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NM_000335.5(SCN5A):c.458C>T (p.Pro153Leu) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 25, 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:
RCV003224533.1

Allele description [Variation Report for NM_000335.5(SCN5A):c.458C>T (p.Pro153Leu)]

NM_000335.5(SCN5A):c.458C>T (p.Pro153Leu)

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.458C>T (p.Pro153Leu)
HGVS:
  • NC_000003.12:g.38622424G>A
  • NG_008934.1:g.32249C>T
  • NM_000335.5:c.458C>TMANE SELECT
  • NM_001099404.2:c.458C>T
  • NM_001099405.2:c.458C>T
  • NM_001160160.2:c.458C>T
  • NM_001160161.2:c.458C>T
  • NM_001354701.2:c.458C>T
  • NM_198056.3:c.458C>T
  • NP_000326.2:p.Pro153Leu
  • NP_001092874.1:p.Pro153Leu
  • NP_001092875.1:p.Pro153Leu
  • NP_001153632.1:p.Pro153Leu
  • NP_001153633.1:p.Pro153Leu
  • NP_001341630.1:p.Pro153Leu
  • NP_932173.1:p.Pro153Leu
  • LRG_289t1:c.458C>T
  • LRG_289:g.32249C>T
  • NC_000003.11:g.38663915G>A
  • NM_198056.2:c.458C>T
Protein change:
P153L
Links:
dbSNP: rs1298498462
NCBI 1000 Genomes Browser:
rs1298498462
Molecular consequence:
  • NM_000335.5:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.458C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Brugada syndrome 1 (BRGDA1)
Synonyms:
Right bundle branch block, ST segment elevation, and sudden death syndrome
Identifiers:
MONDO: MONDO:0011001; MedGen: C4551804; Orphanet: 130; OMIM: 601144
Name:
Long QT syndrome 3 (LQT3)
Identifiers:
MONDO: MONDO:0011377; MedGen: C1859062; Orphanet: 101016; Orphanet: 768; OMIM: 603830
Name:
Sick sinus syndrome 1
Synonyms:
SICK SINUS SYNDROME, CONGENITAL; SINUS BRADYCARDIA SYNDROME, FAMILIAL; SINUS NODE DISEASE, FAMILIAL, AUTOSOMAL RECESSIVE; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0024562; MedGen: C1837845; Orphanet: 166282; OMIM: 608567
Name:
Progressive familial heart block, type 1A (PFHB1A)
Synonyms:
HEART BLOCK, PROGRESSIVE FAMILIAL, TYPE I; Heart block progressive familial type 1; Cardiac conduction defect progressive; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007240; MedGen: C1879286; Orphanet: 871; OMIM: 113900
Name:
Ventricular fibrillation, paroxysmal familial, type 1
Identifiers:
MONDO: MONDO:0011376; MedGen: C2751898; Orphanet: 228140; OMIM: 603829
Name:
Dilated cardiomyopathy 1E (CMD1E)
Synonyms:
CARDIOMYOPATHY, DILATED, WITH CONDUCTION DEFECT 2; CARDIOMYOPATHY, DILATED, WITH CONDUCTION DISORDER AND ARRHYTHMIA; SCN5A-Associated Dilated Cardiomyopathy
Identifiers:
MONDO: MONDO:0011003; MedGen: C1832680; Orphanet: 154; OMIM: 601154
Name:
SUDDEN INFANT DEATH SYNDROME (SIDS)
Synonyms:
Sudden Infant Death
Identifiers:
EFO: EFO_0005303; MeSH: D013398; MedGen: C0038644; OMIM: 272120
Name:
Atrial fibrillation, familial, 10 (ATFB10)
Identifiers:
MONDO: MONDO:0013530; MedGen: C3151464; OMIM: 614022

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003920453Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jul 25, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920453.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest rpeorted MAF: 0.007% [1/15288]; https://gnomad.broadinstitute.org/variant/3-38622424-G-A?dataset=gnomad_r3), and in ClinVar (Variation ID:956871). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 14, 2024