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Variant: NM_000527.5(LDLR):c.1553A>G (p.Lys518Arg)

CA10585500

251895 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: 111b0c96-1b53-4da7-bb1f-045450283a51

HGVS expressions

NM_000527.5:c.1553A>G
NM_000527.5(LDLR):c.1553A>G (p.Lys518Arg)
NC_000019.10:g.11113729A>G
CM000681.2:g.11113729A>G
NC_000019.9:g.11224405A>G
CM000681.1:g.11224405A>G
NC_000019.8:g.11085405A>G
NG_009060.1:g.29349A>G
ENST00000558518.6:c.1553A>G
ENST00000252444.9:n.1807A>G
ENST00000455727.6:c.1049A>G
ENST00000535915.5:c.1430A>G
ENST00000545707.5:c.1172A>G
ENST00000557933.5:c.1553A>G
ENST00000558013.5:c.1553A>G
ENST00000558518.5:c.1553A>G
ENST00000559340.1:n.274A>G
NM_000527.4:c.1553A>G
NM_001195798.1:c.1553A>G
NM_001195799.1:c.1430A>G
NM_001195800.1:c.1049A>G
NM_001195803.1:c.1172A>G
NM_001195798.2:c.1553A>G
NM_001195799.2:c.1430A>G
NM_001195800.2:c.1049A>G
NM_001195803.2:c.1172A>G

Uncertain Significance

Met criteria codes 4
PS4_Supporting PP4 PM2 BP4
Not Met criteria codes 3
PS3 PP3 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5 (LDLR):c.1553A>G (p. Lys518Arg) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP4, PS4_Supporting, BP4) 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 = 0.00001 in European (Non-Finnish) population in gnomAD (gnomAD v2.1.1). PP4: Variant meets PM2 and is identified in ˃1 index case who fulfil criteria for FH diagnosis from 2 labs after alternative causes of high cholesterol were excluded. PS4_Supporting: Variant meets PM2 and is identified in 2 unrelated index cases who fulfil FH diagnosis criteria. One index case met MedPed definite FH criteria from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); one index case fulfil Simon Broome criteria for FH, reported by Usifo et al, 2012, British Heart Foundation Laboratories, Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK (PMID22881376). BP4: REVEL = 0.371, it is below 0.5, 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. PP3 not met: REVEL = 0.371, it is not above 0.75. Alternative splicing is not predicted. PS3 not met: Functional data on splicing is not available. PM5 not met: There is one other variant in the same codon: LDLR: NM_000527:c.1552A>G (p.Lys518Glu) is classified as Uncertain significance - insufficient evidence by these guidelines. Therefore PM5 is not met.
Met criteria codes
PS4_Supporting
Variant meets PM2 and is identified in 2 unrelated index cases who fulfil FH diagnosis criteria. One index case met MedPed definite FH criteria from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); one index case fulfil Simon Broome criteria for FH, reported by Usifo et al, 2012, British Heart Foundation Laboratories, Centre for Cardiovascular Genetics, Institute of Cardiovascular Sciences, University College London, London, UK (PMID22881376).
PP4
Variant meets PM2 and is identified in ˃1 index case who fulfil criteria for FH diagnosis from 2 labs after alternative causes of high cholesterol were excluded.
PM2
PopMax MAF = 0.00001 in European (Non-Finnish) population in gnomAD (gnomAD v2.1.1).
BP4
REVEL = 0.371, it is below 0.5, 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.
Not Met criteria codes
PS3
Functional data on splicing is not available.
PP3
REVEL = 0.371, it is not above 0.75. Alternative splicing is not predicted.
PM5
There is one other variant in the same codon: LDLR: NM_000527:c.1552A>G (p.Lys518Glu) is classified as Uncertain significance - insufficient evidence by these guidelines. Therefore PM5 is not met.
Approved on: 2022-08-26
Published on: 2022-12-23
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