NM_001330723.2(SNX27):c.543+6T>C AND Severe myoclonic epilepsy in infancy

Clinical significance:Uncertain significance (Last evaluated: Aug 17, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000820527.1

Allele description [Variation Report for NM_001330723.2(SNX27):c.543+6T>C]

NM_001330723.2(SNX27):c.543+6T>C

Gene:
SNX27:sorting nexin 27 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q21.3
Genomic location:
Preferred name:
NM_001330723.2(SNX27):c.543+6T>C
HGVS:
  • NC_000001.11:g.151639125T>C
  • NM_001330723.2:c.543+6T>CMANE SELECT
  • NM_030918.6:c.543+6T>C
  • NC_000001.10:g.151611601T>C
  • NM_030918.5:c.543+6T>C
Links:
dbSNP: rs1571793465
NCBI 1000 Genomes Browser:
rs1571793465
Molecular consequence:
  • NM_001330723.2:c.543+6T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_030918.6:c.543+6T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Severe myoclonic epilepsy in infancy (DRVT)
Synonyms:
Epilepsy, Myoclonic, Infantile, Severe; Dravet syndrome; Epileptic encephalopathy, early infantile, 6 (Dravet syndrome)
Identifiers:
MONDO: MONDO:0100135; MedGen: C0751122; Orphanet: 33069; OMIM: 607208

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000961244Invitaecriteria provided, single submitter
Uncertain significance
(Aug 17, 2018)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000961244.1

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

Description

This sequence change falls in intron 2 of the SNX27 gene. It does not directly change the encoded amino acid sequence of the SNX27 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SNX27-related disease. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 7, 2021

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