chr19-11120523-G-A

Position:

• chr19-11120523-G-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS4_Moderate PP1_Strong PS3_Supporting PM2 PVS1 PP4

This summary comes from the ClinGen Evidence Repository: NM_000527.5(LDLR):c.2140+1G>A variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PVS1, PP1_Strong, PM2, PS4_Moderate, PP4 and PS3_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: PVS1 - Variant is in canonical splice site and predicts a frameshift in exon 15.PP1_strong - Variant segregates with FH phenotype in 9 members of 4 families (9 informative meioses).PM2 - No population data was found for this allele in gnomAD (gnomAD v2.1.1).PS4_moderate - Variant meets PM2. Variant identified in 7 unrelated index cases fulfilling validated clinical criteria for FH from different labs.PP4 - Variant meets PM2. Variant found in 7 unrelated index cases fulfilling validated clinical criteria for FH.PS3_supporting - PMID:12522687 - Level 3 assay - study on htz patient's lymphocytes. An additional mRNA transcript of ~730 bp was detected; 214 bp retention of intron 14 causing a premature stop codon 99 amino acids later was the identified using cDNA sequencing. 46% LDLR particle clearance. LINK:https://erepo.genome.network/evrepo/ui/classification/CA023643/MONDO:0007750/013

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: LDLR NM_000527.5 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:19
• Conservation: PhyloP100: 7.97

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 18 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5	c.2140+1G>A		splice_donor_variant, intron_variant		ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.2140+1G>A		splice_donor_variant, intron_variant		1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1460792 Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3 AN XY: 726750

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.00000647 Hom.: 0

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:19

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:13

Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	research	Fundacion Hipercolesterolemia Familiar	Mar 01, 2016	- -
Pathogenic, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	May 10, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2004	- -
Pathogenic, criteria provided, single submitter	research	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	0/200 non-FH alleles -
Pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Jun 18, 2021	NM_000527.5(LDLR):c.2140+1G>A variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PVS1, PP1_Strong, PM2, PS4_Moderate, PP4 and PS3_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: PVS1 - Variant is in canonical splice site and predicts a frameshift in exon 15. PP1_strong - Variant segregates with FH phenotype in 9 members of 4 families (9 informative meioses). PM2 - No population data was found for this allele in gnomAD (gnomAD v2.1.1). PS4_moderate - Variant meets PM2. Variant identified in 7 unrelated index cases fulfilling validated clinical criteria for FH from different labs. PP4 - Variant meets PM2. Variant found in 7 unrelated index cases fulfilling validated clinical criteria for FH. PS3_supporting - PMID:12522687 - Level 3 assay - study on htz patient's lymphocytes. An additional mRNA transcript of ~730 bp was detected; 214 bp retention of intron 14 causing a premature stop codon 99 amino acids later was the identified using cDNA sequencing. 46% LDLR particle clearance. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 29, 2022	- -
Pathogenic, no assertion criteria provided	clinical testing	Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	Jun 10, 2008	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 13, 2018	The LDLR c.2140+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. The c.2140+1G>A variant has been reported in at least three studies and is found in at least four probands with familial hypercholesterolemia in a heterozygous state (Mozas et al. 2004; Medeiros et al. 2010; Hooper et al. 2012). One of these patients also had a second splice site variant (Mozas et al. 2004). The c.2140+1G>A variant is reported at a frequency of 0.000116 in the European American population of the Exome Sequencing Project, but this is based on one allele in a region of good sequence coverage, so the variant is presumed to be rare. Due to the potential impact of splice donor variants, the c.2140+1G>A variant is classified as likely pathogenic for familial hypercholesterolemia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Nov 21, 2021	- -
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	subject mutated among 2600 FH index cases screened = 1 -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 07, 2024	The c.2140+1G>A intronic variant, also known as IVS14+1G>A, of the LDLR gene is located at the canonical donor splice site of intron 14. This variant has been reported in several (>7) individuals affected with Familial Hypercholesterolemia (FH) and segregated with disease in 14 members in a large pedigree (PMID: 12522687, 15241806, 20828696, 22883975, 23054246, 24627126, 27784735, 11313767). In-silico computational prediction tools suggest that the c.2140+1G>A variant likely leads to disturbed splicing (SpliceAI: 0.99), resulting in an aberrant or absence of protein product (PMID: 16199547). cDNA analysis using leukocyte derived mRNA revealed an insertion of a 214-bp intronic sequence between exons 14 and 15 due to activation of a cryptic splicing-donor site, resulting in the creation of a premature stop codon and production of a truncated protein that lacked transmembrane and cytoplasmic domains (PMID: 12522687). Experimental functional studies using heterozygous patient-derived peripheral lymphocytes have shown that this variant causes significant decrease in LDLR expression levels and LDL binding activity (PMID: 12522687). This variant is found to be absent in the general population database, gnomAD and interpreted as likely pathogenic/pathogenic by several ClinVar submitters including the ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel (ClinVar ID: 3744). Therefore, the c.2140+1G>A intronic variant in LDLR gene is classified as pathogenic. -

