ClinVar Genomic variation as it relates to human health

subjects mutated among 2600 FH index cases screened = 2, family members = 2, with co-segregation / Software predictions: Conflicting

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Published in vitro studies show that this variant causes a reduction in membrane-associated LDLR (Le et al., 2015) while other published functional studies show PCSK9 protein with this variant is cleaved normally and secreted efficiently (Fasano et al., 2009) and binding and degradation of LDLR protein is similar to that of wild type PCSK9 activity (Ahmad et al., 2012); This variant is associated with the following publications: (PMID: 23064986, 23680767, 28994502, 34037665, 29261184, 26374825, 31491741, 33955087, 26195630, 19081568)

In the published literature, this variant has been reported in affected individuals with familial hypercholesterolemia (PMIDs: 19081568 (2009), 23064986 (2012), 23680767 (2013), 26374825 (2015), 31491741 (2019), 33955087 (2021), and 34037665 (2021)). One functional study demonstrated that this variant may reduce cell surface expression of LDLR (PMID: 26195630 (2015)), while two additional functional studies found that this variant performed similar to wild type (PMIDs: 19081568 (2009) and 23064986 (2012)). The frequency of this variant in the general population, 0.000026 (3/113682 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.

This missense variant replaces aspartic acid with asparagine at codon 129 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 studies for this variant are conflicted as some have shown that this variant causes a reduction of the cell surface expression of LDLR and LDL uptake compared to wild type (PMID: 26195630, 34948399), while other studies have shown no significant difference (PMID: 19081568, 23064986). This variant has been reported in several unrelated individuals affected with familial hypercholesterolemia (PMID: 19081568, 23680767, 26195630, 26374825, 28994502, 31491741, 33955087, 34407635). This variant has also been reported in five individuals from a family affected with hypercholesterolemia, including three affected and two unaffected, suggesting a reduced penetrance for this variant (PMID: 23064986). This variant has been identified in 4/251360 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 sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 129 of the PCSK9 protein (p.Asp129Asn). This variant is present in population databases (rs778738291, gnomAD 0.003%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 19081568, 23064986, 23680767, 26374825, 31491741, 34037665; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 375844). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on PCSK9 function (PMID: 19081568, 23064986, 26195630, 34948399). This variant disrupts the p.Asp129 amino acid residue in PCSK9. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17765244, 26195630, 27280970, 29259136; 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.

This missense variant replaces aspartic acid with asparagine at codon 129 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 studies for this variant are conflicted as some have shown that this variant causes a reduction of the cell surface expression of LDLR and LDL uptake compared to wild type (PMID: 26195630, 34948399), while other studies have shown no significant difference (PMID: 19081568, 23064986). This variant has been reported in several unrelated individuals affected with familial hypercholesterolemia (PMID: 19081568, 23680767, 26195630, 26374825, 28994502, 31491741, 33955087, 34407635). This variant has also been reported in five individuals from a family affected with hypercholesterolemia, including three affected and two unaffected, suggesting a reduced penetrance for this variant (PMID: 23064986). This variant has been identified in 4/251360 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.385G>A (p.D129N) alteration is located in exon 2 (coding exon 2) of the PCSK9 gene. This alteration results from a G to A substitution at nucleotide position 385, causing the aspartic acid (D) at amino acid position 129 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

Variant summary: PCSK9 c.385G>A (p.Asp129Asn) results in a conservative amino acid change located in the Peptidase S8 propeptide/proteinase inhibitor I9 domain (IPR010259) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251360 control chromosomes. c.385G>A has been reported in the literature segregating with disease in the heterozygous state in multiple individuals affected with autosomal dominant Familial Hypercholesterolemia (example, Ahmad_2012, Bjornsson_2021, Cao_2021, Fasano_2009), and was also observed de novo in at least 1 affected individual with confirmed parentage (ClinVar, deCODE entry). In at least 1 family, there was evidence to suggest incomplete penetrance. In vitro experiments carried out in HEK293 and HepG2 cell lines found this variant to have a relatively mild gain-of-function impact on the activity of PCSK9 (example, Ahmad_2012, Chorba_2018, Fasano_2009, Uribe_2021). The following publications have been ascertained in the context of this evaluation (PMID: 23064986, 34407635, 36338372, 29259136, 19081568, 34948399). ClinVar contains an entry for this variant (Variation ID: 375844). Based on the evidence outlined above, the variant was classified as likely pathogenic.

The variant NM_174936.4:c.385G>A (chr1:55044020) in PCSK9 was detected in 1 heterozygote out of 58K WGS Icelanders (MAF= 0,001%). The variant occurred de novo (confirmed absence from parents’ WGS data) in an individual with highly elevated LDL cholesterol. This variant has been reported in ClinVar previously as benign, likely pathogenic, and as a variant of uncertain significance. Based on ACMG criteria (PS2, PM2, PM5, PP5) this variant classifies as likely pathogenic.