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.1432G>T (p.Gly478Trp)

CA404085992

548076 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: d4e8f2e5-1bec-4614-8a2f-e85ce94c2aa3

HGVS expressions

NM_000527.5:c.1432G>T
NM_000527.5(LDLR):c.1432G>T (p.Gly478Trp)
NC_000019.10:g.11113608G>T
CM000681.2:g.11113608G>T
NC_000019.9:g.11224284G>T
CM000681.1:g.11224284G>T
NC_000019.8:g.11085284G>T
NG_009060.1:g.29228G>T
ENST00000558518.6:c.1432G>T
ENST00000252444.9:n.1686G>T
ENST00000455727.6:c.928G>T
ENST00000535915.5:c.1309G>T
ENST00000545707.5:c.1051G>T
ENST00000557933.5:c.1432G>T
ENST00000558013.5:c.1432G>T
ENST00000558518.5:c.1432G>T
ENST00000559340.1:n.153G>T
ENST00000560467.1:n.912G>T
NM_000527.4:c.1432G>T
NM_001195798.1:c.1432G>T
NM_001195799.1:c.1309G>T
NM_001195800.1:c.928G>T
NM_001195803.1:c.1051G>T
NM_001195798.2:c.1432G>T
NM_001195799.2:c.1309G>T
NM_001195800.2:c.928G>T
NM_001195803.2:c.1051G>T

Uncertain Significance

Met criteria codes 3
PP3 PM5 PM2
Not Met criteria codes 23
BA1 PP4 PP1 PP2 PM3 PM1 PM4 PM6 PVS1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Familial Hypercholesterolemia VCEP
The NM_000527.5(LDLR):c.1432G>T (p.Gly478Trp) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes PM2, PM5 and PP3 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), so PM2 is met. PM5 - 2 other missense variants in the same codon: (1) NM_000527.5(LDLR):c.1432G>A (p.Gly478Arg) - 1 star, Conflicting interpretations of pathogenicity​: Likely pathogenic(8);Pathogenic(1);Uncertain significance(4) - Pathogenic by these guidelines (FH VCEP training Aug 2021) (2) NM_000527.4(LDLR):c.1433G>A (p.Gly478Glu) - 0 stars, Pathogenic - Likely pathogenic by these guidelines --- 1 Pathogenic variant in the same codon, so PM5 is met. PP3 - REVEL = 0.985. It is above 0.75, so PP3 is met.
Met criteria codes
PP3
REVEL = 0.985. It is above 0.75, so PP3 is met
PM5
2 other missense variants in the same codon: (1) NM_000527.5(LDLR):c.1432G>A (p.Gly478Arg) - 1 star, Conflicting interpretations of pathogenicity​: Likely pathogenic(8);Pathogenic(1);Uncertain significance(4) in ClinVar - Pathogenic by these guidelines (FH VCEP training Aug 2021) (2) NM_000527.4(LDLR):c.1433G>A (p.Gly478Glu) - 0 stars, Pathogenic in ClinVar - Likely pathogenic by these guidelines 1 Pathogenic variant in the same codon, so PM5 is met
PM2
This variant is absent from gnomAD (gnomAD v2.1.1), so PM2 is met
Not Met criteria codes
BA1
This variant is absent from gnomAD (gnomAD v2.1.1), so not met
PP4
there is no case data for this variant, so not met
PP1
there is no case data for this variant, so not met
PP2
not applicable
PM3
there is no case data for this variant, so not met
PM1
variant is missense and meets PM2, but it is not in exon 4 and does not alter Cys, so not met
PM4
variant is missense, so not applicable
PM6
there is no case data for this variant, so not met
PVS1
variant is missense and not in initiation codon, so not applicable
BS4
there is no case data for this variant, so not met
BS3
there are no published functional studies for this variant
BS1
This variant is absent from gnomAD (gnomAD v2.1.1), so not met
BS2
there is no case data for this variant, so not met
BP5
not applicable
BP7
variant is missense, so not applicable
BP2
there is no case data for this variant, so not met
BP3
not applicable
BP4
REVEL = 0.985. It is not below 0.50, so BP4 is not met
BP1
not applicable
PS2
there is no case data for this variant, so not met
PS4
there is no case data for this variant, so not met
PS3
there are no published functional studies for this variant
PS1
no other missense variant leads to the same amino acid change, so not met
Approved on: 2022-01-28
Published on: 2022-07-11
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