LRP3

LDL receptor related protein 3, the group of Low density lipoprotein receptors

Basic information

Region (hg38): 19:33177603-33208864

Links

ENSG00000130881 ∙ NCBI:4037 ∙ OMIM:603159 ∙ HGNC:6695 ∙ Uniprot:O75074 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			64	1	1	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	64	3	4

Variants in LRP3

This is a list of pathogenic ClinVar variants found in the LRP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-33196745-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-33196763-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-33202848-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-33202884-G-A		not specified	Uncertain significance (Jun 22, 2023)
19-33202920-A-G		not specified	Uncertain significance (Mar 21, 2023)
19-33202926-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-33204646-A-G		not specified	Uncertain significance (Jun 10, 2022)
19-33204744-G-A		not specified	Uncertain significance (Mar 13, 2023)
19-33204756-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-33204795-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-33204816-G-A		not specified	Uncertain significance (Jul 08, 2022)
19-33204835-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-33204849-C-G		not specified	Uncertain significance (May 23, 2023)
19-33205372-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-33205375-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-33205431-G-A		not specified	Uncertain significance (Jun 13, 2024)
19-33205437-C-T		not specified	Uncertain significance (Nov 03, 2022)
19-33205467-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-33205468-G-A		not specified	Uncertain significance (May 15, 2023)
19-33205520-C-T			Benign (May 08, 2018)
19-33205524-C-A		not specified	Uncertain significance (Dec 12, 2023)
19-33205528-C-T		not specified	Uncertain significance (Dec 30, 2023)
19-33205630-A-G		not specified	Uncertain significance (Dec 12, 2023)
19-33205659-C-A		not specified	Uncertain significance (Oct 29, 2021)
19-33205721-C-T			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP3	protein_coding	protein_coding	ENST00000253193	7	30186

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000646	0.995	125714	0	23	125737	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	386	472	0.818	0.0000345	4782
Missense in Polyphen		171	231.88	0.73744		2198
Synonymous	-0.513	221	212	1.04	0.0000169	1590
Loss of Function	2.49	13	26.9	0.483	0.00000145	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.000215	0.000198
East Asian	0.0000604	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000141
Middle Eastern	0.0000604	0.0000544
South Asian	0.00	0.00
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. Its precise role is however unclear, since it does not bind to very low density lipoprotein (VLDL) or to LRPAP1 in vitro.

Recessive Scores

• pRec: 0.152

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.618
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lrp3

Gene ontology

• Biological process: receptor-mediated endocytosis
• Cellular component: clathrin-coated pit;integral component of membrane