NM_174936.4(PCSK9):c.1537A>G (p.Asn513Asp) AND Cardiovascular phenotype

Germline classification:: Likely benign (1 submission)
Last evaluated:: May 20, 2024
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:: RCV004649143.1

Allele description [Variation Report for NM_174936.4(PCSK9):c.1537A>G (p.Asn513Asp)]

NM_174936.4(PCSK9):c.1537A>G (p.Asn513Asp)

Gene:

PCSK9:proprotein convertase subtilisin/kexin type 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p32.3

Genomic location:

Preferred name:

NM_174936.4(PCSK9):c.1537A>G (p.Asn513Asp)

Other names:

p.Asn513Asp

HGVS:

NC_000001.11:g.55059519A>G
NG_009061.1:g.24973A>G
NM_001407240.1:c.1660A>G
NM_001407241.1:c.1579A>G
NM_001407242.1:c.1540A>G
NM_001407243.1:c.1480A>G
NM_001407244.1:c.1363A>G
NM_001407245.1:c.1345A>G
NM_001407246.1:c.1162A>G
NM_174936.4:c.1537A>GMANE SELECT
NP_001394169.1:p.Asn554Asp
NP_001394170.1:p.Asn527Asp
NP_001394171.1:p.Asn514Asp
NP_001394172.1:p.Asn494Asp
NP_001394173.1:p.Asn455Asp
NP_001394174.1:p.Asn449Asp
NP_001394175.1:p.Asn388Asp
NP_777596.2:p.Asn513Asp
NP_777596.2:p.Asn513Asp
NP_777596.2:p.N513D
LRG_275t1:c.1537A>G
LRG_275:g.24973A>G
LRG_275p1:p.Asn513Asp
NC_000001.10:g.55525192A>G
NM_174936.3:c.1537A>G
NR_110451.2:n.1144A>G
NR_110451.3:n.1818A>G
NR_176318.1:n.1511A>G
NR_176319.1:n.2096A>G
NR_176320.1:n.1950A>G
NR_176321.1:n.1775A>G
NR_176322.1:n.1730A>G
NR_176324.1:n.2037A>G

Protein change:

N388D

Links:

dbSNP: rs1057516136

NCBI 1000 Genomes Browser:

rs1057516136

Molecular consequence:

NM_001407240.1:c.1660A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407241.1:c.1579A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407242.1:c.1540A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407243.1:c.1480A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407244.1:c.1363A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407245.1:c.1345A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407246.1:c.1162A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_174936.4:c.1537A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005147444	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (May 20, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005147444

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(May 20, 2024)

germline

clinical testing

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

Citation Link

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

Polygenic Versus Monogenic Causes of Hypercholesterolemia Ascertained Clinically.

Wang J, Dron JS, Ban MR, Robinson JF, McIntyre AD, Alazzam M, Zhao PJ, Dilliott AA, Cao H, Huff MW, Rhainds D, Low-Kam C, Dubé MP, Lettre G, Tardif JC, Hegele RA.

Arterioscler Thromb Vasc Biol. 2016 Dec;36(12):2439-2445. Epub 2016 Oct 20.

PubMed [citation]

PMID:: 27765764

Details of each submission

From Ambry Genetics, SCV005147444.1

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Nov 30, 2024

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