chr1-55057454-G-T

Variant names:

• chr1-55057454-G-T
• rs137852912
• NM_174936.4:c.1120G>T

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_174936.4(PCSK9):​c.1120G>T​(p.Asp374Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D374N) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: PCSK9 NM_174936.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9 O:1
• Conservation: PhyloP100: 8.03
• Publications: 256 publications found

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]

PCSK9 Gene-Disease associations (from GenCC):

• hypercholesterolemia, autosomal dominant, 3

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
• homozygous familial hypercholesterolemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-55057454-G-C is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 265939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.911
• PP5: Variant 1-55057454-G-T is Pathogenic according to our data. Variant chr1-55057454-G-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 2875.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCSK9	NM_174936.4	c.1120G>T	p.Asp374Tyr	missense_variant	Exon 7 of 12	ENST00000302118.5	NP_777596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCSK9	ENST00000302118.5	c.1120G>T	p.Asp374Tyr	missense_variant	Exon 7 of 12	1	NM_174936.4	ENSP00000303208.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461694 Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1 AN XY: 727152

African (AFR) AF: 0.00 AC: 0 AN: 33476

American (AMR) AF: 0.00 AC: 0 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53284

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5750

European-Non Finnish (NFE) AF: 0.00000270 AC: 3 AN: 1111992

Other (OTH) AF: 0.0000166 AC: 1 AN: 60394

GnomAD4 genome Cov.: 33

Alfa AF: 0.000332 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, autosomal dominant, 3 Pathogenic:4 Other:1

Feb 12, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Jan 22, 2020

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The p.Asp374Tyr variant in PCSK9 has been reported in at least 10 families with hypercholesterolemia, segregated with disease in 20 affected relatives from 5 families, and was absent from large population studies. This variant has also been reported in ClinVar (VariationID: 2875) as likely pathogenic by the Instituto Nacional de Saude Doutor Ricardo Jorge and as pathogenic by Roberts Research Institute, Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, OMIM, and GeneReviews. In vitro functional studies demonstrating that cells transfected with the variant result in a near complete disappearance of LDLR protein provide some evidence that the p.Asp374Tyr variant may impact protein function (PMID: 19081568, 15772090). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. One additional likely pathogenic variant, resulting in a different amino acid change at the same position, p.Asp374His, has been reported in association with disease in the literature and ClinVar, slightly supporting that a change at this position may not be tolerated (PMID: 19081568, 26374825/Variation ID: 265939). The p.Asp374Tyr variant is located in a region of PCSK9 that is essential to protein folding and stability, suggesting that this variant is in a functional domain and slightly supports pathogenicity (PMID: 19081568). In summary, this variant meets criteria to be classified as pathogenic for hypercholesterolemia in an autosomal dominant manner based on the increased prevalence and cosegregation of the variant in affected individuals compared to controls, in vitro functional studies, and computational evidence. ACMG/AMP Criteria applied: PP1_strong, PM2, PS4_moderate, PP3, PM5_supporting, PS3_supporting, PM1_supporting (Richards 2015). -

Feb 02, 2022

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with hypercholesterolemia, familial, 3 (MIM#603776) (PMID: 33173529). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from aspartic acid to tyrosine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (20 heterozygotes, 0 homozygotes). (SP) 0600 - Variant is located in the annotated Peptidase S8 domain (Pfam). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been submitted as pathogenic in the ClinVar database, and has been reported in multiple families with familial hypercholesterolaemia (PMID: 14727179, 15099351, 16224054, 28777095). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been shown to segregate with disease in multiple families (PMID: 14727179, 15099351, 16224054). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. In vitro functional studies show that this variant results in increased binding affinity to LDLR and reduced LDLR protein levels (PMID: 17435765, 19081568). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Feb 29, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 374 of the PCSK9 protein (p.Asp374Tyr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 14727179, 19797716, 28777095, 33740630). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2875). 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 expected to disrupt PCSK9 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects PCSK9 function (PMID: 15358785, 16912035, 18197702, 19081568, 23283366, 27280970). This variant disrupts the p.Asp374 amino acid residue in PCSK9. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17765246, 26374825; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Hypercholesterolemia, familial, 1 Pathogenic:3

Mar 01, 2016

Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation;literature only

- -

Jan 02, 2018

Robarts Research Institute, Western University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Homozygous familial hypercholesterolemia Pathogenic:1

Apr 18, 2019

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Asp374Tyr variant in PCSK9 has been reported in at least 12 individuals with hypercholesterolemia and segregated with disease in at least 9 affected individuals from 1 family (Timms 2004, Humphries 2009, Kaya 2017). It was absent from large population studies, but has been reported in ClinVar (Variation ID: 2875). Computational prediction tools and conservation analysis are consistent with pathogenicity. In vitro functional studies support an impact on protein function (Benjannet 2004, Bottomley 2009, Al-Mashhadi 2013). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hypercholesterolemia. ACMG/AMP Criteria applied: PP1_Strong, PM2, PS4_Moderate, PP3, PS3_Supporting. -

Cardiovascular phenotype Pathogenic:1

Oct 26, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1120G>T (p.D374Y) alteration is located in coding exon 7 of the PCSK9 gene. This alteration results from a G to T substitution at nucleotide position 1120, causing the aspartic acid (D) at amino acid position 374 to be replaced by a tyrosine (Y). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported in numerous individuals with familial hypercholesterolemia (Gill, 2021; Leren, 2021; Kaya, 2017; Humphries, 2009). This variant has also been shown to segregate with disease in multiple affected families (Sun, 2005). This amino acid position is highly conserved in available vertebrate species. Numerous studies have demonstrated that this variant significantly decreases LDL uptake and has significantly increased binding affinity to LDLr compared to wildtype (Larrea-Sebal, 2023; Huijgen, 2021; S&aacute;nchez-Hern&aacute;ndez, 2019; Fasano, 2009). Published structural analyses shows that this variant likely improves the binding affinity of PCSK9 to the LDLr EGF(A) domain (Martin, 2020; Fasano, 2009). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.43	T
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.93	D
M_CAP	Uncertain	0.10	D
MetaRNN	Pathogenic	0.91	D
MetaSVM	Uncertain	0.57	D
MutationAssessor	Uncertain	2.1	M
PhyloP100		8.0
PrimateAI	Pathogenic	0.80	T
PROVEAN	Pathogenic	-4.9	D
REVEL	Pathogenic	0.92
Sift	Uncertain	0.013	D
Sift4G	Uncertain	0.011	D
Polyphen		1.0	D
Vest4		0.84
MutPred		0.78		Loss of disorder (P = 0.0641);
MVP		0.95
MPC		0.94
ClinPred		0.99	D
GERP RS		4.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.95
gMVP		0.89
Mutation Taster		=8/92	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs137852912; hg19: chr1-55523127;