NM_174936.4:c.1394C>T

Variant names:

• chr1-55058538-C-T
• rs778849441
• NM_174936.4:c.1394C>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 6P and 4B. PM1 PM5 PP3 PP5 BS2

The NM_174936.4(PCSK9):​c.1394C>T​(p.Ser465Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000753 in 1,459,884 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S465W) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: PCSK9 NM_174936.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:6
• Conservation: PhyloP100: 3.73

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 Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 11 uncertain in NM_174936.4
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-55058538-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 2418130.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=1}.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.77
• PP5: Variant 1-55058538-C-T is Pathogenic according to our data. Variant chr1-55058538-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 403292.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=6, Pathogenic=2}. Variant chr1-55058538-C-T is described in Lovd as [Likely_pathogenic]. Variant chr1-55058538-C-T is described in Lovd as [Pathogenic].
• BS2: High AC in GnomAdExome4 at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCSK9	NM_174936.4	c.1394C>T	p.Ser465Leu	missense_variant	Exon 9 of 12	ENST00000302118.5	NP_777596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCSK9	ENST00000302118.5	c.1394C>T	p.Ser465Leu	missense_variant	Exon 9 of 12	1	NM_174936.4	ENSP00000303208.5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD3 exomes AF: 0.0000239 AC: 6 AN: 251370 Hom.: 0 AF XY: 0.0000368 AC XY: 5 AN XY: 135888

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.00000753 AC: 11 AN: 1459884 Hom.: 0 Cov.: 85 AF XY: 0.00000826 AC XY: 6 AN XY: 726246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000899

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

Alfa AF: 0.0000675 Hom.: 0

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:6

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:1

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 29, 2023

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a damaging effect through defective PCSK9-LDL binding (Sarkar et al., 2022); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in association with FH in published literature (Sturm et al., 2021; Hopkins et al., 2015; Di Taranto et al., 2017; Ruotolo et al., 2014); This variant is associated with the following publications: (PMID: 29259136, 32058034, 26165249, 26374825, 29127338, 24607922, 31653860, 34037665, 36187800) -

-

Clinical Genetics, Academic Medical Center

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

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

Nov 09, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 465 of the PCSK9 protein (p.Ser465Leu). This variant is present in population databases (no rsID available, gnomAD 0.006%). This missense change has been observed in individuals with hypercholesterolemia (PMID: 24607922, 26374825). ClinVar contains an entry for this variant (Variation ID: 403292). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt PCSK9 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. -

May 03, 2023

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS4_SUP -

Jun 09, 2024

All of Us Research Program, National Institutes of Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces serine with leucine at codon 465 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). Functional studies have shown that this variant may cause a decrease in PCSK9 secretion and noted that this finding is not consistent with reported high LDL-C levels (PMID: 29259136, 32058034). Another functional study in transfected HEK293 cells has shown that this variant significantly decreased LDL binding (PMID: 36187800). This variant has been reported in two related individuals affected with hypercholesterolemia (PMID: 24607922). Cells from these carriers showed partially reduced LDLR activity but no change in the amount of LDLR protein at the cell surface. This variant has been reported in over ten unrelated individuals affected with hypercholesterolemia who showed mildly elevated LDL-C levels (PMID: 29127338, 26374825, 34037665; Color internal data). This variant has also been identified in 6/251370 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease, the role of this variant cannot be determined conclusively, due to the unclear impact of this variant on the LDLR function and the observation of this variant in the general population. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Familial hypercholesterolemia Pathogenic:1 Uncertain:2

Jan 22, 2020

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

The p.Ser465Leu variant in PCSK9 has been reported in 13 individuals with familial hypercholesterolemia, segregated with disease in 2 affected relatives from 1 family (PMID: 24607922, 26374825, 29127338), and has been identified in 0.005% (1/18392) of East Asian chromosomes and 0.004% (4/113662) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs778849441). Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. This variant has also been reported in ClinVar as a VUS, likely pathogenic, and pathogenic (Variation ID#: 403292). Computational prediction tools, including splice predictors, and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, the clinical significance of the p.Ser465Leu variant is uncertain. ACMG/AMP Criteria applied: PS4_moderate, BP4 (Richards 2015). -

Oct 18, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces serine with leucine at codon 465 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). Functional studies have shown that this variant may cause a decrease in PCSK9 secretion and noted that this finding is not consistent with reported high LDL-C levels (PMID: 29259136, 32058034). Another functional study in transfected HEK293 cells has shown that this variant significantly decreased LDL binding (PMID: 36187800). This variant has been reported in two related individuals affected with hypercholesterolemia (PMID: 24607922). Cells from these carriers showed partially reduced LDLR activity but no change in the amount of LDLR protein at the cell surface. This variant has been reported in over ten unrelated individuals affected with hypercholesterolemia who showed mildly elevated LDL-C levels (PMID: 29127338, 26374825, 34037665; Color internal data). This variant has also been identified in 6/251370 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease, the role of this variant cannot be determined conclusively, due to the unclear impact of this variant on the LDLR function and the observation of this variant in the general population. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Oct 07, 2024

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: PCSK9 c.1394C>T (p.Ser465Leu) results in a non-conservative amino acid change located in the Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 (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 2.4e-05 in 251370 control chromosomes, predominantly at a frequency of 5.4e-05 within the East Asian subpopulation in the gnomAD database. c.1394C>T has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia, four of which had developed coronary artery disease (example, Hopkins_2015). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in diminished LDL binding in HEK293 (Sarkar_2022). The following publications have been ascertained in the context of this evaluation (PMID: 26374825, 36187800). ClinVar contains an entry for this variant (Variation ID: 403292). Based on the evidence outlined above, the variant was classified as pathogenic. -

Hypercholesterolemia, familial, 1 Pathogenic:1

-

Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

not specified Uncertain:1

Jan 31, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 2 papers, not sig diff LDLR -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.44	T
Eigen	Benign	0.079
Eigen_PC	Benign	-0.10
FATHMM_MKL	Benign	0.63	D
LIST_S2	Uncertain	0.86	D
M_CAP	Benign	0.026	D
MetaRNN	Pathogenic	0.77	D
MetaSVM	Benign	-0.42	T
MutationAssessor	Uncertain	2.6	M
PrimateAI	Uncertain	0.68	T
PROVEAN	Uncertain	-3.6	D
REVEL	Uncertain	0.32
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.010	D
Polyphen		1.0	D
Vest4		0.73
MutPred		0.50		Loss of glycosylation at S465 (P = 0.0374);
MVP		0.85
MPC		0.29
ClinPred		0.74	D
GERP RS		1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
Varity_R		0.61
gMVP		0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs778849441; hg19: chr1-55524211; COSMIC: COSV105120113;