NM_000335.5(SCN5A):c.6013C>G (p.Pro2005Ala) AND not provided

Germline classification:: Likely benign (5 submissions)
Last evaluated:: Jul 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000058824.40

Allele description [Variation Report for NM_000335.5(SCN5A):c.6013C>G (p.Pro2005Ala)]

NM_000335.5(SCN5A):c.6013C>G (p.Pro2005Ala)

Gene:

SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.6013C>G (p.Pro2005Ala)

Other names:

p.P2006A:CCT>GCT

HGVS:

NC_000003.12:g.38550356G>C
NG_008934.1:g.104317C>G
NM_000335.5:c.6013C>GMANE SELECT
NM_001099404.1:c.6016C>G
NM_001099404.2:c.6016C>G
NM_001099405.2:c.5962C>G
NM_001160160.2:c.5917C>G
NM_001160161.2:c.5854C>G
NM_001354701.2:c.5959C>G
NM_198056.3:c.6016C>G
NP_000326.2:p.Pro2005Ala
NP_001092874.1:p.Pro2006Ala
NP_001092875.1:p.Pro1988Ala
NP_001153632.1:p.Pro1973Ala
NP_001153633.1:p.Pro1952Ala
NP_001341630.1:p.Pro1987Ala
NP_932173.1:p.Pro2006Ala
NP_932173.1:p.Pro2006Ala
LRG_289t1:c.6016C>G
LRG_289t3:c.6016C>G
LRG_289:g.104317C>G
LRG_289p1:p.Pro2006Ala
NC_000003.11:g.38591847G>C
NM_198056.2:c.6016C>G
Q14524:p.Pro2006Ala

Protein change:

P1952A

Links:

UniProtKB: Q14524#VAR_055222; dbSNP: rs45489199

NCBI 1000 Genomes Browser:

rs45489199

Molecular consequence:

NM_000335.5:c.6013C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.6016C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.5962C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.5917C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.5854C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.5959C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.6016C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000090344	Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	no classification provided	not provided	germline	literature only	PubMed (12) [See all records that cite these PMIDs] 10961955, 15851227, 16379539, 16712702, 17210839, 19841300, 19597050, 21109022, 21410720, 21070882, 20129283, 22581653
SCV000235311	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Oct 5, 2020)	germline	clinical testing	Citation Link,
SCV000291828	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000884485	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Mar 20, 2020)	germline	clinical testing	Citation Link,
SCV001153852	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	12	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, literature only

Citations

PubMed

The elusive link between LQT3 and Brugada syndrome: the role of flecainide challenge.

Priori SG, Napolitano C, Schwartz PJ, Bloise R, Crotti L, Ronchetti E.

Circulation. 2000 Aug 29;102(9):945-7.

PubMed [citation]

PMID:: 10961955

Spectrum and prevalence of cardiac sodium channel variants among black, white, Asian, and Hispanic individuals: implications for arrhythmogenic susceptibility and Brugada/long QT syndrome genetic testing.

Ackerman MJ, Splawski I, Makielski JC, Tester DJ, Will ML, Timothy KW, Keating MT, Jones G, Chadha M, Burrow CR, Stephens JC, Xu C, Judson R, Curran ME.

Heart Rhythm. 2004 Nov;1(5):600-7.

PubMed [citation]

PMID:: 15851227

See all PubMed Citations (13)

Details of each submission

From Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust, SCV000090344.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (12)

Description

This variant has been reported in the following publications (PMID:10961955;PMID:15851227;PMID:16379539;PMID:16712702;PMID:17210839;PMID:19841300;PMID:19597050;PMID:21109022;PMID:21410720;PMID:21070882;PMID:20129283).

#	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

From GeneDx, SCV000235311.13

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

Description

This variant is associated with the following publications: (PMID: 22378279, 22360817, 21215473, 19597050, 26749013, 20875080, 2107088, 23714088, 27153395, 28988457, 10961955, 23631430, 23465283, 21070882, 17210839, 17210841, 15851227, 21410720, 21109022, 26159999, 23571586, 20129283, 29032884, 28831623, 28807990, 28798025, 16712702, 16379539, 19841300, 25351510, 26746457, 28301460, 29728395, 29672598, 30762279, 31337358, 31043699, 32880476)

#	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

From Invitae, SCV000291828.9

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

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884485.3

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001153852.25

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	12	not provided	not provided	clinical testing	not provided

Description

SCN5A: BS2

#	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		12	not provided	not provided	not provided

Last Updated: Sep 16, 2024

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