19-11100222-G-C

Variant names:

• chr19-11100222-G-C
• rs879254397
• NM_000527.5:c.68-1G>C

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000527.5(LDLR):​c.68-1G>C variant causes a splice acceptor, intron 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, intron
• Scores: Splicing: ADA: 0.9996
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 2.32
• Publications: 2 publications found

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]

LDLR Gene-Disease associations (from GenCC):

• hypercholesterolemia, familial, 1

  Inheritance: AD, SD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, ClinGen
• homozygous familial hypercholesterolemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.04761905 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
• PP5: Variant 19-11100222-G-C is Pathogenic according to our data. Variant chr19-11100222-G-C is described in ClinVar as Pathogenic. ClinVar VariationId is 251005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000527.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDLR	NM_000527.5	MANE Select	c.68-1G>C		splice_acceptor intron	N/A	NP_000518.1
	LDLR	NM_001195798.2		c.68-1G>C		splice_acceptor intron	N/A	NP_001182727.1
	LDLR	NM_001195799.2		c.68-1G>C		splice_acceptor intron	N/A	NP_001182728.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDLR	ENST00000558518.6	TSL:1 MANE Select	c.68-1G>C		splice_acceptor intron	N/A	ENSP00000454071.1
	LDLR	ENST00000252444.10	TSL:1	c.326-1G>C		splice_acceptor intron	N/A	ENSP00000252444.6
	LDLR	ENST00000558013.5	TSL:1	c.68-1G>C		splice_acceptor intron	N/A	ENSP00000453346.1

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

Mar 25, 2016

LDLR-LOVD, British Heart Foundation

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: literature only

Mar 01, 2016

Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation;literature only

not provided Pathogenic:1

Oct 23, 2017

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Jun 21, 2018

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Nov 28, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 v4.9

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
PhyloP100		2.3
GERP RS		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=0/100	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs879254397; hg19: chr19-11210898;