rs879254770

chr19-11110764-ATGCGAAGG-A

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1_Moderate PM2 PP3 PP5_Very_Strong

The NM_000527.5(LDLR):c.1056_1060+3del variant causes a splice donor, coding sequence change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,240 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. C352C) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: LDLR NM_000527.5 splice_donor, coding_sequence
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:12
• Conservation: PhyloP100: 9.55

Genes affected

LDLR (HGNC:6547): (low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.04607046 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.5, offset of 3, new splice context is: cggGTggga. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 19-11110764-ATGCGAAGG-A is Pathogenic according to our data. Variant chr19-11110764-ATGCGAAGG-A is described in ClinVar as [Pathogenic]. Clinvar id is 251620.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11110764-ATGCGAAGG-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.1056_1060+3del		splice_donor_variant, coding_sequence_variant	7/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.1056_1060+3del		splice_donor_variant, coding_sequence_variant	7/18	1	NM_000527.5	P3

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152178 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461062 Hom.: 0 AF XY: 0.00000138 AC XY: 1 AN XY: 726854

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152178 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74338

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 18, 2023	This variant deletes eight nucleotides spanning the boundary of exon 7 and intron 7 of the LDLR gene, deleting the canonical splice donor site, and creating a premature translation stop signal at the deletion boundary. Use of a downstream cryptic donor would allow use of this stop codon and would result in a protein truncation (p.Cys352*). However in-frame skipping of exon 7 may also occur. To our knowledge RNA studies on this variant have not been reported. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 16389549, 28008010, 32220565, 34037665). This variant has also been observed in compound heterozygous state with a known pathogenic LDLR variant in an individual affected with severe homozygous familial hypercholesterolemia, a phenotype expected of having two deleterious LDLR variants (PMID: 34029164). This variant has been identified in 1/31382 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	Dec 16, 2016	subjects mutated among 2600 FH index cases screened = 4 , family member =1 -
Pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Jun 05, 2017	This c.1056_1060+3del (p.Cys352*) variant has not been observed in our cohort database nor has been detected in the ExAC population database. This variant deletes 8 nucleotides from cDNA postion c.1056 to c.1060+3, which includes the donor splice site of intron 7 of the LDLR gene. Computer algorithm predict the use of an alternative splice site at position c.1060+12_1060+13 and the creation of a non sense variant and a stop codon at amino acid position 352 of the LDLR protein. This variant is thus classified as pathogenic. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 13, 2023	The LDLR c.1056_1060+3del variant disrupts a canonical splice-donor site and interferes with normal LDLR mRNA splicing. It is also predicted to create a premature stop codon (p.Cys352*) that may disrupt normal LDLR protein synthesis. The frequency of this variant in the general population, 0.000032 (1/31382 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. In the published literature, the variant has been reported in multiple individuals with clinical features of familial hypercholesterolemia (PMIDs: 34363016 (2021), 34037665 (2021), 32220565 (2020), 30586733 (2019), 28008010 (2016), 16389549 (2006)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 26, 2021	Not observed at significant frequency in large population cohorts (gnomAD); Deletion involving the last five nucleotides of exon 7 and the first three nucleotides of intron 7, which is predicted to result in aberrant splicing; Affects the LDL-receptor EGF precursor domain A, which contains several cysteine residues critical for correct protein structure (Sudhof et al., 1985; Rudenko et al., 2002); Reported in ClinVar (ClinVar Variant ID#251620); This variant is associated with the following publications: (PMID: 30586733, 16389549, 31447099, 34037665) -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Feb 11, 2022	- -

Familial hypercholesterolemia Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 21, 2023	Variant summary: Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 250660 control chromosomes. c.1056_1060+3delCGAAGGTG has been reported in the literature in individuals affected with Familial Hypercholesterolemia and in an individual with early onset myocardial infarction (Humphries_2006, Khera_2019, Abul-Husn_2016). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 28, 2024	This variant results in the deletion of exon 7 (c.1056_1060+3del) of the LDLR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has been observed in individuals with clinical features of familial hypercholesterolemia (PMID: 16389549, 28008010, 30586733; Invitae). This variant is also known as p.C331fs and p.Cys352fs. ClinVar contains an entry for this variant (Variation ID: 251620). For these reasons, this variant has been classified as Pathogenic. -

Homozygous familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 16, 2017

The c.1056_1060+3del variant in LDLR has been reported in 1 individual with fami lial hypercholesterolemia (FH; Humphries 2006) and in several individuals with F H in ClinVar (Variation ID# 251620). This variant has also been identified in 1/ 8722 African chromosomes by the Genome Aggregation Database (GnomAD, http://gnom ad.broadinstitute.org; dbSNP rs879254770). This frequency is low enough to be co nsistent with the frequency of FH in the general population. This deletion spans the (+/- 1,2) invariant region of the 5' splice consensus sequence and is predi cted to cause altered splicing leading to an abnormal or absent protein. Heteroz ygous loss of function of the LDLR gene is an established disease mechanism in F H. In summary, this variant meets criteria to be classified as pathogenic for FH in an autosomal dominant manner based upon the predicted impact to the protein, presence in multiple affected individuals and very low frequency in the general population. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 21, 2023

The c.1056_1060+3delCGAAGGTG pathogenic mutation results from a deletion of 8 nucleotides between positions 1056 and 1060+3 and involves the canonical splice donor site after coding exon 7 of the LDLR gene. This alteration has been reported in a familial hypercholesterolemia cohort (Humphries SE et al. J. Mol. Med., 2006 Mar;84:203-14). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs879254770; hg19: chr19-11221440;