NM_001165963.4(SCN1A):c.2671G>A (p.Gly891Arg) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 3, 2022
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:: RCV002466353.2

Allele description [Variation Report for NM_001165963.4(SCN1A):c.2671G>A (p.Gly891Arg)]

NM_001165963.4(SCN1A):c.2671G>A (p.Gly891Arg)

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.2671G>A (p.Gly891Arg)

HGVS:

NC_000002.12:g.166038051C>T
NG_011906.1:g.40589G>A
NM_001165963.4:c.2671G>AMANE SELECT
NM_001165964.3:c.2587G>A
NM_001202435.3:c.2671G>A
NM_001353948.2:c.2671G>A
NM_001353949.2:c.2638G>A
NM_001353950.2:c.2638G>A
NM_001353951.2:c.2638G>A
NM_001353952.2:c.2638G>A
NM_001353954.2:c.2635G>A
NM_001353955.2:c.2635G>A
NM_001353957.2:c.2587G>A
NM_001353958.2:c.2587G>A
NM_001353960.2:c.2584G>A
NM_001353961.2:c.229G>A
NM_006920.6:c.2638G>A
NP_001159435.1:p.Gly891Arg
NP_001159436.1:p.Gly863Arg
NP_001189364.1:p.Gly891Arg
NP_001340877.1:p.Gly891Arg
NP_001340878.1:p.Gly880Arg
NP_001340879.1:p.Gly880Arg
NP_001340880.1:p.Gly880Arg
NP_001340881.1:p.Gly880Arg
NP_001340883.1:p.Gly879Arg
NP_001340884.1:p.Gly879Arg
NP_001340886.1:p.Gly863Arg
NP_001340887.1:p.Gly863Arg
NP_001340889.1:p.Gly862Arg
NP_001340890.1:p.Gly77Arg
NP_008851.3:p.Gly880Arg
NP_008851.3:p.Gly880Arg
LRG_8t1:c.2638G>A
LRG_8:g.40589G>A
LRG_8p1:p.Gly880Arg
NC_000002.11:g.166894561C>T
NM_006920.4:c.2638G>A
NR_148667.2:n.3024G>A

Protein change:

G77R

Molecular consequence:

NM_001165963.4:c.2671G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.2587G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.2671G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.2671G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.2635G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.2635G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.2587G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.2587G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.2584G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.229G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.3024G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002761308	Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 3, 2022)	de novo	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

SCV002761308

Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 3, 2022)

de novo

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	de novo	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 Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine, SCV002761308.1

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

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

Last Updated: May 26, 2024

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