rs879255201

Variant names:

• chr19-11129520-CGTCTTCCTTTGCCTGGGG-C
• rs879255201
• NM_000527.5:c.2407_2424delTGCCTGGGGGTCTTCCTT

Your query was ambiguous. Multiple possible variants found:

• chr19-11129520-CGTCTTCCTTTGCCTGGGG-C
• chr19-11129520-CGTCTTCCTTTGCCTGGGG-CGTCTTCCTTTGCCTGGGGGTCTTCCTTTGCCTGGGG

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PS3 PM1 PM4 PP5

The NM_000527.5(LDLR):​c.2407_2424delTGCCTGGGGGTCTTCCTT​(p.Cys803_Leu808del) variant causes a conservative inframe deletion change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). ClinVar reports functional evidence for this variant: "SCV004112251: "In vitro functional analysis suggests that this deletion may reduce protein level (Strøm et al. 2015. PubMed ID: 26220972)."" and additional evidence is available in ClinVar. Synonymous variant affecting the same amino acid position (i.e. C803C) has been classified as Likely benign. The gene LDLR is included in the ClinGen Criteria Specification Registry.

• Frequency: Genomes: not found (cov: 31)
• Consequence: LDLR NM_000527.5 conservative_inframe_deletion
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:1
• Conservation: PhyloP100: 4.94
• Publications: 0 publications found

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]

LDLR Gene-Disease associations (from GenCC):

• hypercholesterolemia, familial, 1

  Inheritance: AD, SD Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen
• homozygous familial hypercholesterolemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Specifications for LDLR are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV004112251: "In vitro functional analysis suggests that this deletion may reduce protein level (Strøm et al. 2015. PubMed ID: 26220972)."; SCV004297885: Experimental studies have shown that this variant affects LDLR function (PMID: 26220972).
• PM1: In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 15 uncertain in NM_000527.5
• PM4: Nonframeshift variant in NON repetitive region in NM_000527.5.
• PP5: Variant 19-11129520-CGTCTTCCTTTGCCTGGGG-C is Pathogenic according to our data. Variant chr19-11129520-CGTCTTCCTTTGCCTGGGG-C is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 438330.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000527.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDLR	NM_000527.5	MANE Select	c.2407_2424delTGCCTGGGGGTCTTCCTT	p.Cys803_Leu808del	conservative_inframe_deletion	Exon 17 of 18	NP_000518.1	P01130-1
	LDLR	NM_001195798.2		c.2407_2424delTGCCTGGGGGTCTTCCTT	p.Cys803_Leu808del	conservative_inframe_deletion	Exon 17 of 18	NP_001182727.1	P01130-5
	LDLR	NM_001195799.2		c.2284_2301delTGCCTGGGGGTCTTCCTT	p.Cys762_Leu767del	conservative_inframe_deletion	Exon 16 of 17	NP_001182728.1	P01130-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDLR	ENST00000558518.6	TSL:1 MANE Select	c.2407_2424delTGCCTGGGGGTCTTCCTT	p.Cys803_Leu808del	conservative_inframe_deletion	Exon 17 of 18	ENSP00000454071.1	P01130-1
	LDLR	ENST00000252444.10	TSL:1	c.2665_2682delTGCCTGGGGGTCTTCCTT	p.Cys889_Leu894del	conservative_inframe_deletion	Exon 17 of 18	ENSP00000252444.6	J3KMZ9
	LDLR	ENST00000558013.5	TSL:1	c.2407_2424delTGCCTGGGGGTCTTCCTT	p.Cys803_Leu808del	conservative_inframe_deletion	Exon 17 of 18	ENSP00000453346.1	P01130-5

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
2	-	-	Hypercholesterolemia, familial, 1 (2)
-	1	-	Cardiovascular phenotype (1)
1	-	-	Familial hypercholesterolemia (1)
1	-	-	LDLR-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.9
Mutation Taster		=21/179	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs879255201; hg19: chr19-11240196;