ClinVar Genomic variation as it relates to human health

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.

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.

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.

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.

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.

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.

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.