953887T>C
NM_001081676.1:c.3967A>G
NM_006922.3:c.4114A>G

Protein change:

M1323V; MET1323VAL

Links:

OMIM: 182391.0003; dbSNP: rs758906955

NCBI 1000 Genomes Browser:

rs758906955

Molecular consequence:

NM_001081676.2:c.3967A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001081677.2:c.3967A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006922.4:c.4114A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Epilepsy, familial focal, with variable foci 4 (FFEVF4)
Identifiers:: MONDO: MONDO:0054776; MedGen: C4693694; OMIM: 617935

Recent activity

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transcription factor-like protein DPB-like isoform 3 [Glycine max]
transcription factor-like protein DPB-like isoform 3 [Glycine max]
gi|1679885267|ref|NP_001242415.2|

Protein
Homo sapiens ubiquitin specific peptidase 9 Y-linked (USP9Y), RefSeqGene on chro...
Homo sapiens ubiquitin specific peptidase 9 Y-linked (USP9Y), RefSeqGene on chromosome Y
gi|2296125382|ref|NG_008311.2|

Nucleotide
ytfR galactofuranose ABC transporter putative ATP binding subunit [Escherichia c...
ytfR galactofuranose ABC transporter putative ATP binding subunit [Escherichia coli str. K-12 substr. MG1655]
Gene ID:2847725

Gene
fbp [Escherichia coli CFT073]
fbp [Escherichia coli CFT073]
Gene ID:1037390

Gene
mgtA [Escherichia coli O157:H7 str. EDL933]
mgtA [Escherichia coli O157:H7 str. EDL933]
Gene ID:959797

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000746210	OMIM	no assertion criteria provided	Pathogenic (Sep 1, 2020)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 24157691, 29466837

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000746210

OMIM

no assertion criteria provided

Pathogenic
(Sep 1, 2020)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Novel SCN3A variants associated with focal epilepsy in children.

Vanoye CG, Gurnett CA, Holland KD, George AL Jr, Kearney JA.

Neurobiol Dis. 2014 Feb;62:313-22. doi: 10.1016/j.nbd.2013.10.015. Epub 2013 Oct 21.

PubMed [citation]

PMID:: 24157691
PMCID:: PMC3877720

Mutations in SCN3A cause early infantile epileptic encephalopathy.

Zaman T, Helbig I, Božović IB, DeBrosse SD, Bergqvist AC, Wallis K, Medne L, Maver A, Peterlin B, Helbig KL, Zhang X, Goldberg EM.

Ann Neurol. 2018 Apr;83(4):703-717. doi: 10.1002/ana.25188. Epub 2018 Mar 30. Erratum in: Ann Neurol. 2019 Jun;85(6):948. doi: 10.1002/ana.25485.

PubMed [citation]

PMID:: 29466837
PMCID:: PMC5912987

Details of each submission

From OMIM, SCV000746210.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

In an individual with familial focal epilepsy with variable foci-4 (FFEVF4; 617935), Vanoye et al. (2014) identified a heterozygous mutation in the SCN3A gene, resulting in a met1323-to-val (M1323V) substitution at a conserved residue in the extracellular linker between transmembrane segment 5 and the pore region of domain 2. The authors noted that nucleotide numbering corresponded to the major SCN53A isoform that includes the exon 5 adult (5A) and exon 12v1 (646 bp) splice variants (NM_001081676.1), although they did not include the nucleotide change that resulted in the M1323V substitution. The mutation was found by exome sequencing; parental DNA was not available for study. The mutation was not found in the Exome Variant Server or in 590 control chromosomes. Zaman et al. (2018) noted that this variant, which they referred to as M1372V, was found at a low frequency in the ExAC database.

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

Last Updated: Sep 29, 2024

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