NM_001165963.4(SCN1A):c.4633A>G (p.Ile1545Val) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 30, 2018
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:: RCV001249684.5

Allele description [Variation Report for NM_001165963.4(SCN1A):c.4633A>G (p.Ile1545Val)]

NM_001165963.4(SCN1A):c.4633A>G (p.Ile1545Val)

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.4633A>G (p.Ile1545Val)

Other names:

NM_001165963.4(SCN1A):c.4633A>G

HGVS:

NC_000002.12:g.165994365T>C
NG_011906.1:g.84275A>G
NM_001165963.4:c.4633A>GMANE SELECT
NM_001165963.4:c.4633A>G
NM_001165964.3:c.4549A>G
NM_001202435.3:c.4633A>G
NM_001353948.2:c.4633A>G
NM_001353949.2:c.4600A>G
NM_001353950.2:c.4600A>G
NM_001353951.2:c.4600A>G
NM_001353952.2:c.4600A>G
NM_001353954.2:c.4597A>G
NM_001353955.2:c.4597A>G
NM_001353957.2:c.4549A>G
NM_001353958.2:c.4549A>G
NM_001353960.2:c.4546A>G
NM_001353961.2:c.2191A>G
NM_006920.6:c.4600A>G
NP_001159435.1:p.Ile1545Val
NP_001159436.1:p.Ile1517Val
NP_001189364.1:p.Ile1545Val
NP_001340877.1:p.Ile1545Val
NP_001340878.1:p.Ile1534Val
NP_001340879.1:p.Ile1534Val
NP_001340880.1:p.Ile1534Val
NP_001340881.1:p.Ile1534Val
NP_001340883.1:p.Ile1533Val
NP_001340884.1:p.Ile1533Val
NP_001340886.1:p.Ile1517Val
NP_001340887.1:p.Ile1517Val
NP_001340889.1:p.Ile1516Val
NP_001340890.1:p.Ile731Val
NP_008851.3:p.Ile1534Val
LRG_8t1:c.4600A>G
LRG_8:g.84275A>G
NC_000002.11:g.166850875T>C
NC_000002.12:g.165994365T>C
NM_001165963.1:c.4633A>G
NM_001202435.1:c.4633A>G
NM_006920.4:c.4600A>G
NR_148667.2:n.5050A>G

Protein change:

I1516V

Links:

UniProtKB/Swiss-Prot: VAR_064265; dbSNP: rs121917975

NCBI 1000 Genomes Browser:

rs121917975

Molecular consequence:

NM_001165963.4:c.4633A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.4549A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.4633A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.4633A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.4600A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.4600A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.4600A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.4600A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.4597A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.4597A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.4549A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.4549A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.4546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.2191A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.4600A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.5050A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Migraine, familial hemiplegic, 3
Identifiers:: MONDO: MONDO:0012320; MedGen: C1864987; Orphanet: 569; OMIM: 609634

Name:: Severe myoclonic epilepsy in infancy (DRVT)
Synonyms:: Epilepsy, Myoclonic, Infantile, Severe; Dravet syndrome; Epileptic encephalopathy, early infantile, 6 (Dravet syndrome); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100135; MedGen: C0751122; Orphanet: 33069; OMIM: 607208

Name:: Generalized epilepsy with febrile seizures plus, type 2 (GEFSP2)
Synonyms:: GEFS+, TYPE 2
Identifiers:: MONDO: MONDO:0011461; MedGen: C1858673; Orphanet: 36387; OMIM: 604403

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matrin-3 isoform b [Homo sapiens]
matrin-3 isoform b [Homo sapiens]
gi|303227928|ref|NP_001181885.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001423679	Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 30, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001423679

Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 30, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital, SCV001423679.1

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

Description

[ACMG/AMP: PS2, PM1, PM2, PP2, PP3] This alteration is de novo in origin as it was not detected in the submitted parental specimens (identity confirmed) [PS2], is located in a mutational hotspot and/or critical and well-established functional domain [PM1], is absent from or rarely observed in large-scale population databases [PM2], is a missense variant in a gene in which missense variants are a common mechanism of disease [PP2], is predicted to be damaging by multiple functional prediction tools [PP3].

#	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: Sep 29, 2024

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