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Variant: NM_000527.5(LDLR):c.313+2T>C

CA023690

189296 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: be57d00e-452f-4bdc-b48a-3ee5b727c648

HGVS expressions

NM_000527.5:c.313+2T>C
NM_000527.5(LDLR):c.313+2T>C
NC_000019.10:g.11102788T>C
CM000681.2:g.11102788T>C
NC_000019.9:g.11213464T>C
CM000681.1:g.11213464T>C
NC_000019.8:g.11074464T>C
NG_009060.1:g.18408T>C
ENST00000558518.6:c.313+2T>C
ENST00000252444.9:n.567+2T>C
ENST00000455727.6:c.313+2T>C
ENST00000535915.5:c.191-2432T>C
ENST00000545707.5:c.313+2T>C
ENST00000557933.5:c.313+2T>C
ENST00000557958.1:n.401T>C
ENST00000558013.5:c.313+2T>C
ENST00000558518.5:c.313+2T>C
NM_000527.4:c.313+2T>C
NM_001195798.1:c.313+2T>C
NM_001195799.1:c.191-2432T>C
NM_001195800.1:c.313+2T>C
NM_001195803.1:c.313+2T>C
NM_001195798.2:c.313+2T>C
NM_001195799.2:c.191-2432T>C
NM_001195800.2:c.313+2T>C
NM_001195803.2:c.313+2T>C

Pathogenic

Met criteria codes 7
PVS1_Strong PS4 PP1_Moderate PP4 PM3 PM2 PS3_Moderate
Not Met criteria codes 15
PS2 PS1 BP2 BP4 BP7 BA1 PP3 PM1 PM4 PM5 PM6 BS2 BS4 BS3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Familial Hypercholesterolemia Expert Panel Specifications to the ACMG/AMP Variant Classification Guidelines Version 1.1

