Submissions for variant NM_000527.5(LDLR):c.979C>T (p.His327Tyr)

gnomAD frequency: 0.00006  dbSNP: rs747507019

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000238224	SCV004022469	uncertain significance	Hypercholesterolemia, familial, 1	2023-04-28	reviewed by expert panel	curation	The NM_000527.5(LDLR):c.979C>T (p.His327Tyr) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PP4 and PS_Supporting) 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 - This variant is absent from gnomAD (gnomAD v2.1.1). PP3 - REVEL = 0.958 PP4 - Variant meets PM2 and is identified in at least one case who fufills clinical criteria for FH (see PS4 for details), after alternative causes of high cholesterol were excluded. PS4_Supporting - Variant meets PM2 and is identified in 3 index cases (1 case with DLCN criteria>=6 from Robarts Research Institute, Canada; 1 case with Simon-Broome criteria in PMID: 9259195 (Day et al., 1997), UK; 1 case with DLCN criteria>=6 in PMID: 11810272 (Fouchier et al., 2001), The Netherlands).
LDLR-LOVD, British Heart Foundation	RCV000238224	SCV000295124	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Robarts Research Institute, Western University	RCV000238224	SCV000484756	likely pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	RCV000238224	SCV000503272	likely benign	Hypercholesterolemia, familial, 1	2016-12-16	criteria provided, single submitter	clinical testing	subjects mutated among 2600 FH index cases screened = 2 / previously described in association with FH (linked to ethnicity ?) / Software predictions: Damaging
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000590256	SCV000697257	uncertain significance	not provided	2016-12-14	criteria provided, single submitter	clinical testing	Variant summary: The LDLR c.979C>T (p.His327Tyr) variant involves the alteration of a conserved nucleotide. 2/3 in silico tools predict a damaging outcome for this variant. This variant is present in 8/120554 control chromosomes, which does not exceed the max expected frequency for a pathogenic variant in this gene. The variant has been reported in affected inviduals in the literature, without strong evidence for causality, including co-occurrence data and co-segregation data. Two independent functional studies reveal that this variant results in a molecular gain-of-function, i.e. enhanced LDLR binding to PCSK9. This increased affinity of PCSK9 to the LDLR would in turn lead to enhanced LDLR destruction, decreased plasma LDL-C clearance, and hypercholesterolemia. However, due to the lack of strong clinical data, this variant can not be definitively classified as pathogenic. Taken together, this variant is classified as VUS-possibly pathogenic.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV001248905	SCV001422595	uncertain significance	Familial hypercholesterolemia	2020-01-22	criteria provided, single submitter	curation	The p.His327Tyr variant in LDLR has been reported in at least 4 individuals with familial hypercholesterolemia (PMID: 9259195, 11810272, 15199436, 23833242), and has been identified in 0.05% (15/30610) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs747507019). This variant has also been reported in ClinVar as having conflicting interpretations of pathogenicity (Variation ID: 251583). In vitro functional studies provide some evidence that the p.His327Tyr variant may slightly impact protein function (PMID: 19224862, 19001363). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PP3, PS4_supporting, PS3_supporting (Richards 2015).
Invitae	RCV001248905	SCV003519744	uncertain significance	Familial hypercholesterolemia	2022-03-21	criteria provided, single submitter	clinical testing	This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 327 of the LDLR protein (p.His327Tyr). This variant is present in population databases (rs747507019, gnomAD 0.05%). This missense change has been observed in individual(s) with familial hypercholesterolemia (PMID: 9259195, 15199436, 23833242, 27765764, 33303402, 33740630). This variant is also known as p.His306Tyr. ClinVar contains an entry for this variant (Variation ID: 251583). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects LDLR function (PMID: 19001363, 19224862, 23675525). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000238224	SCV000606288	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research
Natera, Inc.	RCV001248905	SCV001460261	uncertain significance	Familial hypercholesterolemia	2020-09-16	no assertion criteria provided	clinical testing