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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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000417764Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Likely benign
(Apr 27, 2017)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024