Submissions for variant NM_000527.5(LDLR):c.1217G>C (p.Arg406Pro)

dbSNP: rs552422789

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000211629	SCV002506382	likely pathogenic	Hypercholesterolemia, familial, 1	2022-04-22	reviewed by expert panel	curation	The NM_000527.5(LDLR):c1217G>C (p.Arg406Pro) variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM2, PP3, PM5, PS4_Supporting, PP1, and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: PM2 - This variant is absent from gnomAD (gnomAD v2.1.1). PP3 - REVEL = 0.89, which is above the threshold of 0.75. PM5 - 2 other missense variants in the same codon: 1) NM_000527.5(LDLR):c.1217G>A (p.Arg406Gln) – Likely pathogenic by these guidelines. 2) NM_000527.5(LDLR):c.1217G>C (p.Arg406Trp) – Pathogenic by these guidelines. There is 1 variant in the same codon classified as Pathogenic by these guidelines. – therefore PM5 is met. PS4_Supporting - Variant meets PM2 and is identified in 2 unrelated index cases who fulfill clinical criteria for FH (1 case with SB criteria from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation– FH VCEP member lab; 1 case with DLCN criteria from PMID: 16250003) PP1 - Variant segregates with phenotype in 2 informative meioses from 2 families in data provided by FH VCEP member labs (Laboratory of Genetics and Molecular Cardiology – 1 family: 1 affected family member with the variant; Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation – 1 family: 1 affected family member with the variant). PP4 - Variant meets PM2. Identified in >1 case who met clinical criteria for FH after alternative causes for high cholesterol were excluded.
LDLR-LOVD, British Heart Foundation	RCV000211629	SCV000295308	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation	RCV000211629	SCV000540802	likely pathogenic	Hypercholesterolemia, familial, 1	2016-11-05	criteria provided, single submitter	clinical testing
Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	RCV000211629	SCV000268605	pathogenic	Hypercholesterolemia, familial, 1	2013-03-22	no assertion criteria provided	clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000211629	SCV000606364	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research