LRP10

LDL receptor related protein 10, the group of Low density lipoprotein receptors

Basic information

Region (hg38): 14:22871740-22881713

Links

ENSG00000197324 ∙ NCBI:26020 ∙ OMIM:609921 ∙ HGNC:14553 ∙ Uniprot:Q7Z4F1 ∙ 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 LRP10 gene.

• not_specified (80 variants)
• not_provided (14 variants)
• LRP10-related_disorder (12 variants)
• Myoepithelial_tumor (1 variants)
• Bladder_exstrophy-epispadias-cloacal_extrophy_complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014045.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			80	8	6	94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	80	13	8

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP10	protein_coding	protein_coding	ENST00000359591	7	9968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.98e-8	0.958	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.407	415	439	0.945	0.0000276	4486
Missense in Polyphen		151	164.1	0.92015		1676
Synonymous	0.0739	178	179	0.993	0.0000100	1643
Loss of Function	2.00	16	27.3	0.587	0.00000158	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000326	0.000326
South Asian	0.000235	0.000229
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable receptor, which is involved in the internalization of lipophilic molecules and/or signal transduction. May be involved in the uptake of lipoprotein APOE in liver (By similarity). {ECO:0000250}.
• Pathway: Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.192
• rvis_EVS: -0.13
• rvis_percentile_EVS: 44.03

Haploinsufficiency Scores

• pHI: 0.199
• hipred: N
• hipred_score: 0.285
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.507

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrp10

Gene ontology

• Biological process: lipid metabolic process;lipid transport;receptor-mediated endocytosis;inner ear development
• Cellular component: clathrin-coated pit;membrane;integral component of membrane
• Molecular function: low-density lipoprotein particle receptor activity