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.270T>A (p.Asp90Glu)

CA10584821

251107 (ClinVar)

Gene: LDLR
Condition: hypercholesterolemia, familial
Inheritance Mode: Semidominant inheritance
UUID: c59d43d0-b343-44d0-b9cb-f1b7f782876f

HGVS expressions

NM_000527.5:c.270T>A
NM_000527.5(LDLR):c.270T>A (p.Asp90Glu)
NC_000019.10:g.11102743T>A
CM000681.2:g.11102743T>A
NC_000019.9:g.11213419T>A
CM000681.1:g.11213419T>A
NC_000019.8:g.11074419T>A
NG_009060.1:g.18363T>A
ENST00000558518.6:c.270T>A
ENST00000252444.9:n.524T>A
ENST00000455727.6:c.270T>A
ENST00000535915.5:c.190+2398T>A
ENST00000545707.5:c.270T>A
ENST00000557933.5:c.270T>A
ENST00000557958.1:n.356T>A
ENST00000558013.5:c.270T>A
ENST00000558518.5:c.270T>A
NM_000527.4:c.270T>A
NM_001195798.1:c.270T>A
NM_001195799.1:c.190+2398T>A
NM_001195800.1:c.270T>A
NM_001195803.1:c.270T>A
NM_001195798.2:c.270T>A
NM_001195799.2:c.190+2398T>A
NM_001195800.2:c.270T>A
NM_001195803.2:c.270T>A

Pathogenic

Met criteria codes 6
PP4 PP3 PP1_Strong PS4_Supporting PM2 PM5
Not Met criteria codes 20
PVS1 BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS3 PS1 BA1 PP2 PM6 PM3 PM1 PM4

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.270T>A (p.Asp90Glu) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence PP1_Strong, PM2, PM5, PP3, PP4 and PS4_Supporting as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: PP1_strong - variant segregates with FH phenotype in 11 informative meiosis from 2 families from PMID 20809525 (Marduel et al., 2010): F1: 4 affected relatives have the variant and 3 unaffected relatives do not have the variant; F2: 3 affected relatives have the variant and 1 unaffected relative does not have the variant, so PP1_Strong is met. PM2 - This variant was not identified in gnomAD (gnomAD v2.1.1), so PM2 is met. PM5 - 4 other missense variants is the same codon: - NM_000527.5(LDLR):c.268G>A (p.Asp90Asn) - Likely pathogenic by these guidelines - NM_000527.5(LDLR):c.268G>T (p.Asp90Tyr) - classified as Likely pathogenic​ by the FH VCEP, with these guidelines - NM_000527.5(LDLR):c.269A>C (p.Asp90Ala) - Likely pathogenic by these guidelines - NM_000527.5(LDLR):c.269A>G (p.Asp90Gly) - Pathogenic by these guidelines There is 1 variant classified as Pathogenic by these guidelines, so PM5 is met. PP3 - REVEL = 0.833. It is above 0.75, so PP3 is met. PP4 - variant meets PM2 and was identified in 4 index cases with SB criteria of FH (total and LDL-cholesterol levels above the 95th percentile of a sex and age-matched French population and autosomal dominant transmission of hypercholesterolemia in the family) from PMID 20809525 (Marduel et al., 2010), so PP4 is met. PS4_supporting - variant meets PM2 and was identified in 4 index cases with SB criteria of FH from PMID 20809525 (Marduel et al., 2010), (see PP4 for details), so PS4_Supporting is met.
Met criteria codes
PP4
variant meets PM2 and was identified in 4 index cases with SB criteria of FH (total and LDL-cholesterol levels above the 95th percentile of a sex and age-matched French population and autosomal dominant transmission of hypercholesterolemia in the family) from PMID 20809525 (Marduel et al., 2010), so PP4 is met
PP3
REVEL = 0.833. It is above 0.75, so PP3 is met
PP1_Strong
variant segregates with FH phenotype in 11 informative meiosis from 2 families from PMID 20809525 (Marduel et al., 2010): F1: 4 affected relatives have the variant and 3 unaffected relatives do not have the variant; F2: 3 affected relatives have the variant and 1 unaffected relative does not have the variant (4-3, 3-1 in paper), so PP1_Strong is met
PS4_Supporting
variant meets PM2 and was identified in: - at least 1 index case with DLCN score of definite FH from U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille (SCV000583647.1), France - 4 index cases with SB criteria of FH (total and LDL-cholesterol levels above the 95th percentile of a sex and age-matched French population and autosomal dominant transmission of hypercholesterolemia in the family) from PMID 20809525 (Marduel et al., 2010), France only count 4 cases to avoid double counting, so PS4_Supporting is met
PM2
This variant was not identified in gnomAD (gnomAD v2.1.1), so PM2 is met
PM5
4 other missense variants is the same codon: - NM_000527.5(LDLR):c.268G>A (p.Asp90Asn) - Likely pathogenic by these guidelines - NM_000527.5(LDLR):c.268G>T (p.Asp90Tyr) - classified as Likely pathogenic​ by the FH VCEP, with these guidelines - NM_000527.5(LDLR):c.269A>C (p.Asp90Ala) - Likely pathogenic by these guidelines - NM_000527.5(LDLR):c.269A>G (p.Asp90Gly) - Pathogenic by these guidelines There is 1 variant classified as Pathogenic by these guidelines, so PM5 is met.
Not Met criteria codes
PVS1
variant is missense and not in initiation codon, so not met
BS2
not identified in normolipidemic individuals, so not met
BS4
no lack of segregation was identified, so not met
BS3
no functional studies performed, so not met
BS1
This variant was not identified in gnomAD (gnomAD v2.1.1), so not met
BP5
not applicable
BP7
variant is missense, so not met
BP2
no index cases with more than 1 variant were identified
BP3
not applicable
BP4
REVEL = 0.833. It is not below 0.50, so BP4 is not met
BP1
not applicable
PS2
no de novo occurrence
PS3
no functional studies performed, so not met
PS1
no other missense variant leads to the same amino acid change, so not met
BA1
This variant was not identified in gnomAD (gnomAD v2.1.1), so not met
PP2
not applicable
PM6
no de novo occurrence
PM3
no index cases with more than 1 variant were identified
PM1
variant is not in exon 4 and does not alter Cys, so not met
PM4
variant is missense, so not met
Approved on: 2021-12-30
Published on: 2022-07-11
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.