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NM_006514.4(SCN10A):c.1496C>A (p.Ala499Asp) AND Episodic pain syndrome, familial, 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 11, 2021
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:
RCV003993716.2

Allele description [Variation Report for NM_006514.4(SCN10A):c.1496C>A (p.Ala499Asp)]

NM_006514.4(SCN10A):c.1496C>A (p.Ala499Asp)

Gene:
SCN10A:sodium voltage-gated channel alpha subunit 10 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_006514.4(SCN10A):c.1496C>A (p.Ala499Asp)
Other names:
p.Ala499Asp
HGVS:
  • NC_000003.12:g.38752478G>T
  • NG_031891.2:g.46533C>A
  • NG_031891.3:g.68739C>A
  • NM_001293306.2:c.1496C>A
  • NM_001293307.2:c.1462-2294C>A
  • NM_006514.4:c.1496C>AMANE SELECT
  • NP_001280235.2:p.Ala499Asp
  • NP_006505.4:p.Ala499Asp
  • NC_000003.11:g.38793969G>T
  • NM_006514.3:c.1496C>A
Protein change:
A499D
Molecular consequence:
  • NM_001293307.2:c.1462-2294C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001293306.2:c.1496C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006514.4:c.1496C>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Episodic pain syndrome, familial, 2 (FEPS2)
Identifiers:
MONDO: MONDO:0014246; MedGen: C3809893; Orphanet: 306577; OMIM: 615551

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004811876Clinical Genomics Laboratory, Stanford Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jun 11, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not 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 Clinical Genomics Laboratory, Stanford Medicine, SCV004811876.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

The p.Ala499Asp variant in the SCN10A gene has not been previously reported in association with disease. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Computational tools do not predict that the p.Ala499Asp variant impacts protein function; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Ala499Asp variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PM2]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 7, 2024