rs374603772

chr1-55058630-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM1 PP5 BS2

The NM_174936.4(PCSK9):c.1486C>T(p.Arg496Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000478 in 1,609,304 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R496Q) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000027 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000050 (1 hom.)
• Consequence: PCSK9 NM_174936.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:11 O:1
• Conservation: PhyloP100: 0.532

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 Likely_benign. Variant got -1 ACMG points.

• PM1: In a strand (size 6) in uniprot entity PCSK9_HUMAN there are 5 pathogenic changes around while only 2 benign (71%) in NM_174936.4
• PP5: Variant 1-55058630-C-T is Pathogenic according to our data. Variant chr1-55058630-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 201129.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=11, Pathogenic=2, not_provided=1}. Variant chr1-55058630-C-T is described in Lovd as [Likely_pathogenic].
• BS2: High AC in GnomAdExome at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCSK9	NM_174936.4	c.1486C>T	p.Arg496Trp	missense_variant	9/12	ENST00000302118.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCSK9	ENST00000302118.5	c.1486C>T	p.Arg496Trp	missense_variant	9/12	1	NM_174936.4	P2

Frequencies

GnomAD3 genomes AF: 0.0000266 AC: 4 AN: 150614 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000630

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000444 AC: 11 AN: 247724 Hom.: 0 AF XY: 0.0000521 AC XY: 7 AN XY: 134454

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000262

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000270

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000500 AC: 73 AN: 1458690 Hom.: 1 Cov.: 109 AF XY: 0.0000634 AC XY: 46 AN XY: 725598

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000757

Gnomad4 SAS exome AF: 0.000290

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000369

Gnomad4 OTH exome AF: 0.0000665

GnomAD4 genome AF: 0.0000266 AC: 4 AN: 150614 Hom.: 0 Cov.: 32 AF XY: 0.0000408 AC XY: 3 AN XY: 73442

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000630

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000148

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000659 AC: 8

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00

EpiControl AF: 0.0000595

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:11 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypercholesterolemia, autosomal dominant, 3 Pathogenic:2 Uncertain:2 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Dec 04, 2018	Across a selection of the available literature, the PCSK9 c.1486C>T (p.Arg496Trp) missense variant has been identified in a total of 20 individuals with familial hypercholesterolemia, including in a homozygous state in one individual, in a double heterozygous state with a pathogenic variant in the LDLR gene in one individual, and in a heterozygous state in 18 individuals, 16 of whom are unrelated (Pisciotta et al. 2006; Bertolini et al. 2013; Hopkins et al. 2015; Ohta et al. 2016; Kaya et al. (2017). Pisciotta et al. (2006) postulate an additive effect of the p.Arg496Trp variant on the pathogenic LDLR variant to account for the clinical homozygous FH phenotype in the double heterozygous proband. The p.Arg496Trp variant was absent from 110 controls and is reported at a frequency of 0.00032 in the South Asian population of the Exome Aggregation Consortium. FACS-based determination of the potency of PCSK9 mutants on cell-surface LDLR in EBV-human transformed lymphocytes revealed the p.Arg496Trp variant showed a small but significant increase in its capacity to reduce LDLR compared with WT PCSK9 (Fasano et al. 2009). Based on the collective evidence, the p.Arg496Trp variant is classified as pathogenic for familial hypercholesterolemia. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 14, 2023	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 496 of the PCSK9 protein (p.Arg496Trp). This variant is present in population databases (rs374603772, gnomAD 0.03%). This missense change has been observed in individuals with clinical features of familial hypercholesterolemia (PMID: 26374825, 27206942, 28008010, 28777095, 33269076; Invitae). ClinVar contains an entry for this variant (Variation ID: 201129). 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 with a negative predictive value of 80%. Experimental studies have shown that this missense change affects PCSK9 function (PMID: 31949048). For these reasons, this variant has been classified as Pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	This missense variant replaces arginine with tryptophan at codon 496 in the C-terminal region 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). Evolutionary conservation analysis indicates that arginine at this position is not well conserved and the variant tryptophan amino acid is tolerated in multiple mammalian species, suggesting that this variant is unlikely to adversely affect protein function. Functional studies have shown that this variant does not disrupt PCSK9 secretion (PMID: 27280970) or LDLR expression, uptake or degradation (PMID: 16183066, 19081568, 27280970, 31949048, 32058034). The mutant protein has shown normal ability to bind annexin A2, an extracellular endogenous inhibitor of PCSK9 activity on cell-surface LDLR degradation (PMID: 24808179). Unlike the wild type protein, the mutant protein has shown inability to bind LDL particles in vitro (PMID: 31949048), and the physiological significance of this observation is not clear. This variant has been reported in over ten individuals affected with familial hypercholesterolemia (PMID: 26374825, 27206942, 28777095, 32044282, 33147992, 33533259, 34526433, Color internal data). In a study of 80 Turkish individuals affected with hypercholesterolemia (PMID: 28777095), LDL-C levels of one homozygous individual (197-378 mg/dl) overlapped the LDL-C levels observed in six heterozygous individuals (92-378 mg/dl). A follow-up study of 200 Turkish individuals with primary dyslipidemia and 201 healthy controls has shown that individuals who carry both PCSK9 p.Arg496Trp and p.Asp374Tyr show increased LDL-C levels, when compared to individuals who do not carry these variants (p=0.028) (PMID: 29724976). This study did not provide data specific for the p.Arg496Trp variant. This variant has also been observed in three related, heterozygous individuals affected with hypercholesterolemia (PMID: 16183066, 23375686), one of whom also carried a pathogenic LDLR variant and showed a severe phenotype (PMID: 16183066). This p.Arg496Trp variant has been identified in 12/278942 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this variant has been observed in affected individuals, as well as in unaffected individuals (Color internal data, PMID: 29724976) and in the general population. Multiple functional studies have shown no significant deficit in the mutant protein function. 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	Dec 16, 2016	subjects mutated among 2600 FH index cases screened = 3 / Software predictions: Damaging -

