NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter) AND Familial hemiplegic migraine type 3

Clinical significance:Pathogenic (Last evaluated: Sep 28, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001198880.1

Allele description [Variation Report for NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter)]

NM_001165963.4(SCN1A):c.1702C>T (p.Arg568Ter)

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.1702C>T (p.Arg568Ter)
HGVS:
  • NC_000002.12:g.166044010G>A
  • NG_011906.1:g.34630C>T
  • NM_001165963.4:c.1702C>TMANE SELECT
  • NM_001165964.3:c.1702C>T
  • NM_001202435.3:c.1702C>T
  • NM_001353948.2:c.1702C>T
  • NM_001353949.2:c.1702C>T
  • NM_001353950.2:c.1702C>T
  • NM_001353951.2:c.1702C>T
  • NM_001353952.2:c.1702C>T
  • NM_001353954.2:c.1699C>T
  • NM_001353955.2:c.1699C>T
  • NM_001353957.2:c.1702C>T
  • NM_001353958.2:c.1702C>T
  • NM_001353960.2:c.1699C>T
  • NM_001353961.2:c.-724C>T
  • NM_006920.6:c.1702C>T
  • NP_001159435.1:p.Arg568Ter
  • NP_001159436.1:p.Arg568Ter
  • NP_001189364.1:p.Arg568Ter
  • NP_001340877.1:p.Arg568Ter
  • NP_001340878.1:p.Arg568Ter
  • NP_001340879.1:p.Arg568Ter
  • NP_001340880.1:p.Arg568Ter
  • NP_001340881.1:p.Arg568Ter
  • NP_001340883.1:p.Arg567Ter
  • NP_001340884.1:p.Arg567Ter
  • NP_001340886.1:p.Arg568Ter
  • NP_001340887.1:p.Arg568Ter
  • NP_001340889.1:p.Arg567Ter
  • NP_008851.3:p.Arg568Ter
  • LRG_8:g.34630C>T
  • NC_000002.11:g.166900520G>A
  • NM_001165963.1:c.1702C>T
  • NM_001165963.3:c.1702C>T
  • NR_148667.2:n.2088C>T
Protein change:
R567*
Links:
dbSNP: rs886039430
NCBI 1000 Genomes Browser:
rs886039430
Molecular consequence:
  • NM_001353961.2:c.-724C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_148667.2:n.2088C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001165963.4:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001165964.3:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001202435.3:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353948.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353949.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353950.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353951.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353952.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353954.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353955.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353957.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353958.2:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353960.2:c.1699C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006920.6:c.1702C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Familial hemiplegic migraine type 3 (FHM3)
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
SCV001369875Centre for Mendelian Genomics,University Medical Centre Ljubljanacriteria provided, single submitter
Pathogenic
(Sep 28, 2018)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical 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 Centre for Mendelian Genomics,University Medical Centre Ljubljana, SCV001369875.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS4,PM2,PM4.

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

Last Updated: Oct 8, 2021

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