rs145787161
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS3_SupportingPM2PVS1PP4PP1_StrongPS4_Moderate
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
Consequence
NM_000527.5 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LDLR | NM_000527.5 | c.2140+1G>A | splice_donor_variant, intron_variant | Intron 14 of 17 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460792Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 726750
GnomAD4 genome
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Pathogenic:13
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subject mutated among 2600 FH index cases screened = 1 -
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. -
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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. -
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0/200 non-FH alleles -
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. -
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Familial hypercholesterolemia Pathogenic:3
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. -
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. -
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 altered 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. Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this LDLR variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 363,995 individuals referred to our laboratory for LDLR testing. ClinVar contains an entry for this variant (Variation ID: 3744). Studies have shown that disruption of this splice site results in aberrant splicing, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 12522687). For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:2
The LDLR c.2140+1G>A variant (rs145787161) is reported in the literature in individuals with hypercholesterolemia (Dron 2020, Gill 2021, Lange 2014, Medeiros 2010, Mozas 2004), and is also reported by multiple laboratories in the ClinVar database (Variation ID: 3744). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 14, which is likely to negatively impact gene function. Based on available information, this variant is considered to be pathogenic. References: Dron JS et al. Six years' experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias. BMC Med Genomics. 2020 Feb 10;13(1):23. PMID: 32041611. Gill PK et al. Combined hyperlipidemia is genetically similar to isolated hypertriglyceridemia. J Clin Lipidol. 2021 Jan-Feb;15(1):79-87. PMID: 33303402. Lange LA et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet. 2014 Feb 6;94(2):233-45. PMID: 24507775. Medeiros AM et al. Update of the Portuguese Familial Hypercholesterolaemia Study. Atherosclerosis. 2010 Oct;212(2):553-8. PMID: 20828696. Mozas P et al. Molecular characterization of familial hypercholesterolemia in Spain: identification of 39 novel and 77 recurrent mutations in LDLR. Hum Mutat. 2004 Aug;24(2):187. PMID: 15241806. -
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) -
LDLR-related disorder Pathogenic:1
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. -
Cardiovascular phenotype Pathogenic:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at