APOB apolipoprotein B [Homo sapiens (human)] - Gene

Summary

Official Symbol: APOBprovided by HGNC
Official Full Name: apolipoprotein Bprovided by HGNC
Primary source: HGNC:HGNC:603
See related: Ensembl:ENSG00000084674 MIM:107730; AllianceGenome:HGNC:603
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FLDB; FCHL2; LDLCQ4; apoB-48; apoB-100
Summary: This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins (LDL), and is the ligand for the LDL receptor. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Dec 2019]
Expression: Biased expression in liver (RPKM 415.6), small intestine (RPKM 182.7) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 2p24.1

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (21001429..21044073, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (21034648..21077293, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (21224301..21266945, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Analysis of the association between testosterone and cardiovascular disease potential risk factor apolipoprotein B in adult males without cancer: national health and nutrition examination survey 2011-2016.
Title: Analysis of the association between testosterone and cardiovascular disease potential risk factor apolipoprotein B in adult males without cancer: national health and nutrition examination survey 2011-2016.
ApoA1, ApoB, ApoA1/B for Pathogenic Prediction of Chronic Obstructive Pulmonary Disease Complicated by Acute Lower Respiratory Tract Infection: A Cross-Sectional Study.
Title: ApoA1, ApoB, ApoA1/B for Pathogenic Prediction of Chronic Obstructive Pulmonary Disease Complicated by Acute Lower Respiratory Tract Infection: A Cross-Sectional Study.
Haplotype analysis and linkage disequilibrium of ApoB gene polymorphisms and its relationship with hyperlipidemia in patients with acne vulgaris.
Title: Haplotype analysis and linkage disequilibrium of ApoB gene polymorphisms and its relationship with hyperlipidemia in patients with acne vulgaris.
Association of APO B gene polymorphisms with the development of myocardial infarction in Pakistani population.
Title: Association of APO B gene polymorphisms with the development of myocardial infarction in Pakistani population.
Integrative bioinformatics analysis identifies APOB as a critical biomarker in coronary in-stent restenosis.
Title: Integrative bioinformatics analysis identifies APOB as a critical biomarker in coronary in-stent restenosis.
The relationship between genetic liver fat and coronary heart disease is explained by apoB-containing lipoproteins.
Title: The relationship between genetic liver fat and coronary heart disease is explained by apoB-containing lipoproteins.
Screening and verifying the mutations in the LDLR and APOB genes in a Chinese family with familial hypercholesterolemia.
Title: Screening and verifying the mutations in the LDLR and APOB genes in a Chinese family with familial hypercholesterolemia.
Associations between apolipoprotein B and bone mineral density: a population-based study.
Title: Associations between apolipoprotein B and bone mineral density: a population-based study.
Association of oxidized ApoB and oxidized ApoA-I with high-risk coronary plaque features in cardiovascular disease.
Title: Association of oxidized ApoB and oxidized ApoA-I with high-risk coronary plaque features in cardiovascular disease.
Apo B-48 gene expression and low-density lipoprotein as a factor for increased insulin resistance and severity of acne.
Title: Apo B-48 gene expression and low-density lipoprotein as a factor for increased insulin resistance and severity of acne.

Submit: New GeneRIF Correction See all GeneRIFs (616)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Professional guidelines

Description
Professional guideline ACMG 2013 The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in APOB that are pathogenic or expected to be pathogenic. GuidelinePubMed

Associated conditions

Description	Tests
Familial hypercholesterolemia MedGen: C0020445 GeneReviews: Familial Hypercholesterolemia	Compare labs
Familial hypobetalipoproteinemia 1 MedGen: C4551990 OMIM: 615558 GeneReviews: APOB-Related Familial Hypobetalipoproteinemia	Compare labs
Hypercholesterolemia, autosomal dominant, type B MedGen: C1704417 OMIM: 144010 GeneReviews: Familial Hypercholesterolemia	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-04-09) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-04-09) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Bipolar disorder with comorbid binge eating history: A genome-wide association study implicates APOB. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 30 loci contribute to polygenic dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Familial defective apolipoprotein B-100 and increased low-density lipoprotein cholesterol and coronary artery calcification in the old order amish. EBI GWAS Catalog EBI GWAS CatalogPubMed
Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants influencing circulating lipid levels and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association of lipid-lowering response to statins in combined study populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study evaluating lipoprotein-associated phospholipase A2 mass and activity at baseline and after rosuvastatin therapy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study pinpoints a new functional apolipoprotein B variant influencing oxidized low-density lipoprotein levels but not cardiovascular events: AtheroRemo Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
LDL-cholesterol concentrations: a genome-wide association study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. EBI GWAS Catalog EBI GWAS CatalogPubMed
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of apolipoprotein B (APOB) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH68973 (e-PCR)
- UniSTS:67077

