NM_001365536.1(SCN9A):c.5588T>C (p.Met1863Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 12, 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:: RCV001751362.3

Allele description [Variation Report for NM_001365536.1(SCN9A):c.5588T>C (p.Met1863Thr)]

NM_001365536.1(SCN9A):c.5588T>C (p.Met1863Thr)

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.5588T>C (p.Met1863Thr)

HGVS:

NC_000002.12:g.166199051A>G
NG_012798.1:g.181937T>C
NM_001365536.1:c.5588T>CMANE SELECT
NM_002977.4:c.5555T>C
NP_001352465.1:p.Met1863Thr
NP_002968.1:p.Met1852Thr
NP_002968.1:p.Met1852Thr
NP_002968.2:p.Met1852Thr
LRG_369t1:c.5555T>C
LRG_369:g.181937T>C
LRG_369p1:p.Met1852Thr
NC_000002.11:g.167055561A>G
NC_000002.11:g.167055561A>G
NM_002977.2:c.5555T>C
NM_002977.3:c.5555T>C

Protein change:

M1852T

Links:

dbSNP: rs201561928

NCBI 1000 Genomes Browser:

rs201561928

Molecular consequence:

NM_001365536.1:c.5588T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002977.4:c.5555T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001985782	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 12, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001985782

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Aug 12, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001985782.3

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

Description

Identified in a patient with diabetic peripheral neuropathy in the published literature (Blesneac et al., 2018); Published functional studies demonstrate that this variant results in a gain of function (Blesneac et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29176367, 30672368)

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

Last Updated: Mar 5, 2024

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