chr19-11128005-C-A

Variant names:

• chr19-11128005-C-A
• rs875989942
• NM_000527.5:c.2312-3C>A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000527.5(LDLR):​c.2312-3C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: LDLR NM_000527.5 splice_region, intron
• Scores: Splicing: ADA: 0.9919
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11 U:1
• Conservation: PhyloP100: 0.986

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 19-11128005-C-A is Pathogenic according to our data. Variant chr19-11128005-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 226391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11128005-C-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDLR	NM_000527.5	c.2312-3C>A		splice_region_variant, intron_variant	Intron 15 of 17	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.2312-3C>A		splice_region_variant, intron_variant	Intron 15 of 17	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461694 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727156

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

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 Cov.: 31

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:7 Uncertain:1

Oct 22, 2018

Department of Human Genetics, Laborarztpraxis Dres. Walther, Weindel und Kollegen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The mutation leads to a change in the splice acceptor in intron 15 of the LDLR gene. It has already been described in the literature, detected in patients with familial hypercholesterolemia, and associated with elevated cholesterol and LDL-C levels. In in vitro models, the mutation leads to almost complete loss of LDL receptor activity. We observed this mutation in a patient with TC up to 520 mg/dl and LDL-C approx 420 mg/dl at the age of 45 years. PMID: 11317362, 21865347 -

Mar 25, 2016

LDLR-LOVD, British Heart Foundation

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: literature only

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Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Jun 17, 2019

Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia

Significance: Uncertain significance

Review Status: flagged submission

Collection Method: research

- -

Jul 24, 2009

Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 23, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a C to A nucleotide substitution at the -3 position of intron 15 of the LDLR gene. Functional RNA studies have shown that this variant causes in-frame skipping of exon 16, resulting in the loss of the 26-amino acid transmembrane functional domain (PMID: 11317362). In vitro functional studies using EBV-transformed B-lymphocytes have shown that this variant causes a significant reduction in residual LDLR activity (PMID: 20045108, 21865347). This variant has been reported in over 100 individuals affected with familial hypercholesterolemia (PMID: 11317362, 11668640, 12417285, 14624402, 16115486, 18718593, 25014035, 28353356, 28179607, 30710474, 32331935, 33740630). It has been shown that this variant segregates with disease in multiple affected individuals across multiple families (PMID: 11317362, 11668640, 14624402, 16115486). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Mar 01, 2016

Laboratory of Genetics and Molecular Cardiology, University of São Paulo

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

May 24, 2021

Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Reduced activity, in stimulated T-lymphocytes and EBV-transformed B-lymphocytes. -

Familial hypercholesterolemia Pathogenic:2

Sep 06, 2016

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The LDLR c.2312-3C>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant, and 5/5 splicing algorithms predict this variant to reduce the splice acceptor site strength. LDLR residual activity on stimulated T-lymphocytes from multiple heterozygous patients were approximately 50% of normal activity, suggesting that this variant results in little to no residual activity. This variant was not found in large and broad populations from ExAC. It has been reported as one of the common pathogenic variants that causes FH. Furthermore, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely pathogenic/pathogenic. Taken together, this variant is classified as pathogenic. -

Jul 20, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 15 of the LDLR gene. It does not directly change the encoded amino acid sequence of the LDLR protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with familial hypercholesterolemia (PMID: 11317362, 31491741). ClinVar contains an entry for this variant (Variation ID: 226391). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. -

not provided Pathogenic:1

May 22, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate skipping of exon 16 and reduced LDLR activity (PMID: 11317362, 21865347); Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); This variant is associated with the following publications: (PMID: 11317362, 21865347, 25525159, 18718593, 11668640, 30710474, 32331935, 32994617, 12628589, 12417285, 14624402, 16627557, 16115486, 28965616, 31345425, 31491741, 34040191, 33740630, 34756585, 34297352) -

Cardiovascular phenotype Pathogenic:1

Sep 03, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2312-3C>A intronic variant results from a C to A substitution 3 nucleotides upstream from coding exon 16 in the LDLR gene. This alteration has been detected in numerous individuals with familial hypercholesterolemia (FH) from a variety of ethnic backgrounds, and segregation with disease has been reported in multiple families (Liguori R et al. Hum. Mutat., 2001 May;17:433; García-García AB et al. Hum. Mutat., 2001 Nov;18:458-9; Pisciotta L et al. Atherosclerosis, 2005 Sep;182:153-9; Miyake Y et al. Atherosclerosis, 2009 Mar;203:153-60; Rubba P et al. Eur J Prev Cardiol, 2017 Jul;24:1051-1059). In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. Functional studies have demonstrated skipping of exon 16, with the in-frame deletion of 26 amino acids, and reduced LDLR activity to approximately 50% of wild-type (Romano M et al. Atherosclerosis, 2010 Jun;210:493-6). This nucleotide position is highly conserved in available vertebrate species. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Pathogenic	0.77
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.22		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs875989942; hg19: chr19-11238681;