LRP11

LDL receptor related protein 11, the group of Low density lipoprotein receptors

Basic information

Region (hg38): 6:149818757-149864359

Links

ENSG00000120256 ∙ NCBI:84918 ∙ ∙ HGNC:16936 ∙ Uniprot:Q86VZ4 ∙ 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 LRP11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP11 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						0
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in LRP11

This is a list of pathogenic ClinVar variants found in the LRP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149826317-A-G		not specified	Uncertain significance (Nov 09, 2021)
6-149826344-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-149826347-G-A		not specified	Uncertain significance (Dec 03, 2021)
6-149836087-G-A		not specified	Uncertain significance (Jun 03, 2022)
6-149836127-C-T		not specified	Likely benign (Nov 07, 2023)
6-149836167-C-A		not specified	Uncertain significance (Sep 25, 2023)
6-149837370-G-C		not specified	Uncertain significance (May 23, 2023)
6-149837429-G-C		not specified	Uncertain significance (Feb 21, 2024)
6-149843004-G-A		not specified	Uncertain significance (Oct 12, 2021)
6-149843052-C-G		not specified	Uncertain significance (Jul 14, 2021)
6-149853019-G-A		not specified	Uncertain significance (Oct 10, 2023)
6-149853053-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-149853072-G-T		not specified	Uncertain significance (Apr 22, 2022)
6-149853079-C-T		not specified	Uncertain significance (Dec 22, 2023)
6-149853098-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-149853099-G-C		not specified	Uncertain significance (Nov 12, 2021)
6-149863414-G-C		not specified	Uncertain significance (Apr 12, 2024)
6-149863434-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-149863444-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-149863450-C-G		not specified	Uncertain significance (Sep 22, 2022)
6-149863477-T-C		not specified	Uncertain significance (Oct 25, 2023)
6-149863564-G-A		not specified	Uncertain significance (Mar 08, 2024)
6-149863612-C-G		not specified	Uncertain significance (Jan 23, 2024)
6-149863752-G-A		not specified	Uncertain significance (Feb 27, 2024)
6-149863935-C-T		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP11	protein_coding	protein_coding	ENST00000239367	7	46266

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00398	0.989	125708	0	37	125745	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.785	192	225	0.853	0.0000125	3108
Missense in Polyphen		69	82.521	0.83615		1099
Synonymous	0.372	95	99.7	0.953	0.00000623	1079
Loss of Function	2.35	7	17.7	0.396	0.00000104	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000669	0.000669
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000223	0.000217
South Asian	0.000131	0.000131
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.247
• hipred: N
• hipred_score: 0.403
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.493

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrp11

Gene ontology

• Biological process: response to heat;response to cold;response to water deprivation;response to mechanical stimulus;multicellular organismal response to stress;response to immobilization stress;response to starvation
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: phosphoprotein binding