The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000527.5(LDLR):c.1729T>G (p.Trp577Gly)

CA10585585

252000 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: adb0184f-0bcb-4ed0-a59a-783932dac98b

HGVS expressions

NM_000527.5:c.1729T>G
NM_000527.5(LDLR):c.1729T>G (p.Trp577Gly)
NC_000019.10:g.11116882T>G
CM000681.2:g.11116882T>G
NC_000019.9:g.11227558T>G
CM000681.1:g.11227558T>G
NC_000019.8:g.11088558T>G
NG_009060.1:g.32502T>G
ENST00000558518.6:c.1729T>G
ENST00000252444.9:n.1983T>G
ENST00000455727.6:c.1225T>G
ENST00000535915.5:c.1606T>G
ENST00000545707.5:c.1348T>G
ENST00000557933.5:c.1729T>G
ENST00000558013.5:c.1729T>G
ENST00000558518.5:c.1729T>G
ENST00000559340.1:n.426+670T>G
NM_000527.4:c.1729T>G
NM_001195798.1:c.1729T>G
NM_001195799.1:c.1606T>G
NM_001195800.1:c.1225T>G
NM_001195803.1:c.1348T>G
NM_001195798.2:c.1729T>G
NM_001195799.2:c.1606T>G
NM_001195800.2:c.1225T>G
NM_001195803.2:c.1348T>G

Pathogenic

Met criteria codes 6
PM2 PP1_Moderate PS4_Supporting PS3 PP4 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Familial Hypercholesterolemia Expert Panel Specifications to the ACMG/AMP Variant Classification Guidelines Version 1.2

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.1729T>G (p.Trp577Gly) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PS3, PP1_moderate, PM2, PP3, PS4_supporting, 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: PS3: Level 1 assays: PMID 25378237: Heterologous cells, FACS assays -10-15% LDL-LDLR binding; 5% LDL-LDLR uptake; 5% cell surface LDLR ---- activity is below 70% of wild-type, so functional study is consistent with damaging effect. 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) PM2: This variant is absent from gnomAD (gnomAD v2.1.1). PP3: REVEL = 0.937. PS4_supporting: Variant meets PM2 and is identified in 2 index cases (1 case with DLCN criteria>=6 from Robarts Research Institute; 1 case with DLCN criteria>=6 from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation)) PP4: Variant meets PM2 and is identified in 2 index cases who fulfill clinical criteria for FH from several labs (see PS4 for details), after alternative causes of high cholesterol were excluded.
Met criteria codes
PM2
This variant is absent from gnomAD (gnomAD v2.1.1).
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_Supporting
Variant meets PM2 and is identified in 2 index cases (1 case with DLCN criteria>=6 from Robarts Research Institute; 1 case with DLCN criteria>=6 from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation))
PS3
Level 1 assays: PMID 25378237: Heterologous cells, FACS assays -10-15% LDL-LDLR binding; 5% LDL-LDLR uptake; 5% cell surface LDLR ---- activity is below 70% of wild-type, so functional study is consistent with damaging effect.
PP4
Variant meets PM2 and is identified in 2 index cases (1 case with DLCN criteria>=6 from Robarts Research Institute; 1 case with DLCN criteria>=6 from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation)), after alternative causes of high cholesterol were excluded.
PP3
REVEL = 0.937.
Approved on: 2023-04-28
Published on: 2023-04-28
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