19-11113530-C-G

Position:

• chr19-11113530-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PS3_Supporting PP1_Moderate PM2 PP4 PS4_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000527.5(LDLR):c.1359-5C>G variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PP1_moderate, PM2, PP4, PS3_supporting, PS4_supporting) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012).The supporting evidence is as follows:PP1_moderate: Variant segregates with FH phenotype in 4 informative meioses in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo JorgePM2: PopMax MAF = 0.00001766 (0.001766%) in European (non-Finnish) population exomes (gnomAD v2.1.1). PP3: No REVEL, splicing evaluation required. Functional data on splicing not available.A) variant located at -20 to +3 bases from canonical acceptor splice site,MES scores: canonical site variant = 4.09; canonical acceptor wt = 6.76.Ratio variant/wt canonical acceptor: 4.09/6.76 = 0.605 ---- It is below 0.8Variant is predicted to alter splicing.PP4: Variant meets PM2 and is identified in at least 3 index cases (1 index from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge who meets the Simon Broome Possible criteria; 1 case with Simon-Broome criteria of possible FH in PMID:19411563, and 1 case with Simon-Broome criteria of possible FH in PMID:30876530), after alternative causes of high cholesterol were excludedPS3_supporting: Level 3 assay: PMID 19411563:Heterozygous patients' lymphocytes, RNA assays - result - Retention of intron 9 (p.Ser453Argfs*2)---- functional study is consistent with damaging effect.PS4_supporting: Variant meets PM2 and is identified in 3 index cases (1 index from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge who meets the Simon Broome Possible criteria; 1 case with Simon-Broome criteria of possible FH in PMID:19411563, and 1 case with Simon-Broome criteria of possible FH in PMID:30876530). LINK:https://erepo.genome.network/evrepo/ui/classification/CA10585422/MONDO:0007750/013

• Frequency:
  • Genomes: 𝑓 0.000039 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: LDLR NM_000527.5 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.04278
• Clinical Significance: Likely pathogenic reviewed by expert panel P:7 U:5
• Conservation: PhyloP100: -0.789

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]

MIR6886 (HGNC:50121): (microRNA 6886) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.1359-5C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000558518.6
MIR6886	NR_106946.1	n.57C>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.1359-5C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_000527.5	P3
MIR6886	ENST00000619864.1	n.57C>G		mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0000394 AC: 6 AN: 152142 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.0000120 AC: 3 AN: 250802 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135656

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000177

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.00000753 AC: 11 AN: 1461464 Hom.: 0 Cov.: 39 AF XY: 0.00000825 AC XY: 6 AN XY: 727036

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000112

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: 0.0000331

GnomAD4 genome AF: 0.0000394 AC: 6 AN: 152260 Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4 AN XY: 74444

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000655

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.0000282 Hom.: 0

Bravo AF: 0.0000302

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:7 Uncertain:5

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:5 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 16, 2022	- -
Pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Oct 12, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Uncertain significance, criteria provided, single submitter	research	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	0/75 normolipidaemic Portuguese controls -
Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 27, 2023	The c.1359-5C>G variant of the LDLR gene has been identified in a family with familial hypercholesterolemia (FH). mRNA study from patient cells revealed retention of intron 9, resulting in a frame shift and premature truncation of the protein (PMID: 19411563, 17765246). Loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 21310417). In addition, the variant has been identified in 3 index cases and segregates with FH phenotype in 4 informative meiosis from different laboratories according to ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel. The variant has been reported in ClinVar as likely pathogenic and reviewed by the expert panel (ClinVar: 251808). The variant is rare in the general population according to gnomAD (3/250802). Therefore, the c.1359-5C>G variant of LDLR has been classified as likely pathogenic. -
Likely pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Aug 27, 2022	The NM_000527.5(LDLR):c.1359-5C>G variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PP1_moderate, PM2, PP4, PS3_supporting, PS4_supporting) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PP1_moderate: Variant segregates with FH phenotype in 4 informative meioses in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge PM2: PopMax MAF = 0.00001766 (0.001766%) in European (non-Finnish) population exomes (gnomAD v2.1.1). PP3: No REVEL, splicing evaluation required. Functional data on splicing not available. A) variant located at -20 to +3 bases from canonical acceptor splice site, MES scores: canonical site variant = 4.09; canonical acceptor wt = 6.76. Ratio variant/wt canonical acceptor: 4.09/6.76 = 0.605 ---- It is below 0.8 Variant is predicted to alter splicing. PP4: Variant meets PM2 and is identified in at least 3 index cases (1 index from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge who meets the Simon Broome Possible criteria; 1 case with Simon-Broome criteria of possible FH in PMID: 19411563, and 1 case with Simon-Broome criteria of possible FH in PMID: 30876530), after alternative causes of high cholesterol were excluded PS3_supporting: Level 3 assay: PMID 19411563: Heterozygous patients' lymphocytes, RNA assays - result - Retention of intron 9 (p.Ser453Argfs*2) ---- functional study is consistent with damaging effect. PS4_supporting: Variant meets PM2 and is identified in 3 index cases (1 index from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge who meets the Simon Broome Possible criteria; 1 case with Simon-Broome criteria of possible FH in PMID: 19411563, and 1 case with Simon-Broome criteria of possible FH in PMID: 30876530). -
Likely pathogenic, criteria provided, single submitter	clinical testing	New York Genome Center	Jul 31, 2023	The inherited c.1359-5C>G variant identified in the LDLR gene is an intronic variant at the -5 position within intron 9/17. This variant is found with low frequency in population databases (allele frequency=3.80e-5; gnomADv2.1.1, gnomADv3.1.2, BRAVO-TOPMed, All of Us) suggesting it is not a common benign variant in the populations represented in those databases. This variant has been curated by the Hypercholesterolemia Variant Curation Expert Panel of the Clinical Genome Resource (ClinGen) and deposited in ClinVar as Likely Pathogenic (VarID:251808). This variant has been reported in many affected individuals in the literature [PMID:19411563, 24627126, 30876530, others], and functional studies demonstrate this variant leads to the retention of nucleotide sequences within intron 9 and is predicted to lead to a frameshift (p.(Ser453Argfs*2)) [PMID:19411563]. Given the available evidence, the paternally inherited c.1359-5C>G variant identified in the LDLR gene of this fetus is reported here as Likely Pathogenic -

