The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate ... See more...

Aliases for APOM Gene

Aliases for APOM Gene

  • Apolipoprotein M 2 3 4 5
  • NG20 2 3 4
  • Protein G3a 3 4
  • Apo-M 3 4
  • G3a 2 3
  • Alternative Name: G3a, NG20 3
  • NG20-Like Protein 3
  • HSPC336 3
  • APOM 5
  • ApoM 4
  • G3A 4

External Ids for APOM Gene

Previous GeneCards Identifiers for APOM Gene

  • GC06P031687
  • GC06P031390
  • GC06P031727
  • GC06P031731
  • GC06P031620
  • GC06P031410
  • GC06P031660
  • GC06P031678
  • GC06P032322
  • GC06P032508
  • GC06P032613
  • GC06P033408
  • GC06P031743
  • GC06P031800
  • GC06P031861
  • GC06P031901
  • GC06P031944
  • GC06P032010
  • GC06P032197
  • GC06P032220
  • GC06P047315
  • GC06P049359

Summaries for APOM Gene

Entrez Gene Summary for APOM Gene

  • The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Alternate splicing results in both coding and non-coding variants of this gene. [provided by RefSeq, Jan 2012]

GeneCards Summary for APOM Gene

APOM (Apolipoprotein M) is a Protein Coding gene. Diseases associated with APOM include Fetal Macrosomia and Huntington Disease-Like 1. Among its related pathways are Metabolism of water-soluble vitamins and cofactors and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include phospholipid binding and lipid transporter activity.

UniProtKB/Swiss-Prot Summary for APOM Gene

  • Probably involved in lipid transport. Can bind sphingosine-1-phosphate, myristic acid, palmitic acid and stearic acid, retinol, all-trans-retinoic acid and 9-cis-retinoic acid.

Gene Wiki entry for APOM Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for APOM Gene

Genomics for APOM Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for APOM Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J031650 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.1 61 3.3 BCLAF1 SP1 ZNF207 NCOR1 MYC ZNF600 SSRP1 ZNF580 ZMYM3 KLF9 BAG6 APOM HSALNG0049303 lnc-BAG6-1 MDC1 LSM2 LY6G5B DDX39B ATF6B GTF2H4
GH06J031654 Promoter/Enhancer 1.3 EPDnew ENCODE 250.7 +3.0 2963 1.8 SSRP1 ZMYM3 KLF9 CEBPA POLR2A YY1 MXD4 KLF11 ZFP64 HOMEZ APOM HSALNG0049304 BAG6 DDX39B LY6G5B DHX16 MDC1 ATF6B SKIV2L MICA
GH06J031567 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.1 -74.0 -73985 22.2 BCLAF1 SP1 ZNF207 NCOR1 IKZF1 MYC ZNF600 ZNF592 POLR2A ZIC2 TNF ATP6V1G2 LST1 AB675034 LTB lnc-TNF-1 LTA DDX39B LY6G5B MICB
GH06J031614 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 11.4 -36.5 -36543 3.6 BCLAF1 SP1 IKZF1 POLR2A ZNF341 KDM6A SAP130 IRF4 ETV4 DMAP1 AIF1 HSALNG0049293 BAG6 LY6G5B HLA-DRB1 SKIV2L LY6G5C LST1 LTB C4A
GH06J031658 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 0.4 +7.9 7880 4.2 NCOR1 ZNF600 IKZF1 SSRP1 KLF9 POLR2A ZBTB10 MXD4 REST CEBPB BAG6 C6orf47 C6orf47-AS1 NONHSAG045755.2 piR-32214-584 LY6G5C LY6G5B C4A MDC1 PRRC2A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around APOM on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for APOM

Top Transcription factor binding sites by QIAGEN in the APOM gene promoter:
  • COUP
  • COUP-TF
  • COUP-TF1
  • PPAR-gamma1
  • PPAR-gamma2
  • STAT1

Genomic Locations for APOM Gene

Latest Assembly
chr6:31,652,404-31,658,210
(GRCh38/hg38)
Size:
5,807 bases
Orientation:
Plus strand

Previous Assembly
chr6:31,620,181-31,625,987
(GRCh37/hg19 by Entrez Gene)
Size:
5,807 bases
Orientation:
Plus strand

chr6:31,620,193-31,625,987
(GRCh37/hg19 by Ensembl)
Size:
5,795 bases
Orientation:
Plus strand

Alternative Locations (GRCh38/hg38)

  • chr6(ALT_REF_LOCI_2):3,129,694-3,135,499 (+)
  • chr6(ALT_REF_LOCI_3):2,900,175-2,905,981 (+)
  • chr6(ALT_REF_LOCI_4):2,957,450-2,963,256 (+)
  • chr6(ALT_REF_LOCI_5):2,994,276-3,000,082 (+)
  • chr6(ALT_REF_LOCI_6):2,908,223-2,914,028 (+)
  • chr6(ALT_REF_LOCI_7):2,951,682-2,957,487 (+)

Genomic View for APOM Gene

Genes around APOM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APOM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APOM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for APOM Gene

  • Protein details for APOM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95445-APOM_HUMAN
    Recommended name:
    Apolipoprotein M
    Protein Accession:
    O95445
    Secondary Accessions:
    • B0UX98
    • Q5SRP4
    • Q9P046
    • Q9UMP6

    Protein attributes for APOM Gene

    Size:
    188 amino acids
    Molecular mass:
    21253 Da
    Quaternary structure:
    • Interacts with LRP2; LRP2 mediates APOM renal uptake and subsequent lysosomal degradation.

