NM_001349253.2(SCN11A):c.2513G>A (p.Arg838Gln) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 1, 2023
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:: RCV000651875.6

Allele description [Variation Report for NM_001349253.2(SCN11A):c.2513G>A (p.Arg838Gln)]

NM_001349253.2(SCN11A):c.2513G>A (p.Arg838Gln)

Gene:

SCN11A:sodium voltage-gated channel alpha subunit 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_001349253.2(SCN11A):c.2513G>A (p.Arg838Gln)

HGVS:

NC_000003.12:g.38894855C>T
NG_033859.2:g.162132G>A
NM_001349253.2:c.2513G>AMANE SELECT
NM_014139.3:c.2513G>A
NP_001336182.1:p.Arg838Gln
NP_054858.2:p.Arg838Gln
NP_054858.2:p.Arg838Gln
NC_000003.11:g.38936346C>T
NM_014139.2:c.2513G>A

Protein change:

R838Q

Links:

dbSNP: rs149681198

NCBI 1000 Genomes Browser:

rs149681198

Molecular consequence:

NM_001349253.2:c.2513G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014139.3:c.2513G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary sensory and autonomic neuropathy type 7
Synonyms:: HSAN VII; Neuropathy, hereditary sensory and autonomic, type VII
Identifiers:: MONDO: MONDO:0014244; MedGen: C3809882; Orphanet: 391397; OMIM: 615548

Name:: Familial episodic pain syndrome with predominantly lower limb involvement
Synonyms:: Episodic pain syndrome, familial, 3
Identifiers:: MONDO: MONDO:0014247; MedGen: C3809899; Orphanet: 391384; Orphanet: 391392; OMIM: 615552

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000773731	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 1, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 30533233, 30554136, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000773731

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 1, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Multifactorial Origin of Exertional Rhabdomyolysis, Recurrent Hematuria, and Episodic Pain in a Service Member with Sickle Cell Trait.

Sambuughin N, Ren M, Capacchione JF, Mungunsukh O, Chuang K, Horkayne-Szakaly I, O'Connor FG, Deuster PA.

Case Rep Genet. 2018;2018:6898546. doi: 10.1155/2018/6898546.

PubMed [citation]

PMID:: 30533233
PMCID:: PMC6247656

Yield of peripheral sodium channels gene screening in pure small fibre neuropathy.

Eijkenboom I, Sopacua M, Hoeijmakers JGJ, de Greef BTA, Lindsey P, Almomani R, Marchi M, Vanoevelen J, Smeets HJM, Waxman SG, Lauria G, Merkies ISJ, Faber CG, Gerrits MM.

J Neurol Neurosurg Psychiatry. 2019 Mar;90(3):342-352. doi: 10.1136/jnnp-2018-319042. Epub 2018 Dec 15.

PubMed [citation]

PMID:: 30554136

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000773731.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 838 of the SCN11A protein (p.Arg838Gln). This variant is present in population databases (rs149681198, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of SCN11A-related conditions (PMID: 30533233, 30554136). ClinVar contains an entry for this variant (Variation ID: 541570). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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