rs879255051

Positions:

• chr19-11120091-G-A
• chr19-11120091-G-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000527.5(LDLR):​c.1846-1G>A variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,614,010 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: LDLR NM_000527.5 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:15
• Conservation: PhyloP100: 9.78

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: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 5.2, offset of 1, new splice context is: ttccttgctgcctgtttaAGaca. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-11120091-G-A is Pathogenic according to our data. Variant chr19-11120091-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 252079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11120091-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5	c.1846-1G>A		splice_acceptor_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.1846-1G>A		splice_acceptor_variant, intron_variant		1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152190 Hom.: 0 Cov.: 33

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: 0.00000274 AC: 4 AN: 1461820 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 727216

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152190 Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1 AN XY: 74342

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

Alfa AF: 0.0000936 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:15

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:8

Pathogenic, criteria provided, single submitter	research	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	0/220 non-FH alleles -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	-	- -
Pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation	Nov 05, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jul 29, 2024	This variant causes a G to A nucleotide substitution at the -1 position of intron 12 of the LDLR gene. This variant is also known as FH-Tunis and FH-Avellino-2 in the literature. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Functional RNA studies have shown that this variant produces three mutant transcripts, all of which cause the creation of frameshifts and premature translation stop signals, which are expected to result in an absent or non-functional protein products (PMID: 8697568, 9974426). A functional study using cultured fibroblasts derived from a homozygous carrier individual has shown that this variant causes a residual <2% LDLR activity (PMID: 1301956). This variant has been reported in over 40 individuals affected with familial hypercholesterolemia (PMID: 1301956 , 8697568, 8828981, 9712531, 9974426, 10978268, 11317362, 12492446, 15359125, 16542394, 19026292, 19446849, 20828696, 27765764, 31491741, 32331935, 33740630, 33955087, 34100221, 34297352, 34456200, 36507290). This variant has also been observed in homozygous state in several individuals affected with severe homozygous familial hypercholesterolemia (PMID: 1301956, 11317362, 32977124). It has been shown that this variant segregates with disease in multiple affected individuals across multiple families (PMID: 8828981, 10978268, 16542394, 34100221). This variant has been identified in 1/31408 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	Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II	May 24, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 12, 2023	The LDLR c.1846-1G>A variant results in the substitution of a guanine within the consensus splice acceptor site with adenosine, which is predicted to result in splicing defects. Across a selection of the available literature, this variant has been identified in a heterozygous state in 23 unrelated individuals with familial hypercholesterolemia (PMID: 8828981; 30710474; 31491741; 33955087; 33740630). This variant is not observed at a significant frequency in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. Based on the available evidence, the c.1846-1G>A variant is classified as pathogenic for familial hypercholesterolemia. -

Familial hypercholesterolemia Pathogenic:3

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Feb 11, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 15, 2024	This sequence change affects an acceptor splice site in intron 12 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%). Disruption of this splice site has been observed in individuals with hypercholesterolemia (PMID: 8828981, 11317362, 11737238, 15359125, 16542394, 20828696). ClinVar contains an entry for this variant (Variation ID: 252079). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 03, 2020	Variant summary: LDLR c.1846-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: 4/4 tools predict that the variant abolishes or weakens a 3' acceptor site. Several publications report experimental evidence that this variant affects mRNA splicing (examples-Hobbs_1992, Bertolini_1999). The variant allele was found at a frequency of 3.2e-05 in 31408 control chromosomes (gnomAD genomes). c.1846-1G>A has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (examples- Hobbs_1992, Jensen_1996, Bertolini_1999, Kim_2004, Madeiros_2014). These data indicate that the variant is very likely to be associated with disease. The variant has also been referred to in the literature as "FH-Tunis" and FH-Avellino-2". Several publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal LDL-receptor activity (Hobbs_1992). Five ClinVar submitters (evaluation after 2014) have cited the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	LDLR: PVS1, PM2, PS4:Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2022	Not observed at a significant frequency in large population cohorts (gnomAD); Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate this variant results in significantly reduced receptor activity (Hobbs et al., 1992; Jensen et al., 1996; Bertolini et al., 1999); Different variants at this splice acceptor site (c.1846-1 G>C, c.1846-2 A>C) have been reported in the Human Gene Mutation Database in association with FH (HGMD); This variant is associated with the following publications: (PMID: 11317362, 15359125, 25525159, 8828981, 1301956, 9974426, 11737238, 16542394, 20828696, 24627126, 30586733, 31491741, 32977124, 32041611, 32331935, 33740630, 34037665) -

Homozygous familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 06, 2019

The c.1846-1G>A variant in LDLR has been reported in more than 16 individuals with familial hypercholesterolemia (FH) and segregated with disease in at least 13 affected individuals from 9 families (Jensen 1996, Nissen 1998, Bertolini 1999, Descamps 2001, Brusgaard 2006). It has also been identified in 1/8714 African chromosomes by gnomAD (http://gnomad.broadinstitute.org) and has been reported in ClinVar (Variation ID: 252079). This variant occurs within the canonical splice site (+/- 1,2) and sequencing of mRNA from patient cells has shown that this variant causes abnormal splicing, which is predicted to lead to an abnormal or absent protein (Jensen 1996, Bertolini 1999). Loss of function of the LDLR gene is an established disease mechanism in autosomal dominant FH. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant FH. ACMG/AMP criteria applied: PVS1, PS3, PS4, PP1_Strong, PM2. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 02, 2023

The c.1846-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide before coding exon 13 of the LDLR gene. This mutation has been reported in a number of patients with familial hypercholesterolemia, and has segregated with disease in families (Hobbs HH et al. Hum Mutat. 1992;1:445-66; Jensen HK et al. Clin Genet. 1996;49:175-9; Bertolini S et al. Arterioscler. Thromb Vasc Biol. 1999;19:408-18; Descamps OS et al. Eur J Clin Invest. 2001;31:958-65; Kim JH et al. Mol Cells. 2004 Aug;18:63-70; Medeiros AM et al. Atherosclerosis. 2010;212:553-8). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. 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 classified 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	0.35
CADD	Pathogenic	35
DANN	Uncertain	1.0
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	0.98
FATHMM_MKL	Pathogenic	0.99	D
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.91
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.91		Position offset: 20
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: rs879255051; hg19: chr19-11230767;