NM_000335.5(SCN5A):c.567T>C (p.Leu189=) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 23, 2015
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:: RCV000223477.4

Allele description [Variation Report for NM_000335.5(SCN5A):c.567T>C (p.Leu189=)]

NM_000335.5(SCN5A):c.567T>C (p.Leu189=)

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.567T>C (p.Leu189=)

HGVS:

NC_000003.12:g.38620887A>G
NG_008934.1:g.33786T>C
NM_000335.5:c.567T>CMANE SELECT
NM_001099404.2:c.567T>C
NM_001099405.2:c.567T>C
NM_001160160.2:c.567T>C
NM_001160161.2:c.567T>C
NM_001354701.2:c.567T>C
NM_198056.3:c.567T>C
NP_000326.2:p.Leu189=
NP_001092874.1:p.Leu189=
NP_001092875.1:p.Leu189=
NP_001153632.1:p.Leu189=
NP_001153633.1:p.Leu189=
NP_001341630.1:p.Leu189=
NP_932173.1:p.Leu189=
NP_932173.1:p.Leu189=
LRG_289t1:c.567T>C
LRG_289:g.33786T>C
LRG_289p1:p.Leu189=
NC_000003.11:g.38662378A>G
NM_198056.2:c.567T>C
p.Leu189Leu

Links:

dbSNP: rs876657581

NCBI 1000 Genomes Browser:

rs876657581

Molecular consequence:

NM_000335.5:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001099404.2:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001099405.2:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001160160.2:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001160161.2:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354701.2:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_198056.3:c.567T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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RecName: Full=Methylcytosine dioxygenase TET1; AltName: Full=CXXC-type zinc fing...
RecName: Full=Methylcytosine dioxygenase TET1; AltName: Full=CXXC-type zinc finger protein 6; AltName: Full=Leukemia-associated protein with a CXXC domain; AltName: Full=Ten-eleven translocation 1 gene protein
gi|115502139|sp|Q8NFU7.2|TET1_HUMAN

Protein
RecName: Full=General transcription factor IIH subunit 1; AltName: Full=Basic tr...
RecName: Full=General transcription factor IIH subunit 1; AltName: Full=Basic transcription factor 2 62 kDa subunit; Short=BTF2 p62; AltName: Full=General transcription factor IIH polypeptide 1; AltName: Full=TFIIH basal transcription factor complex p62 subunit
gi|416727|sp|P32780.1|TF2H1_HUMAN

Protein
RecName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase sub...
RecName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2; AltName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit; AltName: Full=RIBIIR; AltName: Full=Ribophorin II; Short=RPN-II; AltName: Full=Ribophorin-2; Flags: Precursor
gi|9297108|sp|P04844.3|RPN2_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000270832	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Apr 23, 2015)	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

SCV000270832

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Apr 23, 2015)

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	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000270832.3

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

Description

p.Leu189Leu in exon 5 of SCN5A: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence.

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

Last Updated: Oct 26, 2024

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