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NM_174936.4(PCSK9):c.1621C>T (p.Pro541Ser) AND Familial hypercholesterolemia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 21, 2019
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:
RCV001185954.4

Allele description [Variation Report for NM_174936.4(PCSK9):c.1621C>T (p.Pro541Ser)]

NM_174936.4(PCSK9):c.1621C>T (p.Pro541Ser)

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.1621C>T (p.Pro541Ser)
HGVS:
  • NC_000001.11:g.55059603C>T
  • NG_009061.1:g.25057C>T
  • NM_001407240.1:c.1744C>T
  • NM_001407241.1:c.1663C>T
  • NM_001407242.1:c.1624C>T
  • NM_001407243.1:c.1564C>T
  • NM_001407244.1:c.1447C>T
  • NM_001407245.1:c.1429C>T
  • NM_001407246.1:c.1246C>T
  • NM_174936.4:c.1621C>TMANE SELECT
  • NP_001394169.1:p.Pro582Ser
  • NP_001394170.1:p.Pro555Ser
  • NP_001394171.1:p.Pro542Ser
  • NP_001394172.1:p.Pro522Ser
  • NP_001394173.1:p.Pro483Ser
  • NP_001394174.1:p.Pro477Ser
  • NP_001394175.1:p.Pro416Ser
  • NP_777596.2:p.Pro541Ser
  • NP_777596.2:p.Pro541Ser
  • LRG_275t1:c.1621C>T
  • LRG_275:g.25057C>T
  • LRG_275p1:p.Pro541Ser
  • NC_000001.10:g.55525276C>T
  • NM_174936.3:c.1621C>T
  • NR_110451.2:n.1228C>T
  • NR_110451.3:n.1902C>T
  • NR_176318.1:n.1595C>T
  • NR_176319.1:n.2180C>T
  • NR_176320.1:n.2034C>T
  • NR_176321.1:n.1859C>T
  • NR_176322.1:n.1814C>T
  • NR_176324.1:n.2121C>T
Protein change:
P416S
Links:
dbSNP: rs369996097
NCBI 1000 Genomes Browser:
rs369996097
Molecular consequence:
  • NM_001407240.1:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407241.1:c.1663C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407242.1:c.1624C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407243.1:c.1564C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407244.1:c.1447C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407245.1:c.1429C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407246.1:c.1246C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_174936.4:c.1621C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial hypercholesterolemia
Identifiers:
MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001352272Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Oct 21, 2019) 		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 Color Diagnostics, LLC DBA Color Health, SCV001352272.2

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

Description

This missense variant replaces proline with serine at codon 541 of the PCSK9 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with familial hypercholesterolemia in the literature. This variant has been identified in 2/189310 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 1, 2024