LRP1B

LDL receptor related protein 1B, the group of Low density lipoprotein receptors

Basic information

Region (hg38): 2:140231422-142131016

Links

ENSG00000168702 ∙ NCBI:53353 ∙ OMIM:608766 ∙ HGNC:6693 ∙ Uniprot:Q9NZR2 ∙ 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 LRP1B gene.

• Inborn genetic diseases (143 variants)
• not provided (54 variants)
• LRP1B-related condition (4 variants)
• Preeclampsia (1 variants)
• LRP1B-associated developmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP1B 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				12	13	25
missense			144	14	8	166
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					4	4
non coding				1	3	4
Total	0	0	145	27	24

Variants in LRP1B

This is a list of pathogenic ClinVar variants found in the LRP1B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-140233187-T-C		LRP1B-related disorder	Likely benign (Apr 26, 2019)
2-140233241-C-T		not specified	Uncertain significance (Nov 17, 2022)
2-140233299-C-T		LRP1B-related disorder	Likely benign (Feb 28, 2019)
2-140234776-C-A			Benign (Jul 17, 2018)
2-140234778-T-C		LRP1B-related disorder	Benign (Mar 01, 2019)
2-140238223-T-G		not specified	Uncertain significance (Sep 22, 2023)
2-140238235-G-C		not specified	Uncertain significance (Aug 28, 2023)
2-140239445-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-140239476-C-A		not specified	Uncertain significance (Aug 18, 2021)
2-140239517-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-140270252-G-A		not specified	Uncertain significance (Jul 30, 2023)
2-140274437-C-A		not specified	Uncertain significance (Dec 08, 2023)
2-140274452-T-A		LRP1B-related disorder	Benign/Likely benign (Sep 01, 2023)
2-140274491-C-T		not specified	Uncertain significance (Feb 05, 2024)
2-140274517-C-T		not specified	Uncertain significance (Jul 08, 2022)
2-140274518-G-C		not specified	Uncertain significance (Jun 21, 2022)
2-140274519-C-T		LRP1B-related disorder	Benign (Oct 17, 2019)
2-140274598-T-C		not specified	Uncertain significance (Dec 27, 2023)
2-140297827-G-C		LRP1B-related disorder	Likely benign (Jun 17, 2019)
2-140297930-G-T		not specified	Uncertain significance (Dec 13, 2022)
2-140297947-T-G		LRP1B-related disorder	Likely benign (May 21, 2019)
2-140297972-A-G		LRP1B-related disorder	Likely benign (Nov 12, 2019)
2-140314950-C-G		LRP1B-related disorder	Benign (Apr 23, 2019)
2-140314950-C-T		LRP1B-related disorder	Likely benign (Feb 28, 2019)
2-140314988-T-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP1B	protein_coding	protein_coding	ENST00000389484	91	1900279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000253	1.00	125622	0	125	125747	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	2148	2.41e+3	0.890	0.000126	30637
Missense in Polyphen		251	329.9	0.76083		3595
Synonymous	-2.56	936	842	1.11	0.0000458	8063
Loss of Function	10.8	63	245	0.257	0.0000125	3119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.000439	0.000397
East Asian	0.000982	0.000979
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000367	0.000360
Middle Eastern	0.000982	0.000979
South Asian	0.000857	0.000817
Other	0.000552	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.00916
• rvis_EVS: -2.29
• rvis_percentile_EVS: 1.23

Haploinsufficiency Scores

• pHI: 0.623
• hipred: Y
• hipred_score: 0.540
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.203

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrp1b
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: receptor-mediated endocytosis;protein transport
• Cellular component: integral component of membrane;receptor complex
• Molecular function: calcium ion binding