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

  • See Evidence submitted by expert panel for details.

Variant: NM_000527.5(LDLR):c.3G>T (p.Met1Ile)

CA10584721

250969 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: d6e0032f-77ff-4e94-ad24-e9f089ef4990

HGVS expressions

NM_000527.5:c.3G>T
NM_000527.5(LDLR):c.3G>T (p.Met1Ile)
NC_000019.10:g.11089551G>T
CM000681.2:g.11089551G>T
NC_000019.9:g.11200227G>T
CM000681.1:g.11200227G>T
NC_000019.8:g.11061227G>T
NG_009060.1:g.5171G>T
ENST00000558518.6:c.3G>T
ENST00000455727.6:c.3G>T
ENST00000535915.5:c.3G>T
ENST00000545707.5:c.3G>T
ENST00000557933.5:c.3G>T
ENST00000557958.1:n.89G>T
ENST00000558013.5:c.3G>T
ENST00000558518.5:c.3G>T
ENST00000560502.5:n.89G>T
NM_000527.4:c.3G>T
NM_001195798.1:c.3G>T
NM_001195799.1:c.3G>T
NM_001195800.1:c.3G>T
NM_001195803.1:c.3G>T
NM_001195798.2:c.3G>T
NM_001195799.2:c.3G>T
NM_001195800.2:c.3G>T
NM_001195803.2:c.3G>T
NR_163945.1:n.109C>A

Likely Pathogenic

Met criteria codes 5
PP4 PP1 PVS1_Moderate PM5 PM2
Not Met criteria codes 8
PS3 PS1 BP7 BA1 PM4 BS4 BS3 BS1

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.3G>T (p.Met1Ile) variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM2, PVS1_Moderate, PM5, PP1, 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 - variant is absent from gnomAD (v2.1.1). PVS1_Moderate – variant is predicted to affect the initiation codon. PP1- variant segregates with phenotype in 2 informative meioses in 1 family (Centre for Cardiovascular Surgery and Transplantation - 1 family: 2 affected relatives with the variant). PP4 - variant meets PM2 and is identified in 1 case who met clinical criteria for FH after alternative causes for high cholesterol were excluded. PM5 - Three other missense variants at this same codon have been reported, and one is Pathogenic: 1) NM_000527.5(LDLR):c.1A>C (p.Met1Leu) – Pathogenic by these guidelines. 2) NM_000527.5(LDLR):c.1A>G (p.Met1Val) - Likely pathogenic by these guidelines. 3) NM_000527.4(LDLR):c.2T>C (p.Met1Thr) - Likely pathogenic by these guidelines. Note: One other variant resulting in the same amino acid change at this codon has been reported: 1) NM_000527.4(LDLR):c.3G>A (p.Met1Ile) - Likely pathogenic by these guidelines. -PS1 is not applicable as such variants must be Pathogenic.
Met criteria codes
PP4
Variant meets PM2 and is identified in 1 case who met clinical criteria for FH after alternative causes for high cholesterol were excluded.
PP1
Variant segregates with phenotype in 2 informative meioses in 1 family (Centre for Cardiovascular Surgery and Transplantation - 1 family: 2 affected relatives with the variant)
PVS1_Moderate
Variant is predicted to affect the initiation codon.
PM5
Three other missense variants at this same codon have been reported, and one is Pathogenic: 1) NM_000527.5(LDLR):c.1A>C (p.Met1Leu) – Pathogenic by these guidelines. 2) NM_000527.5(LDLR):c.1A>G (p.Met1Val) - Likely pathogenic by these guidelines. 3) NM_000527.4(LDLR):c.2T>C (p.Met1Thr) - Likely pathogenic by these guidelines.
PM2
Variant is absent from gnomAD (v2.1.1).
Not Met criteria codes
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
Note: One other variant resulting in the same amino acid change at this codon has been reported: 1) NM_000527.4(LDLR):c.3G>A (p.Met1Ile) - Likely pathogenic by these guidelines. -PS1 not applicable as such variants must be Pathogenic.
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-01-22
Published on: 2022-04-22
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