19-11100222-G-C

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.68-1G>C variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LDLR NM_000527.5 splice_acceptor
• Scores: Splicing: ADA: 0.9996
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 2.32

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 0.0472319 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.3, offset of 10, new splice context is: tctctctcactgggcgacAGatg. Cryptic site results in frameshift 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: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 19-11100222-G-C is Pathogenic according to our data. Variant chr19-11100222-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 251005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11100222-G-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.68-1G>C		splice_acceptor_variant		ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.68-1G>C		splice_acceptor_variant		1	NM_000527.5	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	curation;literature only	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 23, 2017

The c.68-1 G>C variant in the LDLR gene has been identified in a homozygous state in one individual with severe hypercholesterolemia and tendon xnathomas. Three maternal relatives were heterozygous for the variant and had serum choleterol levels consistent with heterozygous FH (HeFH). Cultured fibroblasts from the proband showed null LDLR protein synthesis. Additionally, functional mRNA studies supported destruction of the canonical splice acceptor site in intron 1, and utilization of a cryptic acceptor site downstream of exon 2 (Maruyama et al. 1998). This variant was also published in an individual with clinical HeFH, who also harbored a rare variant in the PCSK9 gene (Ohta et al., 2016). This variant is predicted to lead to either an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Other splice site variants in the LDLR gene, including c.68-2 A>T and c.68-2 A>G, have been reported in HGMD in association with FH (Stenson et al., 2014). Furthermore, the c.68-1 G>C variant is not observed in large population cohorts (Lek et al., 2016). -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 21, 2018

The c.68-1G>C intronic pathogenic mutation results from a G to C substitution one nucleotide upstream from coding exon 2 of the LDLR gene, and is located in the region of the ligand binding 1 domain. This variant has been reported in a homozygous Japanese female from consanguineous parents, who had hypercholesterolemia and tendon xanthomas, as well as in an Italian family with heterozygous familial hypercholesterolemia, and in a Japanese female with hypercholesterolemia who also harbored a PCSK9 variant (Maruyama T et al. Hum. Mutat., 1998;11:480-1; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8; Ohta N et al. J Clin Lipidol 2016 Jan;10:547-555.e5). Limited functional studies in fibroblasts from the homozygous individual reportedly showed no LDLR protein was produced, while RNA studies suggested use of a downstream cryptic acceptor site caused a frameshift leading to a premature stop codon (Maruyama T et al. Hum. Mutat., 1998;11:480-1). 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. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 28, 2023

This sequence change affects an acceptor splice site in intron 1 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 not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with familial hypercholesterolemia (PMID: 10200052; Invitae). ClinVar contains an entry for this variant (Variation ID: 251005). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.77
Cadd	Pathogenic	26
Dann	Benign	0.65
Eigen	Benign	0.17
Eigen_PC	Benign	-0.17
FATHMM_MKL	Benign	0.44	N
MutationTaster	Benign	0.94	N;N;N;N;N;N;N
GERP RS		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.73
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.92		Position offset: 11
DS_AL_spliceai		1.0		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs879254397; hg19: chr19-11210898;