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APOB apolipoprotein B [ Homo sapiens (human) ]

Gene ID: 338, updated on 12-Feb-2024

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See APOB in Genome Data Viewer
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_000002.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr2:20893576-20893760 Neighboring gene lipid droplet associated hydrolase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:21021737-21022562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15408 Neighboring gene long intergenic non-protein coding RNA 2850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:21211745-21212246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:21212247-21212746 Neighboring gene APOB 3' scaffold/matrix attachment region Neighboring gene APOB 5' regulatory region Neighboring gene Sharpr-MPRA regulatory region 5245 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:21290821-21291609 Neighboring gene uncharacterized LOC124905593 Neighboring gene uncharacterized LOC124908055 Neighboring gene APOB intestinal control region Neighboring gene tudor domain containing 15

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

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
Bipolar disorder with comorbid binge eating history: A genome-wide association study implicates APOB.
EBI GWAS Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia.
EBI GWAS Catalog
Familial defective apolipoprotein B-100 and increased low-density lipoprotein cholesterol and coronary artery calcification in the old order amish.
EBI GWAS Catalog
Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
EBI GWAS Catalog
Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.
EBI GWAS Catalog
Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
EBI GWAS Catalog
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
EBI GWAS Catalog
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
EBI GWAS Catalog
Genome-wide association of lipid-lowering response to statins in combined study populations.
EBI GWAS Catalog
Genome-wide association study evaluating lipoprotein-associated phospholipase A2 mass and activity at baseline and after rosuvastatin therapy.
EBI GWAS Catalog
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
EBI GWAS Catalog
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
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
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.
EBI GWAS Catalog
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
LDL-cholesterol concentrations: a genome-wide association study.
EBI GWAS Catalog
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
EBI GWAS Catalog
Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
EBI GWAS Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
EBI GWAS Catalog
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
EBI GWAS Catalog

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 PubMed 
located_in extracellular region HDA 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

Preferred Names
apolipoprotein B-100
Names
apolipoprotein B (including Ag(x) antigen)
apolipoprotein B48

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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

  1. NG_011793.2 RefSeqGene

    Range
    5000..47644
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000384.3NP_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:20602490
    235kDa-fam; reticulocyte binding/rhoptry protein
    COG1340
    Location:42584523
    COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]
    pfam01347
    Location:46597
    Vitellogenin_N; Lipoprotein amino terminal region
    pfam12491
    Location:44944550
    ApoB100_C; Apolipoprotein B100 C terminal
    pfam06448
    Location:9611062
    DUF1081; Domain of Unknown Function (DUF1081)
    pfam09172
    Location:632937
    DUF1943; Domain of unknown function (DUF1943)
    cl21487
    Location:14481865
    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) ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    21001429..21044073 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791767.1 Reference GRCh38.p14 PATCHES

    Range
    52097..94741 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    21034648..21077293 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)