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

Variant: NM_000527.5(LDLR):c.169G>A (p.Asp57Asn)

CA10584771

251040 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
Link to MONDO
UUID: 7db92565-5287-495d-97ef-45a26dd534ac
Approved on: 2022-08-29
Published on: 2022-12-23

HGVS expressions

NM_000527.5:c.169G>A
NM_000527.5(LDLR):c.169G>A (p.Asp57Asn)
NC_000019.10:g.11100324G>A
CM000681.2:g.11100324G>A
NC_000019.9:g.11211000G>A
CM000681.1:g.11211000G>A
NC_000019.8:g.11072000G>A
NG_009060.1:g.15944G>A
ENST00000558518.6:c.169G>A
ENST00000252444.9:n.423G>A
ENST00000455727.6:c.169G>A
ENST00000535915.5:c.169G>A
ENST00000545707.5:c.169G>A
ENST00000557933.5:c.169G>A
ENST00000557958.1:n.255G>A
ENST00000558013.5:c.169G>A
ENST00000558518.5:c.169G>A
ENST00000560502.5:n.255G>A
NM_000527.4:c.169G>A
NM_001195798.1:c.169G>A
NM_001195799.1:c.169G>A
NM_001195800.1:c.169G>A
NM_001195803.1:c.169G>A
NM_001195798.2:c.169G>A
NM_001195799.2:c.169G>A
NM_001195800.2:c.169G>A
NM_001195803.2:c.169G>A
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Uncertain Significance

Met criteria codes 3
PP4 PP3 PM2
Not Met criteria codes 10
PS3 PS1 PVS1 PM4 PM5 BA1 BS3 BS1 BP3 BP4

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.169G>A (p.Asp57Asn) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes PM2, PP3, and 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: This variant is absent from gnomAD (gnomAD v2.1.1.). So PM2 is met. PP3: REVEL= 0.791. It is above 0.75, so PP3 is met. PP4: Variant meets PM2 and is identified in 1 case fulfilling WHO criteria published in PMID: 20145306 (Chmara et al., 2010). So PP4 is met.
Met criteria codes
PP4
Variant meets PM2 and is identified in 1 case fulfilling WHO criteria published in PMID: 20145306 (Chmara et al., 2010). So PP4 is met.
PP3
REVEL= 0.791. It is above 0.75, so PP3 is met.
PM2
This variant is absent from gnomAD (gnomAD v2.1.1.). So PM2 is met.
Not Met criteria codes
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
Not a null variant
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Two other missense variants in the same codon: -NM_000527.5(LDLR):c.170A>G (p.Asp57Gly) (ClinVar ID 1380181) Uncertain significance by these guidelines -NM_000527.5(LDLR):c.170A>C (p.Asp57Ala) (ClinVar ID 523722) Uncertain significance by these guidelines
BA1
This variant is absent from gnomAD (gnomAD v2.1.1.).
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
This variant is absent from gnomAD (gnomAD v2.1.1.).
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL= 0.791. It is above 0.5
Curation History
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