APOBR

apolipoprotein B receptor

Basic information

Region (hg38): 16:28494643-28498964

Links

ENSG00000184730 ∙ NCBI:55911 ∙ OMIM:605220 ∙ HGNC:24087 ∙ Uniprot:Q0VD83 ∙ 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 APOBR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBR 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			24	7	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	10	2

Variants in APOBR

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

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

Position	Type	Phenotype	Significance	ClinVar
16-28494694-C-T		not specified	Uncertain significance (Apr 09, 2024)
16-28494728-G-C		not specified	Uncertain significance (Dec 16, 2023)
16-28495108-G-C		not specified	Uncertain significance (Dec 28, 2023)
16-28495139-C-T		not specified	Uncertain significance (Jul 05, 2024)
16-28495144-C-A		not specified	Uncertain significance (Dec 19, 2022)
16-28495157-G-T		not specified	Uncertain significance (Aug 05, 2024)
16-28495263-A-C		not specified	Uncertain significance (Nov 10, 2024)
16-28495340-C-T		not specified	Uncertain significance (Nov 12, 2024)
16-28495351-G-A		not specified	Uncertain significance (Feb 28, 2024)
16-28495408-A-G		not specified	Likely benign (Apr 01, 2024)
16-28495490-A-G		not specified	Likely benign (Mar 01, 2023)
16-28495501-G-A		not specified	Likely benign (Apr 09, 2024)
16-28495506-A-C		not specified	Uncertain significance (Apr 19, 2024)
16-28495524-G-C		not specified	Uncertain significance (May 03, 2023)
16-28495651-G-A		not specified	Likely benign (Nov 17, 2022)
16-28495658-C-T		not specified	Uncertain significance (Dec 28, 2023)
16-28495682-G-A		not specified	Uncertain significance (Dec 13, 2023)
16-28495763-C-G		not specified	Uncertain significance (May 15, 2023)
16-28495769-G-A		not specified	Uncertain significance (Oct 24, 2023)
16-28495811-G-T		not specified	Uncertain significance (Dec 09, 2023)
16-28495876-G-A		not specified	Uncertain significance (Oct 14, 2023)
16-28495916-C-T		not specified	Uncertain significance (Oct 09, 2024)
16-28495933-G-A		not specified	Uncertain significance (Nov 08, 2024)
16-28495986-C-A			Likely benign (Jun 13, 2018)
16-28495987-G-A		not specified	Likely benign (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBR	protein_coding	protein_coding	ENST00000564831	4	4322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.40e-8	0.996	124312	0	37	124349	0.000149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.420	545	573	0.951	0.0000330	6882
Missense in Polyphen		75	89.333	0.83956		1031
Synonymous	-1.47	274	245	1.12	0.0000160	2278
Loss of Function	2.61	17	33.3	0.511	0.00000150	463

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000865	0.000848
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000110
Finnish	0.00	0.00
European (Non-Finnish)	0.0000851	0.0000803
Middle Eastern	0.000116	0.000110
South Asian	0.0000337	0.0000327
Other	0.000173	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Macrophage receptor that binds to the apolipoprotein B48 (APOB) of dietary triglyceride (TG)-rich lipoproteins (TRL) or to a like domain of APOB in hypertriglyceridemic very low density lipoprotein (HTG-VLDL). Binds and internalizes TRL when out of the context of the macrophage. May provide essential lipids to reticuloendothelial cells. Could also be involved in foam cell formation with elevated TRL and remnant lipoprotein (RLP). Mediates the rapid high-affinity uptake of chylomicrons (CM), HTG- VLDL, and trypsinized (tryp) VLDL devoid of APOE in vitro in macrophages. {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15591219, ECO:0000269|PubMed:9633939}.
• Pathway: VLDL clearance;Plasma lipoprotein clearance;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apobr

Gene ontology

• Biological process: triglyceride metabolic process;lipid transport;receptor-mediated endocytosis;cholesterol metabolic process;very-low-density lipoprotein particle clearance
• Cellular component: plasma membrane;membrane;very-low-density lipoprotein particle;low-density lipoprotein particle;chylomicron
• Molecular function: very-low-density lipoprotein particle receptor activity