Hypercholesterolemia, familial, 1 Pathogenic:2 Uncertain:1

Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 03, 2020	The p.Arg496Trp variant in PCSK9 has been reported in the heterozygous state in >25 individuals with hypercholesterolemia or primary dyslipidemia, the majority of whom were from Turkey or the Netherlands, and segregated with disease in 1 affected individual (Bertolini 2013 PMID: 23375686, Hopkins 2015 PMID: 26374825, Ohta 2016 PMID: 27206942, Kaya 2017 PMID: 28777095, Martin-Campos 2018 PMID: 30293936, Eroglu 2018 PMID: 29724976, Invitae pers. comm., GeneDx pers. comm.). In addition, it was identified in an individual with a severe presentation who also carried a pathogenic variant in LDLR. His affected mother also carried the PCSK9 variant (Pisciotta 2006 PMID: 16183066). It has been seen in the homozygous state in 2 individuals with hypercholesterolemia (Kaya 2017 PMID: 28777095, Eroglu 2018 PMID: 29724976, Invitae pers. comm.). A case control study of Turkish individuals showed that individuals harboring this variant were statistically more likely to be affected with primary dyslipidemia compared to controls and had a 12.8-fold higher triglyceride levels compared to controls (Eroglu 2018 PMID: 29724976). This variant has also been identified in 0.026% (8/30508) of South Asian chromosomes and 0.003% (4/126638) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org) and has been reported in ClinVar (Variation ID 201129). An in vitro functional studies showed a modest gain of function impact (Fasano 2009 PMID: 19081568) and 2 additional studies did not demonstrate a significant functional change (Pisciotta 2006 PMID: 16183066, Ly 2014 PMID: 24808179); however, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein and 1 mammal carries Tryptophan (Trp) at this position with high nearby conservation. In summary, although additional studies are required to fully establish its clinical significance particularly because the allele frequency of this variant in the South Asian population of gnomAD is relatively high and functional studies are unclear, this variant meets criteria to be classified as likely pathogenic for autosomal dominant familial hypercholesterolemia. ACMG/AMP Criteria applied: PS4, PM3. -
Uncertain significance, criteria provided, single submitter	curation;literature only	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	- -