APOB_711 (e-PCR)
- UniSTS:276999

RH80663 (e-PCR)
- UniSTS:89102

RH70400 (e-PCR)
- UniSTS:72471

RH68521 (e-PCR)
- UniSTS:21794

SHGC-34591 (e-PCR)
- UniSTS:56355

SHGC-33615 (e-PCR)
- UniSTS:51496

APOB (e-PCR), detects polymorphism
- UniSTS:266032

GDB:185253 (e-PCR)
- UniSTS:155441

GDB:185254 (e-PCR)
- UniSTS:155442

SGC34589 (e-PCR)
- UniSTS:45106

GDB:185282 (e-PCR)
- UniSTS:155444

GDB:185295 (e-PCR)
- UniSTS:155445

D2S2580 (e-PCR)
- UniSTS:58171

RH45452 (e-PCR)
- UniSTS:62271

GDB:181235 (e-PCR)
- UniSTS:155203

GDB:193044 (e-PCR)
- UniSTS:155738

SHGC-56579 (e-PCR)
- UniSTS:45150

GDB:178354 (e-PCR)
- UniSTS:154987

D2S2589 (e-PCR)
- UniSTS:68980

SHGC-33670 (e-PCR)
- UniSTS:55948

RH69077 (e-PCR)
- UniSTS:69261

G44341 (e-PCR)
- UniSTS:95128

GDB:171933 (e-PCR)
- UniSTS:154779

GDB:681390 (e-PCR)
- UniSTS:158620

RH70147 (e-PCR)
- UniSTS:14246

GDB:179436 (e-PCR)
- UniSTS:155047

GDB:177076 (e-PCR)
- UniSTS:154826

GDB:177093 (e-PCR)
- UniSTS:154830

RH69778 (e-PCR)
- UniSTS:64981

GDB:177207 (e-PCR)
- UniSTS:154838

GDB:182191 (e-PCR)
- UniSTS:155360

GDB:182192 (e-PCR)
- UniSTS:155361

GDB:631915 (e-PCR)
- UniSTS:158444

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cholesterol transfer activity	IBA Inferred from Biological aspect of Ancestor more info
enables cholesterol transfer activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables lipase binding	IPI Inferred from Physical Interaction more info	PubMed
enables low-density lipoprotein particle receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables low-density lipoprotein particle receptor binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables low-density lipoprotein particle receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in artery morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cholesterol efflux	IEA Inferred from Electronic Annotation more info
involved_in cholesterol homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cholesterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in fertilization	IEA Inferred from Electronic Annotation more info
involved_in flagellated sperm motility	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in intermembrane lipid transfer	IEA Inferred from Electronic Annotation more info
involved_in lipoprotein biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in lipoprotein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in lipoprotein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in low-density lipoprotein particle clearance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in low-density lipoprotein particle remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cholesterol storage	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of lipid storage	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of macrophage derived foam cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in regulation of cholesterol biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in response to virus	IEP Inferred from Expression Pattern more info	PubMed
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in triglyceride catabolic process	IEA Inferred from Electronic Annotation more info
involved_in triglyceride mobilization	IBA Inferred from Biological aspect of Ancestor more info
involved_in very-low-density lipoprotein particle assembly	IC Inferred by Curator more info	PubMed

Component	Evidence Code	Pubs
part_of chylomicron	IDA Inferred from Direct Assay more info	PubMed
part_of chylomicron remnant	TAS Traceable Author Statement more info	PubMed
located_in clathrin-coated endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome	TAS Traceable Author Statement more info
located_in endocytic vesicle lumen	TAS Traceable Author Statement more info
located_in endoplasmic reticulum exit site	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in endosome lumen	TAS Traceable Author Statement more info
located_in endosome membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	ISS Inferred from Sequence or Structural Similarity more info	PubMed
part_of intermediate-density lipoprotein particle	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lipid droplet	IEA Inferred from Electronic Annotation more info
part_of low-density lipoprotein particle	IBA Inferred from Biological aspect of Ancestor more info
part_of low-density lipoprotein particle	IDA Inferred from Direct Assay more info	PubMed
part_of low-density lipoprotein particle	TAS Traceable Author Statement more info	PubMed
located_in lysosomal lumen	TAS Traceable Author Statement more info
part_of mature chylomicron	IBA Inferred from Biological aspect of Ancestor more info
part_of mature chylomicron	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in smooth endoplasmic reticulum	TAS Traceable Author Statement more info
part_of very-low-density lipoprotein particle	IBA Inferred from Biological aspect of Ancestor more info
part_of very-low-density lipoprotein particle	IDA Inferred from Direct Assay more info	PubMed
part_of very-low-density lipoprotein particle	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: apolipoprotein B-100

Names: apolipoprotein B (including Ag(x) antigen); apolipoprotein B48

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011793.2 RefSeqGene

Range

5000..47644

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000384.3 → NP_000375.3 apolipoprotein B-100 precursor

Status: REVIEWED

Source sequence(s)

AC010872, AC115619, KF456638

Consensus CDS

CCDS1703.1

UniProtKB/Swiss-Prot

O00502, P04114, P78479, P78480, P78481, Q13779, Q13785, Q13786, Q13787, Q13788, Q4ZG63, Q53QC8, Q7Z600, Q9UMN0

UniProtKB/TrEMBL

C0JYY2

Related

ENSP00000233242.1, ENST00000233242.5

Conserved Domains (7) summary

TIGR01612
Location:2060 → 2490

235kDa-fam; reticulocyte binding/rhoptry protein

COG1340
Location:4258 → 4523

COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]

pfam01347
Location:46 → 597

Vitellogenin_N; Lipoprotein amino terminal region

pfam12491
Location:4494 → 4550

ApoB100_C; Apolipoprotein B100 C terminal

pfam06448
Location:961 → 1062

DUF1081; Domain of Unknown Function (DUF1081)

pfam09172
Location:632 → 937

DUF1943; Domain of unknown function (DUF1943)

cl21487
Location:1448 → 1865

OM_channels; Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20) ...