NM_001349253.2(SCN11A):c.240C>G (p.Asp80Glu) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 9, 2022
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:: RCV001243601.4

Allele description [Variation Report for NM_001349253.2(SCN11A):c.240C>G (p.Asp80Glu)]

NM_001349253.2(SCN11A):c.240C>G (p.Asp80Glu)

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.240C>G (p.Asp80Glu)

HGVS:

NC_000003.12:g.38950123G>C
NG_033859.2:g.106864C>G
NM_001349253.2:c.240C>GMANE SELECT
NM_014139.3:c.240C>G
NP_001336182.1:p.Asp80Glu
NP_054858.2:p.Asp80Glu
NC_000003.11:g.38991614G>C
NM_014139.2:c.240C>G

Protein change:

D80E

Links:

dbSNP: rs749020471

NCBI 1000 Genomes Browser:

rs749020471

Molecular consequence:

NM_001349253.2:c.240C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014139.3:c.240C>G - 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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001416769	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 9, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001416769

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 9, 2022)

germline

clinical testing

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

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

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, SCV001416769.4

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

Description

This variant has not been reported in the literature in individuals affected with SCN11A-related conditions. This variant is present in population databases (rs749020471, gnomAD 0.003%). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 80 of the SCN11A protein (p.Asp80Glu). ClinVar contains an entry for this variant (Variation ID: 968465). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SCN11A protein function. 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: Feb 28, 2024

ClinVar

Relating variation to medicine