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NM_174936.4(PCSK9):c.2066A>T (p.Gln689Leu) AND Hypercholesterolemia, autosomal dominant, 3

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 12, 2021
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:
RCV002003504.5

Allele description [Variation Report for NM_174936.4(PCSK9):c.2066A>T (p.Gln689Leu)]

NM_174936.4(PCSK9):c.2066A>T (p.Gln689Leu)

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.2066A>T (p.Gln689Leu)
HGVS:
  • NC_000001.11:g.55063571A>T
  • NG_009061.1:g.29025A>T
  • NM_001407240.1:c.2189A>T
  • NM_001407241.1:c.2108A>T
  • NM_001407242.1:c.2069A>T
  • NM_001407243.1:c.2009A>T
  • NM_001407244.1:c.1892A>T
  • NM_001407245.1:c.1874A>T
  • NM_001407246.1:c.1691A>T
  • NM_001407247.1:c.1565A>T
  • NM_174936.4:c.2066A>TMANE SELECT
  • NP_001394169.1:p.Gln730Leu
  • NP_001394170.1:p.Gln703Leu
  • NP_001394171.1:p.Gln690Leu
  • NP_001394172.1:p.Gln670Leu
  • NP_001394173.1:p.Gln631Leu
  • NP_001394174.1:p.Gln625Leu
  • NP_001394175.1:p.Gln564Leu
  • NP_001394176.1:p.Gln522Leu
  • NP_777596.2:p.Gln689Leu
  • NP_777596.2:p.Gln689Leu
  • LRG_275t1:c.2066A>T
  • LRG_275:g.29025A>T
  • LRG_275p1:p.Gln689Leu
  • NC_000001.10:g.55529244A>T
  • NM_174936.3:c.2066A>T
  • NR_110451.2:n.1673A>T
  • NR_110451.3:n.2347A>T
  • NR_176318.1:n.2150A>T
  • NR_176319.1:n.2625A>T
  • NR_176320.1:n.2589A>T
  • NR_176321.1:n.2304A>T
  • NR_176322.1:n.2259A>T
  • NR_176323.1:n.2178A>T
  • NR_176324.1:n.2566A>T
Protein change:
Q522L
Links:
dbSNP: rs2100344811
NCBI 1000 Genomes Browser:
rs2100344811
Molecular consequence:
  • NM_001407240.1:c.2189A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407241.1:c.2108A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407242.1:c.2069A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407243.1:c.2009A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407244.1:c.1892A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407245.1:c.1874A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407246.1:c.1691A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407247.1:c.1565A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_174936.4:c.2066A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypercholesterolemia, autosomal dominant, 3 (FHCL3)
Synonyms:
Familial hypercholesterolemia 3; Familial Hypercholesterolemia, Autosomal Dominant, 3
Identifiers:
MONDO: MONDO:0011369; MedGen: C1863551; OMIM: 603776

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002271173Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 12, 2021) 		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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002271173.3

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PCSK9 protein function. This variant has not been reported in the literature in individuals affected with PCSK9-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamine with leucine at codon 689 of the PCSK9 protein (p.Gln689Leu). The glutamine residue is weakly conserved and there is a moderate physicochemical difference between glutamine and leucine. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024