not provided Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 28, 2023	The PCSK9 c.1486C>T; p.Arg496Trp variant (rs374603772) is reported in the literature in multiple individuals affected with familial hypercholesterolemia (Fasano 2009, Kaya 2017, Hopkins 2015, Martin-Campos 2018, Miroshnikova 2021). However, in some families this variant was found to co-occur with a pathogenic LDLR variant (Pisciotta 2006). This variant is also reported in ClinVar (Variation ID: 201129) and is found in the general population with an allele frequency of 0.004% (12/278,942 alleles) in the Genome Aggregation Database. Functional analyses of the variant protein show a small increase in the capacity to reduce LDLR (Fasano 2009). Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.456). Due to limited information, the clinical significance of this variant is uncertain at this time. References: Fasano T et al. Degradation of LDLR protein mediated by 'gain of function' PCSK9 mutants in normal and ARH cells. Atherosclerosis. 2009 Mar;203(1):166-71. PMID: 19081568. Kaya E et al. PCSK 9 gain-of-function mutations (R496W and D374Y) and clinical cardiovascular characteristics in a cohort of Turkish patients with familial hypercholesterolemia. Anatol J Cardiol. 2017 Oct;18(4):266-272. PMID: 28777095. Hopkins PN et al. Characterization of Autosomal Dominant Hypercholesterolemia Caused by PCSK9 Gain of Function Mutations and Its Specific Treatment With Alirocumab, a PCSK9 Monoclonal Antibody. Circ Cardiovasc Genet. 2015 Dec;8(6):823-31. PMID: 26374825. Martin-Campos JM et al. Autosomal dominant hypercholesterolemia in Catalonia: Correspondence between clinical-biochemical and genetic diagnostics in 967 patients studied in a multicenter clinical setting. J Clin Lipidol. 2018 Nov-Dec;12(6):1452-1462. PMID: 30293936. Miroshnikova VV et al. Identification of novel variants in the LDLR gene in Russian patients with familial hypercholesterolemia using targeted sequencing. Biomed Rep. 2021 Jan;14(1):15. PMID: 33269076. Pisciotta L et al. Additive effect of mutations in LDLR and PCSK9 genes on the phenotype of familial hypercholesterolemia. Atherosclerosis. 2006 Jun;186(2):433-40. PMID: 16183066. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 09, 2023	BS1, BS3, PS3_moderate -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jan 28, 2022	Functional studies to determine if this variant is damaging have yielded inconsistent results (Fasano et al., 2009; Ly et al., 2014; Deng et al., 2020; Sarkar et al., 2020); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16571601, 23375686, 28777095, 33303402, Ozkara2021 [preprint], 32719484, 16912035, 24808179, 16183066, 27280970, 27206942, 19081568, 33269076, 33147992, 29724976, 33533259, 32106405, 31491741, 33519890, 32058034, 31949048, 30293936) -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Oct 31, 2022

