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NM_174936.4(PCSK9):c.2038C>T (p.Arg680Trp) AND Cardiovascular phenotype

Germline classification:
Likely benign (1 submission)
Last evaluated:
Nov 2, 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:
RCV003168612.2

Allele description [Variation Report for NM_174936.4(PCSK9):c.2038C>T (p.Arg680Trp)]

NM_174936.4(PCSK9):c.2038C>T (p.Arg680Trp)

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.2038C>T (p.Arg680Trp)
HGVS:
  • NC_000001.11:g.55063543C>T
  • NG_009061.1:g.28997C>T
  • NM_001407240.1:c.2161C>T
  • NM_001407241.1:c.2080C>T
  • NM_001407242.1:c.2041C>T
  • NM_001407243.1:c.1981C>T
  • NM_001407244.1:c.1864C>T
  • NM_001407245.1:c.1846C>T
  • NM_001407246.1:c.1663C>T
  • NM_001407247.1:c.1537C>T
  • NM_174936.4:c.2038C>TMANE SELECT
  • NP_001394169.1:p.Arg721Trp
  • NP_001394170.1:p.Arg694Trp
  • NP_001394171.1:p.Arg681Trp
  • NP_001394172.1:p.Arg661Trp
  • NP_001394173.1:p.Arg622Trp
  • NP_001394174.1:p.Arg616Trp
  • NP_001394175.1:p.Arg555Trp
  • NP_001394176.1:p.Arg513Trp
  • NP_777596.2:p.Arg680Trp
  • NP_777596.2:p.Arg680Trp
  • LRG_275t1:c.2038C>T
  • LRG_275:g.28997C>T
  • LRG_275p1:p.Arg680Trp
  • NC_000001.10:g.55529216C>T
  • NM_174936.3:c.2038C>T
  • NR_110451.2:n.1645C>T
  • NR_110451.3:n.2319C>T
  • NR_176318.1:n.2122C>T
  • NR_176319.1:n.2597C>T
  • NR_176320.1:n.2561C>T
  • NR_176321.1:n.2276C>T
  • NR_176322.1:n.2231C>T
  • NR_176323.1:n.2150C>T
  • NR_176324.1:n.2538C>T
Protein change:
R513W
Links:
dbSNP: rs533555352
NCBI 1000 Genomes Browser:
rs533555352
Molecular consequence:
  • NM_001407240.1:c.2161C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407241.1:c.2080C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407242.1:c.2041C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407243.1:c.1981C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407244.1:c.1864C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407245.1:c.1846C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407246.1:c.1663C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407247.1:c.1537C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_174936.4:c.2038C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003911411Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Nov 2, 2022) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Combined hyperlipidemia is genetically similar to isolated hypertriglyceridemia.

Gill PK, Dron JS, Berberich AJ, Wang J, McIntyre AD, Cao H, Hegele RA.

J Clin Lipidol. 2021 Jan-Feb;15(1):79-87. doi: 10.1016/j.jacl.2020.11.006. Epub 2020 Nov 24.

PubMed [citation]
PMID:
33303402

Details of each submission

From Ambry Genetics, SCV003911411.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

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

Last Updated: Sep 29, 2024