NM_001165963.4(SCN1A):c.5864T>C (p.Ile1955Thr) AND Migraine, familial hemiplegic, 3

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 27, 2017
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:: RCV000395905.13

Allele description [Variation Report for NM_001165963.4(SCN1A):c.5864T>C (p.Ile1955Thr)]

NM_001165963.4(SCN1A):c.5864T>C (p.Ile1955Thr)

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.5864T>C (p.Ile1955Thr)

Other names:

p.I1955T:ATA>ACA

HGVS:

NC_000002.12:g.165991411A>G
NG_011906.1:g.87229T>C
NM_001165963.4:c.5864T>CMANE SELECT
NM_001165963.4:c.5864T>C
NM_001165964.3:c.5780T>C
NM_001202435.3:c.5864T>C
NM_001353948.2:c.5864T>C
NM_001353949.2:c.5831T>C
NM_001353950.2:c.5831T>C
NM_001353951.2:c.5831T>C
NM_001353952.2:c.5831T>C
NM_001353954.2:c.5828T>C
NM_001353955.2:c.5828T>C
NM_001353957.2:c.5780T>C
NM_001353958.2:c.5780T>C
NM_001353960.2:c.5777T>C
NM_001353961.2:c.3422T>C
NM_006920.6:c.5831T>C
NP_001159435.1:p.Ile1955Thr
NP_001159436.1:p.Ile1927Thr
NP_001189364.1:p.Ile1955Thr
NP_001340877.1:p.Ile1955Thr
NP_001340878.1:p.Ile1944Thr
NP_001340879.1:p.Ile1944Thr
NP_001340880.1:p.Ile1944Thr
NP_001340881.1:p.Ile1944Thr
NP_001340883.1:p.Ile1943Thr
NP_001340884.1:p.Ile1943Thr
NP_001340886.1:p.Ile1927Thr
NP_001340887.1:p.Ile1927Thr
NP_001340889.1:p.Ile1926Thr
NP_001340890.1:p.Ile1141Thr
NP_008851.3:p.Ile1944Thr
LRG_8:g.87229T>C
NC_000002.11:g.166847921A>G
NM_001165963.1:c.5864T>C
NM_001202435.1:c.5864T>C
NR_148667.2:n.6281T>C
P35498:p.Ile1955Thr

Protein change:

I1141T

Links:

UniProtKB: P35498#VAR_029730; dbSNP: rs35735053

NCBI 1000 Genomes Browser:

rs35735053

Molecular consequence:

NM_001165963.4:c.5864T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001165964.3:c.5780T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001202435.3:c.5864T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353948.2:c.5864T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353949.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353950.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353951.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353952.2:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353954.2:c.5828T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353955.2:c.5828T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353957.2:c.5780T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353958.2:c.5780T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353960.2:c.5777T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001353961.2:c.3422T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006920.6:c.5831T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148667.2:n.6281T>C - 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

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1995274[uid] (1)
Taxonomy
PITG_01919 [Phytophthora infestans T30-4]
PITG_01919 [Phytophthora infestans T30-4]
Gene ID:9469459

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000417764	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22011963, 12610651, 21713554 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000417764

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Generalised epilepsy with febrile seizures plus (GEFS(+)): molecular analysis in a restricted area.

Polizzi A, Incorpora G, Pavone P, Ruggieri M, Annesi G, Gambardella A, Pavone L, Quattrone A.

Childs Nerv Syst. 2012 Jan;28(1):141-5. doi: 10.1007/s00381-011-1592-9. Epub 2011 Oct 20.

PubMed [citation]

PMID:: 22011963

Sodium channels SCN1A, SCN2A and SCN3A in familial autism.

Weiss LA, Escayg A, Kearney JA, Trudeau M, MacDonald BT, Mori M, Reichert J, Buxbaum JD, Meisler MH.

Mol Psychiatry. 2003 Feb;8(2):186-94.

PubMed [citation]

PMID:: 12610651

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000417764.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Last Updated: Nov 3, 2024

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