Variant summary: PCSK9 c.1486C>T (p.Arg496Trp) results in a non-conservative amino acid change located in the C-terminal domain (IPR041254) 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 4.4e-05 in 247724 control chromosomes (gnomAD). The observed variant frequency is approximately equal to the estimated maximal expected allele frequency for a pathogenic variant in PCSK9 causing Familial Hypercholesterolemia phenotype (3.8e-05), suggesting that the variant may be benign. Nevertheless, c.1486C>T has been reported in the literature in multiple heterozygous individuals affected with Familial Hypercholesterolemia, while it was also reported in at least one homozygous individual with a severe phenotype which may however be attributed to possible coexistence of other mutations (e.g. Bertolini_2013, Abul-Husn_2016, Kaya_2017, Hori_2019, Miroshnikova_2020, Setia_2020). One of these studies (Abul-Husn_2016), reported the penetrance of this variant (defined as number of carriers meeting pre-sequencing criteria for a diagnosis of possible, probable, or definite FH [using DLCN criteria]) to be 40% (6 out of 15 heterozygous carriers meeting criteria). Pisciotta et al (2006) detected the variant in one proband affected with a severe phenotype of familial hypercholesterolemia who also carried a pathogenic LDLR variant; the mother of the proband who only carried the variant of interest exhibited a less severe phenotype. The authors concluded that the variant may have an additive effect on the LDLR mutation. A case-control study in Turkish individuals determined that the variant may be a significant risk factor in the development of primary dyslipidemia and may have significant impact on lipid parameters (Eroglu_2018). These data indicate that the variant may be associated with disease. Experimental evidence evaluating an impact on protein function provided inconsistent results. Some functional studies demonstrated the variant exhibits normal LDLR-dependent uptake, has similar secretion efficiency as the wild-type PCSK9 and does not affect the proteins ability to bind Annexin A2 (an extracellular endogenous inhibitor of PCSK9 activity on cell-surface LDL receptor degradation) (Ly_2014, Deng_2020, Sarkar_2020). Other studies found the variant to completely abolish LDL binding, and show slightly but significantly increased activity on cell-surface LDLR compared to the wild-type, consistent with a small gain-of-function effect (Fasano_2009, Sarkar_2020). Seven ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance and three ClinVar submitters (evaluation after 2014) cite it as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Hypercholesterolemia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University Hospital Muenster

Dec 16, 2021

ACMG categories: BP4 -

Hypobetalipoproteinemia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 24, 2019

The c.1486C>T (p.R496W) alteration is located in exon 9 (coding exon 9) of the PCSK9 gene. This alteration results from a C to T substitution at nucleotide position 1486, causing the arginine (R) at amino acid position 496 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Familial hypercholesterolemia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Dec 06, 2023

This missense variant replaces arginine with tryptophan at codon 496 in the C-terminal region of the PCSK9 protein. Computational prediction tools indicate that this variant has a neutral impact on protein structure and function. Functional studies have shown that this variant does not disrupt PCSK9 secretion (PMID: 27280970) or LDLR expression, uptake or degradation (PMID: 16183066, 19081568, 27280970, 31949048, 32058034). This variant has been reported in over ten individuals affected with familial hypercholesterolemia (PMID: 26374825, 27206942, 28777095, 32044282, 33147992, 33533259, 34526433, 35929461, 36087353, 37469559; Color internal data). In a study of 80 Turkish individuals affected with hypercholesterolemia (PMID: 28777095), LDL-C levels of one homozygous individual overlapped levels observed in six heterozygous individuals. A follow-up study of 200 Turkish individuals with primary dyslipidemia has shown that individuals who carry both PCSK9 p.Arg496Trp and p.Asp374Tyr show increased LDL-C levels, when compared to individuals who do not carry both variants (p=0.028; PMID: 29724976). This variant has also been observed in three related, heterozygous individuals affected with hypercholesterolemia (PMID: 16183066, 23375686), one of whom also carried a pathogenic LDLR variant and showed a severe phenotype (PMID: 16183066). This variant has been identified in 12/278942 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this variant has been observed in affected individuals, as well as in unaffected individuals (PMID: 29724976; Color internal data) and in the general population. Multiple functional studies have shown no significant effect on protein function. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.24
Cadd	Benign	22
Dann	Uncertain	1.0
DEOGEN2	Benign	0.14	T
Eigen	Benign	-0.19
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.27	N
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.53	D
MetaSVM	Benign	-0.71	T
MutationAssessor	Uncertain	2.3	M
MutationTaster	Benign	1.0	N;N
PrimateAI	Uncertain	0.60	T
PROVEAN	Benign	-1.7	N
REVEL	Uncertain	0.46
Sift	Uncertain	0.027	D
Sift4G	Uncertain	0.019	D
Polyphen		1.0	D
Vest4		0.70
MVP		0.86
MPC		0.24
ClinPred		0.49	T
GERP RS		-0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.38
gMVP		0.77

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: rs374603772; hg19: chr1-55524303; COSMIC: COSV56165035;