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.

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.

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				5	2	7
missense			33	5	7	45
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	33	10	11

Variants in LRP10

This is a list of pathogenic ClinVar variants found in the LRP10 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-22872119-A-G			Benign (May 13, 2021)
14-22872320-T-G		not specified	Uncertain significance (Jun 29, 2022)
14-22872328-C-T		not specified	Uncertain significance (Feb 05, 2024)
14-22872457-G-C			Benign (May 12, 2021)
14-22872742-C-T		LRP10-related disorder	Benign (May 05, 2021)
14-22872755-C-A		not specified	Uncertain significance (Apr 09, 2024)
14-22872760-C-T			Likely benign (May 01, 2022)
14-22873373-C-T		LRP10-related disorder	Benign (Feb 01, 2023)
14-22873383-G-A		not specified	Uncertain significance (Mar 15, 2024)
14-22873430-C-A		not specified	Uncertain significance (Oct 12, 2022)
14-22875090-G-A		not specified	Likely benign (Dec 21, 2022)
14-22875102-G-A		not specified	Uncertain significance (Jan 26, 2022)
14-22875150-C-T		not specified	Uncertain significance (Dec 20, 2021)
14-22875184-T-A			Likely benign (Aug 01, 2022)
14-22875213-T-C		not specified	Uncertain significance (Jul 14, 2021)
14-22875219-A-T		not specified	Uncertain significance (Mar 08, 2024)
14-22875222-G-A		not specified	Uncertain significance (Dec 09, 2023)
14-22875363-A-G		LRP10-related disorder	Benign (May 05, 2021)
14-22875552-G-A		not specified	Uncertain significance (Jun 01, 2023)
14-22875591-T-C		LRP10-related disorder	Benign (Dec 06, 2019)
14-22875636-C-G		not specified	Uncertain significance (Apr 21, 2022)
14-22875639-C-T		LRP10-related disorder	Benign (Jun 17, 2019)
14-22875648-G-A		not specified	Uncertain significance (Jul 13, 2021)
14-22875652-G-A		not specified	Uncertain significance (Oct 17, 2023)
14-22875693-G-A		not specified	Uncertain significance (Nov 01, 2022)

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