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.

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.

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				3		3
missense			36	3	1	40
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	6	2

Variants in LRP12

This is a list of pathogenic ClinVar variants found in the LRP12 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-104490707-TC-T			Uncertain significance (Feb 21, 2020)
8-104490738-C-T			Likely benign (May 01, 2024)
8-104490771-G-A			Likely benign (Dec 01, 2022)
8-104490869-A-G			Benign (Mar 01, 2024)
8-104490903-A-C		Inborn genetic diseases	Uncertain significance (Nov 08, 2021)
8-104490949-T-A		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
8-104490971-T-C		Inborn genetic diseases	Uncertain significance (May 03, 2023)
8-104491026-T-C		Inborn genetic diseases	Uncertain significance (May 20, 2024)
8-104491032-G-A		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
8-104491059-G-A		Inborn genetic diseases	Uncertain significance (Jun 12, 2023)
8-104491085-C-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
8-104491086-G-A		LRP12-related disorder	Uncertain significance (Jun 27, 2024)
8-104491151-C-T		Inborn genetic diseases	Uncertain significance (May 10, 2024)
8-104491187-A-C		Inborn genetic diseases	Uncertain significance (Nov 28, 2023)
8-104491202-G-A		Inborn genetic diseases	Uncertain significance (Jun 30, 2022)
8-104491366-G-A			Likely benign (Nov 01, 2023)
8-104491533-C-T		Inborn genetic diseases	Uncertain significance (Aug 30, 2022)
8-104495159-T-C		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
8-104497093-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
8-104497110-T-C		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
8-104497336-C-T		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
8-104497345-T-G		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
8-104497434-C-T		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
8-104497472-A-G			Likely benign (Aug 01, 2024)
8-104497489-A-C		LRP12-related disorder	Benign (May 01, 2024)

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