rs141502002

chr1-55058549-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1 BP4_Strong BP6 BS2

The NM_174936.4(PCSK9):c.1405C>T(p.Arg469Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000481 in 1,612,150 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R469Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0025 (4 hom., cov: 33)
  • Exomes 𝑓: 0.00027 (3 hom.)
• Consequence: PCSK9 NM_174936.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:5 B:7
• Conservation: PhyloP100: 0.0310

Genes affected

PCSK9 (HGNC:20001): (proprotein convertase subtilisin/kexin type 9) This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway. The encoded protein undergoes an autocatalytic processing event with its prosegment in the ER and is constitutively secreted as an inactive protease into the extracellular matrix and trans-Golgi network. It is expressed in liver, intestine and kidney tissues and escorts specific receptors for lysosomal degradation. It plays a role in cholesterol and fatty acid metabolism. Mutations in this gene have been associated with autosomal dominant familial hypercholesterolemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 5 benign, 10 uncertain in NM_174936.4
• BP4: Computational evidence support a benign effect (MetaRNN=0.011399835).
• BP6: Variant 1-55058549-C-T is Benign according to our data. Variant chr1-55058549-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 201128.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Likely_benign=5, Uncertain_significance=5}. Variant chr1-55058549-C-T is described in UniProt as null.
• BS2: High AC in GnomAd at 386 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCSK9	NM_174936.4	c.1405C>T	p.Arg469Trp	missense_variant	9/12	ENST00000302118.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCSK9	ENST00000302118.5	c.1405C>T	p.Arg469Trp	missense_variant	9/12	1	NM_174936.4	P2

Frequencies

GnomAD3 genomes AF: 0.00254 AC: 386 AN: 152170 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.00888

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.000605 AC: 152 AN: 251352 Hom.: 1 AF XY: 0.000427 AC XY: 58 AN XY: 135886

Gnomad AFR exome AF: 0.00837

Gnomad AMR exome AF: 0.000231

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000163

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000264

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000268 AC: 391 AN: 1459862 Hom.: 3 Cov.: 86 AF XY: 0.000256 AC XY: 186 AN XY: 726236

Gnomad4 AFR exome AF: 0.00868

Gnomad4 AMR exome AF: 0.000335

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000139

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000297

Gnomad4 OTH exome AF: 0.000664

GnomAD4 genome AF: 0.00253 AC: 385 AN: 152288 Hom.: 4 Cov.: 33 AF XY: 0.00236 AC XY: 176 AN XY: 74452

Gnomad4 AFR AF: 0.00883

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000735

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.000436 Hom.: 1

Bravo AF: 0.00277

ESP6500AA AF: 0.00794 AC: 35

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000700 AC: 85

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:5 Benign:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:1 Uncertain:1 Benign:1

Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Uncertain significance, criteria provided, single submitter	research	Laboratory of Genetics and Molecular Cardiology, University of São Paulo	Mar 01, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	Aug 22, 2019	- -

