NM_001365536.1(SCN9A):c.1555G>A (p.Glu519Lys) AND Paroxysmal extreme pain disorder

Clinical significance:Likely benign (Last evaluated: Apr 28, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000388718.2

Allele description [Variation Report for NM_001365536.1(SCN9A):c.1555G>A (p.Glu519Lys)]

NM_001365536.1(SCN9A):c.1555G>A (p.Glu519Lys)

Genes:
SCN1A-AS1:SCN1A and SCN9A antisense RNA 1 [Gene - HGNC]
SCN9A:sodium voltage-gated channel alpha subunit 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.3
Genomic location:
Preferred name:
NM_001365536.1(SCN9A):c.1555G>A (p.Glu519Lys)
HGVS:
  • NC_000002.12:g.166286383C>T
  • NG_012798.1:g.94605G>A
  • NM_001365536.1:c.1555G>AMANE SELECT
  • NM_002977.3:c.1555G>A
  • NP_001352465.1:p.Glu519Lys
  • NP_002968.1:p.Glu519Lys
  • LRG_369t1:c.1555G>A
  • LRG_369:g.94605G>A
  • LRG_369p1:p.Glu519Lys
  • NC_000002.11:g.167142893C>T
  • Q15858:p.Glu519Lys
Protein change:
E519K
Links:
UniProtKB: Q15858#VAR_064603; dbSNP: rs187453572
NCBI 1000 Genomes Browser:
rs187453572
Molecular consequence:
  • NM_001365536.1:c.1555G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002977.3:c.1555G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Paroxysmal extreme pain disorder (PEXPD)
Synonyms:
PAIN, SUBMANDIBULAR, OCULAR, AND RECTAL, WITH FLUSHING; RECTAL PAIN, FAMILIAL
Identifiers:
MONDO: MONDO:0008179; MedGen: C1833661; Orphanet: 46348; OMIM: 167400

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000418694Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 28, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000418694.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

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). No publications were found based on this search. Allele frequency data from public databases allowed determination 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: Oct 7, 2021

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