The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000527.5(LDLR):c.662A>G (p.Asp221Gly)

CA023739

183092 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: f2f41bd9-ad4d-4237-b618-832f5cbc6885

HGVS expressions

NM_000527.5:c.662A>G
NM_000527.5(LDLR):c.662A>G (p.Asp221Gly)
NC_000019.10:g.11105568A>G
CM000681.2:g.11105568A>G
NC_000019.9:g.11216244A>G
CM000681.1:g.11216244A>G
NC_000019.8:g.11077244A>G
NG_009060.1:g.21188A>G
ENST00000558518.6:c.662A>G
ENST00000252444.9:n.916A>G
ENST00000455727.6:c.314-1824A>G
ENST00000535915.5:c.539A>G
ENST00000545707.5:c.314-997A>G
ENST00000557933.5:c.662A>G
ENST00000558013.5:c.662A>G
ENST00000558518.5:c.662A>G
ENST00000560467.1:n.262A>G
NM_000527.4:c.662A>G
NM_001195798.1:c.662A>G
NM_001195799.1:c.539A>G
NM_001195800.1:c.314-1824A>G
NM_001195803.1:c.314-997A>G
NM_001195798.2:c.662A>G
NM_001195799.2:c.539A>G
NM_001195800.2:c.314-1824A>G
NM_001195803.2:c.314-997A>G

Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Conflicting Evidence"
Met criteria codes 9
PP1_Strong PS3_Moderate PS4 PP4 PP3 PM2 BS4 PM3 PM1
Not Met criteria codes 17
PS2 PS1 PVS1 PP2 BA1 PM6 BS3 BS1 PM4 PM5 BS2 BP5 BP7 BP2 BP3 BP4 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
NM_000527.5(LDLR): c.662A>G (p.Asp221Gly) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PP1_strong, PS3_moderate, PS4, PM1, PM2, PM3, PP3, PP4 and BS4) 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: PP1_strong - Variant segregates with FH phenotype in 92 informative meiosis in at least 37 families from different labs (Robarts Research Institute; Laboratory of Genetics and Molecular Cardiology, University of São Paulo; Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA)): 55 affected family members have the variant, 37 unaffected family members don’t have the variant. PS3_moderate - PMID: 9974426 - Level 2 assay - Homozygous patients' fibroblasts, 125I-LDL assays: 8% LDLR activity; PMID: 25647241 - Level 3 assay - Heterologous cells (HeLa), CLSM assay: most of mutant LDLR is in ER, LDLR activity decreased compared to WT - considered as disruptive. PS4 - Variant meets PM2. Variant identified in 48 unrelated index cases (2 cases with DLCN≥6 from Robarts Research Institute; 21 cases (13 patients with DLCN≥6, and 8 patients with possible FH (Simon Broome)) from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); 17 cases with possible/definite FH (Simon-Broome) from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); 1 case with Possible FH (Simon-Broome) from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; 5 cases with DLCN≥6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); 2 cases with DLCN≥6 from Color Health, Inc. PM1 - Variant meets PM2 and is missense in exon 4. PM2 - PopMax MAF = 0.0001152 (0.01152%) in European (non-Finnish) exomes+genomes (gnomAD v2.1.1). PM3 - Index case from Ambry Genetics has LDL = 750 mg/dl and also LDLR c.2140+1G>T (pathogenic by these guidelines, confirmed to be in trans). PP3 - REVEL = 0.986. PP4 - Variant meets PM2. Identified in 48 FH cases from different labs (for list see PS4) with clinical Dutch Lipid Clinic Network Criteria score ≥ 6 or Simon-Broome possible/definite FH, after alternative causes of high cholesterol were excluded. BS4 - 30 nonsegregations in 12 families (Laboratory of Genetics and Molecular Cardiology, University of São Paulo). Variant has 2 Strong plus 4 Moderate plus 2 Supporting evidence codes towards Pathogenic, enough to classify as Pathogenic, and only 1 Strong evidence codes towards Benign. The Pathogenic criteria overwhelms the Benign criteria, so we are confident in classifying this variant as Pathogenic.
Met criteria codes
PP1_Strong
Variant segregates with FH phenotype in 92 informative meiosis in at least 37 families from different labs (Robarts Research Institute; Laboratory of Genetics and Molecular Cardiology, University of São Paulo; Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA)): 55 affected family members have the variant, 37 unaffected family members don’t have the variant.
PS3_Moderate
PMID: 9974426 - Level 2 assay - Homozygous patients' fibroblasts, 125I-LDL assays: 8% LDLR activity; PMID: 25647241 - Level 3 assay - Heterologous cells (HeLa), CLSM assay: most of mutant LDLR is in ER, LDLR activity decreased compared to WT - considered as disruptive.
PS4
Variant meets PM2. Variant identified in 48 unrelated index cases (2 cases with DLCN≥6 from Robarts Research Institute; 21 cases (13 patients with DLCN≥6, and 8 patients with possible FH (Simon Broome)) from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); 17 cases with possible/definite FH (Simon-Broome) from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); 1 case with Possible FH (Simon-Broome) from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; 5 cases with DLCN≥6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); 2 cases with DLCN≥6 from Color Health, Inc.
PP4
Variant meets PM2. Identified in 48 FH cases from different labs (for list see PS4) with clinical Dutch Lipid Clinic Network Criteria score ≥ 6 or Simon-Broome possible/definite FH, after alternative causes of high cholesterol were excluded.
PP3
REVEL = 0.986
PM2
PopMax MAF = 0.0001152 (0.01152%) in European (non-Finnish) exomes+genomes (gnomAD v2.1.1).
BS4
30 nonsegregations in 12 families (Laboratory of Genetics and Molecular Cardiology, University of São Paulo).
PM3
Index case from Ambry Genetics has LDL = 750 mg/dl and also LDLR c.2140+1G>T (pathogenic by these guidelines, confirmed to be in trans).
PM1
Variant meets PM2 and is missense in exon 4.
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
If PM1 is met, PM5 is not applicable.
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-05-30
Published on: 2022-06-30
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