Familial hypercholesterolemia Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Oct 21, 2023	The c.2140+1G>A intronic variant, also known as IVS14+1G>A, of the LDLR gene is located at the canonical donor splice site of intron 14. This variant has been reported in several (>7) individuals affected with Familial Hypercholesterolemia (FH) and segregated with disease in 14 members in a large pedigree (PMID: 12522687, 15241806, 20828696, 22883975, 23054246, 24627126, 27784735, 11313767). In-silico computational prediction tools suggest that the c.2140+1G>A variant likely leads to disturbed splicing (SpliceAI: 0.99), resulting in an aberrant or absence of protein product (PMID: 16199547). cDNA analysis using leukocyte derived mRNA revealed an insertion of a 214-bp intronic sequence between exons 14 and 15 due to activation of a cryptic splicing-donor site, resulting in the creation of a premature stop codon and production of a truncated protein that lacked transmembrane and cytoplasmic domains (PMID: 12522687). Experimental functional studies using heterozygous patient-derived peripheral lymphocytes have shown that this variant causes significant decrease in LDLR expression levels and LDL binding activity (PMID: 12522687). This variant is found to be absent in the general population database, gnomAD and interpreted as likely pathogenic/pathogenic by several ClinVar submitters including the ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel (ClinVar ID: 3744). Therefore, the c.2140+1G>A intronic variant in LDLR gene is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 15, 2023	This intronic variant is predicted to abolish the canonical splice donor site of intron 14 in the LDLR gene. An experimental RNA study has shown that this variant causes an insertion of a 214-base pair intronic sequence between exons 14 and 15 due to a cryptic splice donor activation, resulting in a frameshift and premature truncation (PMID: 12522687). An additional experimental functional study has shown that this variant causes a significant decrease in LDLR activity (PMID: 12522687). This variant has been reported in over 100 individuals affected with familial hypercholesterolemia (PMID: 15241806, 20828696, 22883975, 23054246, 24507775, 24627126,27784735, 31345425; Color internal data), including over 90 individuals from a large pedigree where the variant has been shown to segregate with disease (PMID: 12522687). 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: 27784735). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 22, 2023	This sequence change affects a donor splice site in intron 14 of the LDLR gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with familial hypercholesterolemia (PMID: 12522687, 15241806, 20828696, 23054246). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3744). Studies have shown that disruption of this splice site results in aberrant splicing and introduces a premature termination codon (PMID: 12522687). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

LDLR-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 23, 2024

The LDLR c.2140+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant is also referred to as IVS14+1G>A in the literature. This variant has been reported in many individuals with familial hypercholesterolemia and segregated with disease in a large family (see, for example, Takada et al 2002. PubMed ID: 12522687; eTable1, Sturm et al 2021. PubMed ID: 34037665, Supplementary Table 6, Marco-Benedí. 2021. PubMed ID: 34456049). RT-PCR studies suggest this variant impacts mRNA splicing (Takada et al 2002. PubMed ID: 12522687). This variant has not been reported in a large population database, indicating this variant is rare. Variants that disrupt the consensus splice donor site in LDLR are expected to be pathogenic. This variant is interpreted as pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Nov 23, 2021

Not observed in large population cohorts (Lek et al., 2016); Canonical splice site variant predicted to result in abnormal gene splicing, which was confirmed by published PCR functional studies showing the insertion of 214 nucleotides into the intronic sequence resulting in a truncated protein product (Takada et al., 2002); Two other splice site variants affecting the same nucleotide (c.2140+1 G>T, c.2140+1 G>C) have been reported in the Human Gene Mutation Database in association with FH (Stenson et al., 2014); Reported in ClinVar (ClinVar Variant ID# 3744; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 31345425, 24507775, 25525159, 12522687, 15241806, 20828696, 14673705, 22883975, 19837725, 32041611, 33303402, 34037665) -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 26, 2022

The c.2140+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 14 of the LDLR gene. This canonical splice site alteration has been reported in individuals with familial hypercholesterolemia (FH) and shown to segregate with the disease in a multi-generational family (Takada D et al. J. Hum. Genet., 2002;47:656-64; Mozas P et al. Hum. Mutat., 2004 Aug;24:187; Medeiros AM et al. Atherosclerosis, 2010 Oct;212:553-8). Moreover, this alteration has been shown to cause aberrant splicing that results in loss of the protein (Takada D et al. J. Hum. Genet., 2002;47:656-64). Additional alterations impacting the same donor site (c.2140+1G>T and c.2140+1G>C) have also been described in FH cases (Peeters AV et al. Mol Cell Probes, 1999 Aug;13:257-60; Heath KE et al. Eur J Hum Genet, 2001 Apr;9:244-52). 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_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.34
CADD	Pathogenic	32
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.88
FATHMM_MKL	Pathogenic	1.0	D
GERP RS		5.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.99		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: rs145787161; hg19: chr19-11231199;