LRP12

LDL receptor related protein 12, the group of Low density lipoprotein receptors

Basic information

Region (hg38): 8:104489231-104589258

Links

ENSG00000147650 ∙ NCBI:29967 ∙ OMIM:618299 ∙ HGNC:31708 ∙ Uniprot:Q9Y561 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oculopharyngodistal myopathy 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oculopharyngodistal myopathy 1; Amyotrophic lateral sclerosis 28	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	31332380; 37339631

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRP12 gene.

• Inborn_genetic_diseases (84 variants)
• not_provided (12 variants)
• Long_QT_syndrome_2 (2 variants)
• Oculopharyngodistal_myopathy_1 (2 variants)
• Amyotrophic_lateral_sclerosis_28 (2 variants)
• LRP12-related_disorder (2 variants)
• Hereditary_breast_ovarian_cancer_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRP12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013437.5. 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			1	3		4
missense			92	4	1	97
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	95	7	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRP12	protein_coding	protein_coding	ENST00000276654	7	99794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00201	125721	0	17	125738	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	397	477	0.832	0.0000250	5641
Missense in Polyphen		152	219.61	0.69212		2551
Synonymous	-0.896	179	164	1.09	0.00000839	1663
Loss of Function	4.92	4	35.8	0.112	0.00000205	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. May act as a tumor suppressor. {ECO:0000269|PubMed:12809483}.
• 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: 0.197

Intolerance Scores

• loftool: 0.0876
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.19

Haploinsufficiency Scores

• pHI: 0.830
• hipred: Y
• hipred_score: 0.640
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrp12

Gene ontology

• Biological process: neuron migration;endocytosis;receptor-mediated endocytosis;signal transduction;neuron projection development;regulation of growth
• Cellular component: integral component of plasma membrane;clathrin-coated pit;integral component of membrane
• Molecular function: low-density lipoprotein particle receptor activity;protein binding