NM_001165963.4(SCN1A):c.5882T>C (p.Ile1961Thr) AND Generalized epilepsy with febrile seizures plus, type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 23, 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:: RCV000678302.3

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5882T>C (p.Ile1961Thr)]

NM_001165963.4(SCN1A):c.5882T>C (p.Ile1961Thr)

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.5882T>C (p.Ile1961Thr)

HGVS:

NC_000002.12:g.165991393A>G
NG_011906.1:g.87247T>C
NM_001165963.4:c.5882T>CMANE SELECT
NM_001165964.3:c.5798T>C
NM_001202435.3:c.5882T>C
NM_001353948.2:c.5882T>C
NM_001353949.2:c.5849T>C
NM_001353950.2:c.5849T>C
NM_001353951.2:c.5849T>C
NM_001353952.2:c.5849T>C
NM_001353954.2:c.5846T>C
NM_001353955.2:c.5846T>C
NM_001353957.2:c.5798T>C
NM_001353958.2:c.5798T>C
NM_001353960.2:c.5795T>C
NM_001353961.2:c.3440T>C
NM_006920.6:c.5849T>C
NP_001159435.1:p.Ile1961Thr
NP_001159436.1:p.Ile1933Thr
NP_001189364.1:p.Ile1961Thr
NP_001340877.1:p.Ile1961Thr
NP_001340878.1:p.Ile1950Thr
NP_001340879.1:p.Ile1950Thr
NP_001340880.1:p.Ile1950Thr
NP_001340881.1:p.Ile1950Thr
NP_001340883.1:p.Ile1949Thr
NP_001340884.1:p.Ile1949Thr
NP_001340886.1:p.Ile1933Thr
NP_001340887.1:p.Ile1933Thr
NP_001340889.1:p.Ile1932Thr
NP_001340890.1:p.Ile1147Thr
NP_008851.3:p.Ile1950Thr
LRG_8:g.87247T>C
NC_000002.11:g.166847903A>G
NM_001165963.1:c.5882T>C
NR_148667.2:n.6299T>C

Protein change:

I1147T

Links:

dbSNP: rs760676898

NCBI 1000 Genomes Browser:

rs760676898

Molecular consequence:

NM_001165963.4:c.5882T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.5798T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5882T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5882T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5849T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5849T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5849T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5849T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5846T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5846T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.5798T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.5798T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.5795T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.3440T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5849T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.6299T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV000804361	Geisinger Autism and Developmental Medicine Institute, Geisinger Health System	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 23, 2018)	paternal	provider interpretation, 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

SCV000804361

Geisinger Autism and Developmental Medicine Institute, Geisinger Health System

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 23, 2018)

paternal

provider interpretation, 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	paternal	unknown	1	not provided	not provided	1	not provided	clinical testing, provider interpretation

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 Geisinger Autism and Developmental Medicine Institute, Geisinger Health System, SCV000804361.2

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

Description

This variant was identified in an 11 year old female with autism spectrum disorder, global developmental delay, microcephaly, coordination disorder, a single seizure, imperforate anus, intermittent exotropia, and history of hydronephrosis. Initial EEG at age 3 was normal; EEG at age 4 following a single unprovoked seizure showed biposterior slowing. There is no paternal history of developmental delays or seizures. The variant is present in the gnomAD South Asian population at 0.0032%. Computational prediction models are inconsistent.

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

Last Updated: Feb 20, 2024

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