chr1-55043847-C-T

Position:

• chr1-55043847-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BS2_Supporting

The NM_001407246.1(PCSK9):​c.-164C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000050 (0 hom.)
• Consequence: PCSK9 NM_001407246.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:6 B:3
• Conservation: PhyloP100: 1.62

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.036026895).
• BS2: High AC in GnomAd4 at 5 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCSK9	NM_174936.4	c.212C>T	p.Pro71Leu	missense_variant	2/12	ENST00000302118.5	NP_777596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCSK9	ENST00000302118.5	c.212C>T	p.Pro71Leu	missense_variant	2/12	1	NM_174936.4	ENSP00000303208.5

Frequencies

GnomAD3 genomes AF: 0.0000329 AC: 5 AN: 152206 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000108 AC: 27 AN: 250360 Hom.: 0 AF XY: 0.000148 AC XY: 20 AN XY: 135440

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000163

Gnomad SAS exome AF: 0.000653

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000266

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000499 AC: 73 AN: 1461752 Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58 AN XY: 727186

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.000684

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000629

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000328 AC: 5 AN: 152324 Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4 AN XY: 74484

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000828

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ExAC AF: 0.0000906 AC: 11

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:6 Benign:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Uncertain significance, criteria provided, single submitter	clinical testing	New York Genome Center	May 11, 2022	The c.212C>T variant in PCSK9 has previously been reported in individuals with clinical features of familial hypercholesterolemia, coronary artery disease (CAD) and stroke [PMID: 26374825, 27920219, 34526433] and it has been deposited in ClinVar [ClinVar ID: 440711] as a Variant of Uncertain Significance. The c.212C>T variant is observed in 34 alleles (0.0063 % minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.212C>T variant in PCSK9 is located in exon 2 of this 12-exon gene and is predicted to replace a weakly conserved proline amino acid with leucine at position 71 of this 692-amino-acid protein. In silico tools predict the p.(Pro71Leu) variant tobe benign [(CADD v1.6 = 15.72, REVEL = 0.079)]; however, there are no functional studies to support or refute these predictions. Based on the available evidence, the c.212C>T p.(Pro71Leu) missense variant identified in the PCSK9 gene is reported as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Apr 16, 2024	This missense variant replaces proline with leucine at codon 71 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 26374825, 36499307) and in an individual affected with acute coronary syndrome (PMID: 34526433). This variant has been identified in 27/250360 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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. -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 08, 2024	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Phosphorus, Inc.	Jan 15, 2022	This missense variant results in an amino acid substitution of proline with leucine at codon 71 of the PCSK9 gene. The variant has an entry in ClinVar (440711) NM_174936.4 (PCSK9): c.212C>T (p.Pro71Leu) and has occurred in GnomAD with a total MAF of 0.0106% and highest MAF of 0.0650% in the South Asian population. This position is not conserved. In silico functional algorithms disagreed, with PolyPhen calling it benign, and SIFT deleterious, but no functional studies were performed to confirm these predictions. The variant has previously been identified in an individual with a coronary artery disease who suffered from a stroke (PMID: 27920219) and in an individual affected with hypercholesterolemia where the variant was considered a gain-of-function mutation (PMID: 26374825). Further evidence is needed to establish whether this variant contributes to disease formation. The variant has therefore been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 09, 2024	Variant summary: PCSK9 c.212C>T (p.Pro71Leu) results in a non-conservative amino acid change in 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 0.00011 in 250360 control chromosomes, predominantly at a frequency of 0.00065 within the South Asian subpopulation in the gnomAD database. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 17-fold of the estimated maximal expected allele frequency for a pathogenic variant in PCSK9 causing autosomal dominant Familial Hypercholesterolemia phenotype (3.8e-05). The variant, c.212C>T, has been reported in the literature to be found in hypercholesterolemia cohorts, i.e. in the heterozygous state in six individuals (e.g. Hopkins_2015, Razman_2022), and in homozygous state in one individual (e.g. Reijman_2023), however patient level clinical details were limited. The variant was also reported in a heterozygous patient affected with coronary artery disease; however the patient was noted to have no familial hypercholesterolemia (FH) history, or FH diagnosis (Harada-Shiba_2022). These data do not allow clear conclusions about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 26374825, 36499307, 36752612, 34526433). ClinVar contains an entry for this variant (Variation ID: 440711). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -

not provided Uncertain:1 Benign:1

Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Aug 28, 2017	p.Pro71Leu (c.212C>T) in the PCSK9 gene (NM_174936.3) - variant of uncertain significance, probably benign Given the unconvincing case data and its prevalence in the general population, we consider this variant a variant of uncertain significance and we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). However, it may be suitable for family studies (testing only related, affected individuals) to determine its effect on cholesterol levels in this family. Gain of function variants in PCSK9 cause autosomal dominant hypercholesterolemia. This variant is not reported in ClinVar. It has been reported in a total of 6 individuals (not including our patient). This variant was reported in 6 individuals from the Netherlands with a total cholesterol of ~220 mg/dL and LDL cholesterol of ~115g mg/dL (Hopkins et al 2015). It is not clear whether any or all of these individuals were related. It is notable that 11/164 patients in this study had a variant in both PCSK9 and LDLR (pathogenicity of these variants has not been included in this review). An editorial by McNutt & Ahmad in 2015 questions whether this variant is truly pathogenic given that these patients had total cholesterol and LDL-C levels that are lower than typical for familial hypercholesterolemia (FH). Family studies may be useful to determine whether this variant has a synergistic effect with the LDLR variant. Per the test report, "Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on he potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0")." The variant was reported online in 26 of 122,596 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 20 of 15,389 individuals of South Asian descent (MAF=0.065%), 2 of 8,623 individuals of East Asian descent, 1 out of 16,787 individuals of Latino descent and 3 of 55,386 individuals of European descent. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. -
Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 13, 2023	- -

Hypercholesterolemia, familial, 1 Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum

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- -

Familial hypercholesterolemia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Jun 22, 2023

This missense variant replaces proline with leucine at codon 71 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 26374825, 36499307) and in an individual affected with acute coronary syndrome (PMID: 34526433). This variant has been identified in 27/250360 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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. -

Cardiovascular phenotype Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 16, 2024

This alteration is classified as 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	17
DANN	Benign	0.71
DEOGEN2	Benign	0.12	T
Eigen	Benign	-0.86
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.40	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.027	D
MetaRNN	Benign	0.036	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.079
Sift	Benign	0.098	T
Sift4G	Uncertain	0.037	D
Polyphen		0.012	B
Vest4		0.21
MutPred		0.49		Gain of MoRF binding (P = 0.0389);
MVP		0.67
MPC		0.23
ClinPred		0.033	T
GERP RS		3.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.18
gMVP		0.75

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: rs569379713; hg19: chr1-55509520;