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NM_174936.4(PCSK9):c.520C>T (p.Pro174Ser) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 6, 2016
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:
RCV000586165.1

Allele description [Variation Report for NM_174936.4(PCSK9):c.520C>T (p.Pro174Ser)]

NM_174936.4(PCSK9):c.520C>T (p.Pro174Ser)

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.520C>T (p.Pro174Ser)
HGVS:
  • NC_000001.11:g.55046643C>T
  • NG_009061.1:g.12097C>T
  • NM_174936.4:c.520C>TMANE SELECT
  • NP_777596.2:p.Pro174Ser
  • NP_777596.2:p.Pro174Ser
  • LRG_275t1:c.520C>T
  • LRG_275:g.12097C>T
  • LRG_275p1:p.Pro174Ser
  • NC_000001.10:g.55512316C>T
  • NM_174936.3:c.520C>T
Protein change:
P174S
Links:
dbSNP: rs533273863
NCBI 1000 Genomes Browser:
rs533273863
Molecular consequence:
  • NM_174936.4:c.520C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000699997Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Apr 6, 2016) 		germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Effect of mutations in LDLR and PCSK9 genes on phenotypic variability in Tunisian familial hypercholesterolemia patients.

Slimani A, Jelassi A, Jguirim I, Najah M, Rebhi L, Omezzine A, Maatouk F, Hamda KB, Kacem M, Rabès JP, Abifadel M, Boileau C, Rouis M, Slimane MN, Varret M.

Atherosclerosis. 2012 May;222(1):158-66. doi: 10.1016/j.atherosclerosis.2012.02.018. Epub 2012 Feb 19.

PubMed [citation]
PMID:
22417841

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699997.1

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

Description

Variant summary: The c.520C>T variant affects a non-conserved nucleotide, resulting in amino acid change from Pro to Ser. 2/4 in-silico tools predict this variant to be damaging. This variant was found in 7/120144 control chromosomes including the broad and large populations of ExAC at a frequency of 0.0000583, which is more than 2 times greater than the maximal expected frequency of a pathogenic allele (0.0000188) based on the disease prevalence of FH, suggesting this variant may be benign with respect to FH. However, the same population frequency may not indicate benign outcome for recessive hypocholesterolemia. From a family study, this variant was found to reduce the severity of FH, acting as a putative loss-of-function variant (Slimani_2012). Although it may not be causing FH, its role in hypocholesterolemia (as evidenced by its lowering effect on LDL-C from the family study) needs to be further evaluated so as to clarify its pathogenicity. Taken together, this variant has been classified as VUS until more information becomes available.

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

Last Updated: May 7, 2024