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.313+2T>C variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM2, PS3_moderate, PVS1_strong, PP1_moderate, PS4, PM3, 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 = 0.00002941 (0.002941%) in European (non-Finnish) exomes (gnomAD v3.1.2), so PM2 is Met. PS3_moderate - Level 2 assays: PMID 19026292: Homozygous patient cells, 125I-LDL assays - result - 10% LDLR activity. ---- functional study is consistent with damaging effect, so PS3_Moderate is Met. PVS1_strong - Variant is in +2 intronic position, but there are no studies on effect predicted, so give PVS1_Strong to be conservative. PP1_moderate - Variant segregates with FH phenotype in 4 informative meiosis from 2 families: 2 relatives with the phenotype and the variant from Robarts Research Institute, and 2 affected family members with the variant from Germany (PMID: 26036859), so PP1_Moderate is Met. PS4 - Variant meets PM2 and is identified in 19 unrelated index cases from different labs (4 index cases with DLCN>6 from Robarts Research Institute; 4 index cases with DLCN>6 from Color Health, Inc; 1 index case who fulfills the following criteria for FH: i) total cholesterol >= 9.5 mmol/l, ii) triglycerides < 2 mmol/l, iii) presence of tendon xanthomas; or iv) occurrence of hypercholesterolemia or early onset of coronary artery disease in first degree relatives, from The Netherlands (PMID: 7616128); 3 index cases with DLCN>6 (LDL between 7,98 - 9,50 mmol/l and hypercholesterolemia in 1st degree relative) from Germany (PMID: 11462246); 1 index case who fulfills the following criteria for FH: (1) LDL > 95th percentile and triglycerides below 2 mmol/l, and (2) the presence of xanthoma or CHD in the proband or 1st degree relative with type IIa hypercholesterolemia, xanthoma, or CVD, from France (PMID: 12436241); 1 index case with SB criteria for FH (Total cholesterol >290 mg/dL and LDL >200 mg/dL and severe hypercholesterolemia in 1st degree relatives), from Germany (PMID: 14974088); 1 index case with definite FH according to SB criteria from Northern Ireland (PMID: 16159606); 3 index cases fulfilling the following criteria for FH: i) total cholesterol > 8.0 mmol/l and LDL > 6 mmol/l; (ii) premature coronary or vascular disease, or a family history of cardiovascular disorder; and (iii) the presence of tendon xanthoma, from Denmark (PMID: 16542394); 1 index case with definite FH according to SB criteria (total cholesterol = 658 mg/dl and presence of xanthomas, and primary hypercholesterolemia in the probands’ parents or 1st degree relatives), from USA (PMID: 19026292)), so PS4 is Met. PM3 - Variant meets PM2 and is identified in a true homozygous with total cholesterol = 658 mg/dl (PMID: 19026292), so PM3 is Met. PP4 - Variant meets PM2 and is identified in 19 unrelated index cases from different labs as described, so PP4 is Met.
Met criteria codes
PVS1_Strong
Variant is in +2 intronic position, but there are no studies on effect predicted, so give PVS1_Strong to be conservative.
PS4
Variant meets PM2 and is identified in 19 unrelated index cases from different labs (4 index cases with DLCN>6 from Robarts Research Institute; 4 index cases with DLCN>6 from Color Health, Inc; 1 index case who fulfills the following criteria for FH: i) total cholesterol >= 9.5 mmol/l, ii) triglycerides < 2 mmol/l, iii) presence of tendon xanthomas; or iv) occurrence of hypercholesterolemia or early onset of coronary artery disease in first degree relatives, from The Netherlands (PMID: 7616128); 3 index cases with DLCN>6 (LDL between 7,98 - 9,50 mmol/l and hypercholesterolemia in 1st degree relative) from Germany (PMID: 11462246); 1 index case who fulfills the following criteria for FH: (1) LDL > 95th percentile and triglycerides below 2 mmol/l, and (2) the presence of xanthoma or CHD in the proband or 1st degree relative with type IIa hypercholesterolemia, xanthoma, or CVD, from France (PMID: 12436241); 1 index case with SB criteria for FH (Total cholesterol >290 mg/dL and LDL >200 mg/dL and severe hypercholesterolemia in 1st degree relatives), from Germany (PMID: 14974088); 1 index case with definite FH according to SB criteria from Northern Ireland (PMID: 16159606); 3 index cases fulfilling the following criteria for FH: i) total cholesterol > 8.0 mmol/l and LDL > 6 mmol/l; (ii) premature coronary or vascular disease, or a family history of cardiovascular disorder; and (iii) the presence of tendon xanthoma, from Denmark (PMID: 16542394); 1 index case with definite FH according to SB criteria (total cholesterol = 658 mg/dl and presence of xanthomas, and primary hypercholesterolemia in the probands’ parents or 1st degree relatives), from USA (PMID: 19026292)), so PS4 is Met.
PP1_Moderate
Variant segregates with FH phenotype in 4 informative meiosis from 2 families: 2 relatives with the phenotype and the variant from Robarts Research Institute, and 2 affected family members with the variant from Germany (PMID: 26036859), so PP1_Moderate is Met.
PP4
Variant meets PM2 and is identified in 19 unrelated index cases from different labs (4 index cases with DLCN>6 from Robarts Research Institute; 4 index cases with DLCN>6 from Color Health, Inc; 1 index case who fulfills the following criteria for FH: i) total cholesterol >= 9.5 mmol/l, ii) triglycerides < 2 mmol/l, iii) presence of tendon xanthomas; or iv) occurrence of hypercholesterolemia or early onset of coronary artery disease in first degree relatives, from The Netherlands (PMID: 7616128); 3 index cases with DLCN>6 (LDL between 7,98 - 9,50 mmol/l and hypercholesterolemia in 1st degree relative) from Germany (PMID: 11462246); 1 index case who fulfills the following criteria for FH: (1) LDL > 95th percentile and triglycerides below 2 mmol/l, and (2) the presence of xanthoma or CHD in the proband or 1st degree relative with type IIa hypercholesterolemia, xanthoma, or CVD, from France (PMID: 12436241); 1 index case with SB criteria for FH (Total cholesterol >290 mg/dL and LDL >200 mg/dL and severe hypercholesterolemia in 1st degree relatives), from Germany (PMID: 14974088); 1 index case with definite FH according to SB criteria from Northern Ireland (PMID: 16159606); 3 index cases fulfilling the following criteria for FH: i) total cholesterol > 8.0 mmol/l and LDL > 6 mmol/l; (ii) premature coronary or vascular disease, or a family history of cardiovascular disorder; and (iii) the presence of tendon xanthoma, from Denmark (PMID: 16542394); 1 index case with definite FH according to SB criteria (total cholesterol = 658 mg/dl and presence of xanthomas, and primary hypercholesterolemia in the probands’ parents or 1st degree relatives), from USA (PMID: 19026292)), so PP4 is Met.
PM3
Variant meets PM2 and is identified in a true homozygous with total cholesterol = 658 mg/dl (PMID: 19026292), so PM3 is Met.
PM2
PopMax MAF = 0.00002941 (0.002941%) in European (non-Finnish) exomes (gnomAD v3.1.2), so PM2 is Met.
PS3_Moderate
Level 2 assays: PMID 19026292: Homozygous patient cells, 125I-LDL assays - result - 10% LDLR activity. ---- functional study is consistent with damaging effect, so PS3_Moderate is Met.
Not Met criteria codes
PS2
de novo occurrence data not reported, so PS2 is Not Met.
PS1
Variant is in a non-coding region, so PS1 is Not Met.
BP2
Variant identified in 8 cases with heterozygous FH phenotype (LDL means of 6.19 mmol/l and 6.11 mmol/l) and LDLR variant c.313+1G>C, but is not in trans (PMID: 22095935), so BP2 is not met.
BP4
Functional data available and PVS1 is given, so BP4 is not applicable.
BP7
Variant is not synonymous, so BP7 is Not Met.
BA1
FAF = 0.000004880 (0.0004880%) in European (non-Finnish) exomes (gnomAD v3.1.1), so BA1 is not met.
PP3
Functional data available and PVS1 is given, so PP3 is not applicable.
PM1
Variant meets PM2 but is not missense, so PM1 is Not Met.
PM4
Variant meets PM2 and is not in frame, so PM4 is Not Met.
PM5
Variant is in a non-coding region, so PM5 is Not Met.
PM6
de novo occurrence data not reported, so PM6 is Not Met.
BS2
Not observed in 1000 normolipidemic individuals from Robarts Research Institute, so BS2 is Not Met.
BS4
Variant does not segregate with FH phenotype in 2 informative meiosis from 1 family from Germany (PMID: 26036859), so BS4 is Not Met.
BS3
Level 2 assays: PMID 19026292: Homozygous patient cells, 125I-LDL assays - result - 10% LDLR activity. ---- functional study is consistent with damaging effect, so BS3 is not met.
BS1
FAF = 0.000004880 (0.0004880%) in European (non-Finnish) exomes (gnomAD v3.1.2), so BS1 is not met.
Approved on: 2022-02-14
Published on: 2022-07-12
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