LDLR p.Gln378Pro

NM_000527.5(LDLR):c.1133A>C (p.Gln378Pro) variant is classified as likely pathogenic for Familial Hypercholesterolemia by applying evidence code PM2, PS4_Moderate, PM3, PP1_Moderate, PP3, and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2: PopMax MAF = 0.00001760 (0.001760%) in European (non-Finnish) exomes (gnomAD v2.1.1). PP3: REVEL = 0.754. PP1_moderate: Variant segregates with FH phenotype in at least 4 informative meiosis from 1 family from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation). PS4_moderate: Variant meets PM2 and is identified in at least 6 unrelated index cases: 1 case from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation) with Simon Broome definite criteria; 1 case from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA) with Dutch lipid clinic network >=6; 1 case from Mayo Clinic Atherosclerosis and Lipid Genomics Laboratory with Dutch lipid clinic network >=6; 1 case from South Africa in PMID: 9664576; 1 case from Spain in PMID: 15241806; 1 case from Italy in PMID: 23375686. PM3: PMID: 27784735 - variant identified in two children with homozygous FH: in one patient confirmed in trans with LDLR p.Ile792Thr and in the second patient confirmed in trans with a LP/P LDLR exonic deletion; given this exonic deletion is LP/P, PM3 applies. PP4: Variant meets PM2 and is identified in >1 index case who fulfill clinical criteria for FH, after alternative causes of high cholesterol were excluded. Note: BS3 not met: PMID: 32015373 - Level 1 assay: Heterologous cells, FACS assays – results - cell surface LDLR (96%), binding (101%) were normal; LDL uptake (80%) activity is not above 90%, so BS3 not met. This result suggests this variant may only have a minor effect (i.e. 20% reduction in LDL uptake), although this is not insignificant.