Hypercholesterolemia, autosomal dominant, 3 Uncertain:1 Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Feb 02, 2018	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Mar 21, 2017	The R469W variant has been reported in one individual with severe hypercholesterolemia, who was also heterozygous for a variant in the LDLR gene (Allard et al., 2005). Subsequently, an individual with elevated LDL-C was found to harbor this variant in isolation (Wang et al., 2016). The R469W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Nevertheless, this substitution occurs at a position that is not conserved across species, where W469 is wild-type in at least one mammalian species. Additionally, the majority of in silico analyses (2 out of 3) predict this variant likely does not alter the protein structure/function. Though R469W was presumed to be a gain-of-function variant by Hampton et al. (2007), in vitro functional analysis showed no effect on the ability of the PCSK9-encoded protein to bind Annexin A2, a protein responsible for inhibiting PCSK9-endoded protein activity (Ly et al,. 2014). Therefore, the mechanism by which this variant may result in disease is unclear. Furthermore, the Exome Aggregation Consortium reports R469W was observed in 80/10392 (0.8%) alleles from individuals of African background, including two individuals of African background who were homozygous for the variant. Of note, this variant has been reported in individuals of African descent with high LDL, though the association was not statistically significant (Kotowski et al., 2006). It has also been identified in two individuals of African Canadian descent from the general population who also harbored other PCSK9 variants (Mayne et al., 2013). Ultimately, the possibility that this variant may have a mild clinical effect and/or function as a genetic modifier for disease can not be excluded, at this time. -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 28, 2021	Variant summary: PCSK9 c.1405C>T (p.Arg469Trp) results in a non-conservative amino acid change located in the Proprotein convertase subtilisin/kexin type 9, C-terminal domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0006 in 252032 control chromosomes, predominantly at a frequency of 0.0084 within the African or African-American subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 90 fold of the estimated maximal expected allele frequency for a pathogenic variant in PCSK9 causing Familial Hypercholesterolemia phenotype (9.4e-05), suggesting that the variant may not be associated with Familial Hypercholesterolemia. c.1405C>T has been reported in the literature in sequencing studies of individuals affected with Familial Hypercholesterolemia (example, Allard_2005, Kotowski_2006, Mayne_2013, Wang_2016 and Taranto_2017). At-least one patient with tendinous xanthomata and an elevated lipid profile in whom a co-occurring LDL-R variant, c.1209delC ( p.Phe403fs) that could have explained the phenotype, has been described (Allard_2005). The authors postulated a digenic/additive role for this variant. At least one study of 57,850 individuals with African ancestry showed that this variant is associated with elevated maxLDL levels (Sun_2018). This association was not found in individuals with European or Chinese ancestry (Sun_2018, Lu_2016). Furthermore, this variant was identified among carriers who did not meet the Dutch Lipid Clinic Network (DLCN) criteria for a diagnosis of possible, probable or definite FH, thereby resulting in an estimated clinical penetrance of 0% (Abul-Husn_2016). These report(s) do not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. Multiple experimental showed that this variant may result in loss of function effect (Geschwindner_2015), no effect on binding activity to AnxA2 (Ly_2014), and no effect on protein processing (Chorba_2017). PCSK9 normally degrades LDL-Receptor. Defective PCSK9 results in impaired LDL-receptor degradation, resulting in an increased uptake of plasma LDL than necessary, leading to hypocholesterolemia. Therefore, a GOF mechanism has been attributed to variants in PCSK9 that are causative of FH. However, none of the ascertained functional studies provide concrete evidence supporting an association of this variant with the pathognomic mechanism of FH attributed to variants in PCSK9. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation with conflicting assessments (benign, n=1; likely benign, n=3; VUS, n=3). Based on the evidence outlined above, although some residual association as a risk factor for high LDL levels cannot be entirely ruled out, the variant was classified as likely benign in the context of an association with inherited autosomal dominant Familial Hypercholesterolemia, -

PCSK9-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 23, 2023

The PCSK9 c.1405C>T variant is predicted to result in the amino acid substitution p.Arg469Trp. This variant has been reported in individuals with hypercholesterolemia (Allard et al. 2005. PubMed ID: 16211558; Kotowski et al. 2006. PubMed ID: 16465619; Wang et al. 2016. PubMed ID: 27765764. Table SI; Di Taranto et al. 2017. PubMed ID: 29127338). Functional study showed that this variant has no effect on binding activity to Annexin A2 and protein processing (Ly et al. 2014. PubMed ID: 24808179; Chorba et al. 2017. PubMed ID: 29259136), but another study showed that it may affect the protein activity (Geschwindner et al. 2015. PubMed ID: 25744035). This variant is reported in 0.93% of alleles in individuals of African descent including 1 homozygous individual in gnomAD (http://gnomad.broadinstitute.org/variant/1-55524222-C-T). In ClinVar, this variant has conflicting interpretations of benign, likely benign, uncertain significance and pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/201128/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Hypobetalipoproteinemia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Feb 02, 2018

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Jun 08, 2023

- -

Cardiovascular phenotype Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 30, 2019

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. -

Familial hypercholesterolemia Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Feb 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.36
Cadd	Benign	18
Dann	Uncertain	1.0
DEOGEN2	Benign	0.21	T
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.52
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.85	T
M_CAP	Benign	0.035	D
MetaRNN	Benign	0.011	T
MetaSVM	Benign	-0.78	T
MutationAssessor	Uncertain	2.2	M
MutationTaster	Benign	1.0	N;N
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-1.8	N
REVEL	Benign	0.24
Sift	Uncertain	0.010	D
Sift4G	Uncertain	0.020	D
Polyphen		1.0	D
Vest4		0.71
MVP		0.84
MPC		0.24
ClinPred		0.017	T
GERP RS		1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.9
Varity_R		0.38
gMVP		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs141502002; hg19: chr1-55524222; COSMIC: COSV56160629;