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.1552A>G (p.Lys518Glu)

CA10585499

251894 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: e938aec0-0c40-48f1-8b32-8ccbc7bdb969

HGVS expressions

NM_000527.5:c.1552A>G
NM_000527.5(LDLR):c.1552A>G (p.Lys518Glu)
NC_000019.10:g.11113728A>G
CM000681.2:g.11113728A>G
NC_000019.9:g.11224404A>G
CM000681.1:g.11224404A>G
NC_000019.8:g.11085404A>G
NG_009060.1:g.29348A>G
ENST00000558518.6:c.1552A>G
ENST00000252444.9:n.1806A>G
ENST00000455727.6:c.1048A>G
ENST00000535915.5:c.1429A>G
ENST00000545707.5:c.1171A>G
ENST00000557933.5:c.1552A>G
ENST00000558013.5:c.1552A>G
ENST00000558518.5:c.1552A>G
ENST00000559340.1:n.273A>G
NM_000527.4:c.1552A>G
NM_001195798.1:c.1552A>G
NM_001195799.1:c.1429A>G
NM_001195800.1:c.1048A>G
NM_001195803.1:c.1171A>G
NM_001195798.2:c.1552A>G
NM_001195799.2:c.1429A>G
NM_001195800.2:c.1048A>G
NM_001195803.2:c.1171A>G

Uncertain Significance

Met criteria codes 3
PP1 PP4 PM2
Not Met criteria codes 4
PS4 PS3 PP3 PM5

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.1552A>G (p. Lys518Glu) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP4, PP1) 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). PP4: Variant meets PM2 and is identified in 1 index case who fulfils Simon Broome criteria for Definite FH after alternative causes of high cholesterol were excluded, from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation. PP1: Variant segregates with FH phenotype in 2 informative meiosis from 1 family: 1 affected relative tested positive and 1 unaffected relative tested negative for the variant, reported from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation. PP3 not met: REVEL = 0.593, it is not above 0.75, splicing evaluation required. Variant is exonic and is not on limit creating de novo acceptor site. It is located at least 50bp downstream from canonical acceptor site but does not create GT. Variant is not predicted to alter splicing. PS3 not met: Functional data is not available for this variant. PS4 not met: Variant meets PM2 and is identified in less than 2 index case who fulfil FH diagnosis criteria. PM5 not met: There is one other variant in the same codon: LDLR: NM_000527:c.1553A>G (p.Lys518Arg) is classified as Uncertain significance - insufficient evidence by these guidelines. Therefore PM5 is not met.
Met criteria codes
PP1
Variant segregates with FH phenotype in 2 informative meiosis from 1 family: 1 affected relative tested positive and 1 unaffected relative tested negative for the variant, reported from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation.
PP4
Variant meets PM2 and is identified in 1 index case who fulfils Simon Broome criteria for Definite FH after alternative causes of high cholesterol were excluded, from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation.
PM2
This variant is absent from gnomAD (gnomAD v2.1.1).
Not Met criteria codes
PS4
Variant meets PM2 and is identified in less than 2 index case who fulfil FH diagnosis criteria.
PS3
Functional data is not available for this variant.
PP3
REVEL = 0.593, it is not above 0.75, splicing evaluation required. Variant is exonic and is not on limit creating de novo acceptor site. It is located at least 50bp downstream from canonical acceptor site but does not create GT. Variant is not predicted to alter splicing.
PM5
There is one other variant in the same codon: LDLR: NM_000527:c.1553A>G (p.Lys518Arg) is classified as Uncertain significance - insufficient evidence by these guidelines. Therefore PM5 is not met.
Approved on: 2023-04-28
Published on: 2023-05-01
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