Familial hypercholesterolemia Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 31, 2023	This variant causes a C>G nucleotide substitution at the -5 position of intron 9 of the LDLR gene. A transcriptional study using RNA from a heterozygous carrier individual has shown that this variant causes a retention of intron 9 and results in a frameshift and premature protein truncation (PMID: 19411563). This variant has been reported in four individuals affected with familial hypercholesterolemia from two unrelated families (PMID: 19411563, 24627126). One affected individual from one of these families was not a carrier (PMID: 19411563). It has been shown that this variant segregates with disease in multiple affected individuals across two families (PMID: 19411563, 24627126; ClinVar SCV000322946.1). This variant has also been reported in one individual affected with myocardial infarction (PMID: 30876530). This variant has been identified in 3/250802 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease. Based on the available evidence, this variant is classified as Likely Pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Sep 27, 2022	This sequence change falls in intron 9 of the LDLR gene. It does not directly change the encoded amino acid sequence of the LDLR protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs531005522, gnomAD 0.002%). This variant has been observed in individual(s) with familial hypercholesterolemia (PMID: 19411563, 24627126). ClinVar contains an entry for this variant (Variation ID: 251808). Studies have shown that this variant results in intron 9 inclusion and introduces a premature termination codon (PMID: 19411563). The resulting mRNA is expected to undergo nonsense-mediated decay. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2023

Published functional studies of patient cDNA showed that the c.1359-5 C>G variant results in an abnormally spliced protein that includes intron 9, and that intron 9 contains an in-frame stop codon resulting in a transcript with premature termination (Bourbon et al., 2009); however, wild type mRNA appears to be expressed at a higher level than variant mRNA, suggesting the c.1359-5 C>G variant may not result in a complete null allele (Bourbon et al., 2009); Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20828696, 22881376, 20964105, 24075752, 30876530, 27821657, 24627126, 31447099, 19411563, 32719484) -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jan 27, 2021

Variant classified as Uncertain Significance - Favor Pathogenic. The c.1359-5G>C variant in LDLR has been reported in 2 Portuguese individuals with Familial hypercholesterolemia (FH) and segregated with disease in 2 affected individuals from 2 families, although in at least 1 of the families segregation was incomplete and 2 affected individuals were not carriers of this variant (Bourbon 2009 PMID: 19411563, Medeiros 2014 PMID:24627126, Gaspar 2019 PMID: 30876530). It has also been identified in 0.002% (2/113226) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 251808). This variant is located in the 3' splice region. Computational tools do not predict a splicing impact, though this information is not predictive enough to rule out pathogenicity. Amplification of patient mRNA by RT-PCR has shown that this variant causes retention of intron 9 and is predicted to result in a frameshift, which alters the protein's amino acid sequence beginning at position 453 and leads to a premature termination codon 1 amino acid downstream (Bourbon 2009 PMID: 19411563). This alteration is then predicted to lead to a truncated or absent protein. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2_Supporting, PS3_Supporting, PS4_Supporting. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.043
dbscSNV1_RF	Benign	0.64
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs531005522; hg19: chr19-11224206;