    Three dimensional structures from OCA and Proteopedia for APOM Gene

    Alternative splice isoforms for APOM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for APOM Gene

Post-translational modifications for APOM Gene

  • Glycosylation at Asn135
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for APOM Gene

No data available for DME Specific Peptides for APOM Gene

Domains & Families for APOM Gene

Gene Families for APOM Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for APOM Gene

InterPro:

Suggested Antigen Peptide Sequences for APOM Gene

GenScript: Design optimal peptide antigens:
  • Protein G3a (APOM_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95445

UniProtKB/Swiss-Prot:

APOM_HUMAN :
  • Belongs to the calycin superfamily. Lipocalin family. Highly divergent.
Family:
  • Belongs to the calycin superfamily. Lipocalin family. Highly divergent.
genes like me logo Genes that share domains with APOM: view

Function for APOM Gene

Molecular function for APOM Gene

UniProtKB/Swiss-Prot Function:
Probably involved in lipid transport. Can bind sphingosine-1-phosphate, myristic acid, palmitic acid and stearic acid, retinol, all-trans-retinoic acid and 9-cis-retinoic acid.

Phenotypes From GWAS Catalog for APOM Gene

Gene Ontology (GO) - Molecular Function for APOM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005319 lipid transporter activity IDA 16682745
GO:0005543 phospholipid binding IDA 22204862
GO:0016209 antioxidant activity IDA 22204862
genes like me logo Genes that share ontologies with APOM: view
genes like me logo Genes that share phenotypes with APOM: view

Animal Models for APOM Gene

MGI Knock Outs for APOM:
  • Apom Apom<tm1.1(KOMP)Vlcg>
  • Apom Apom<tm1Cchr>
  • Apom Apom<tm1Stf>

Animal Models for research

  • Taconic Biosciences Mouse Models for APOM

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APOM

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for APOM Gene

Localization for APOM Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOM Gene

Secreted. Note=Present in high density lipoprotein (HDL) and to a lesser extent in triglyceride-rich lipoproteins (TGRLP) and low density lipoproteins (LDL).

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for APOM gene
Compartment Confidence
extracellular 5
plasma membrane 2
mitochondrion 2
nucleus 2
cytosol 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for APOM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA --
GO:0034361 very-low-density lipoprotein particle IBA,IDA 17154273
GO:0034362 low-density lipoprotein particle IBA,IDA 16682745
GO:0034364 high-density lipoprotein particle IBA,IDA 22204862
genes like me logo Genes that share ontologies with APOM: view

Pathways & Interactions for APOM Gene

genes like me logo Genes that share pathways with APOM: view

Pathways by source for APOM Gene

Gene Ontology (GO) - Biological Process for APOM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0006869 lipid transport IEA --
GO:0009749 response to glucose IEA --
GO:0033344 cholesterol efflux IEA,IMP 15793583
GO:0034375 high-density lipoprotein particle remodeling IBA,IMP 18006500
genes like me logo Genes that share ontologies with APOM: view

No data available for SIGNOR curated interactions for APOM Gene

Drugs & Compounds for APOM Gene

(3) Drugs for APOM Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Myristic acid Experimental Pharma Carrier 0

(3) Additional Compounds for APOM Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with APOM: view

Transcripts for APOM Gene

mRNA/cDNA for APOM Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APOM

Alternative Splicing Database (ASD) splice patterns (SP) for APOM Gene

No ASD Table

Relevant External Links for APOM Gene

GeneLoc Exon Structure for
APOM

Expression for APOM Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for APOM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for APOM Gene

This gene is overexpressed in Liver (x29.6) and Kidney - Cortex (x6.0).

Protein differential expression in normal tissues from HIPED for APOM Gene

This gene is overexpressed in Plasma (27.6), Serum (15.8), and Synovial fluid (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for APOM Gene



Protein tissue co-expression partners for APOM Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for APOM

SOURCE GeneReport for Unigene cluster for APOM Gene:

Hs.534468

mRNA Expression by UniProt/SwissProt for APOM Gene:

O95445-APOM_HUMAN
Tissue specificity: Plasma protein. Expressed in liver and kidney.

Evidence on tissue expression from TISSUES for APOM Gene

  • Liver(4.7)
  • Blood(4.5)
  • Bone marrow(4.2)
  • Kidney(3.3)
  • Heart(2.3)
genes like me logo Genes that share expression patterns with APOM: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for APOM Gene

Orthologs for APOM Gene

This gene was present in the common ancestor of chordates.

Orthologs for APOM Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia APOM 29 30
  • 99.29 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia APOM 29 30
  • 91.13 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia APOM 29 30
  • 89.18 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Apom 29 16 30
  • 84.4 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Apom 29
  • 83.51 (n)
Oppossum
(Monodelphis domestica)
Mammalia APOM 30
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 56 (a)
OneToMany
-- 30
  • 42 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia APOM 30
  • 45 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia apom 29
  • 53.48 (n)
Zebrafish
(Danio rerio)
Actinopterygii apom 30
  • 19 (a)
OneToOne
Species where no ortholog for APOM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for APOM Gene

ENSEMBL:
Gene Tree for APOM (if available)
TreeFam:
Gene Tree for APOM (if available)
Aminode:
Evolutionary constrained regions (ECRs) for APOM: view image
Alliance of Genome Resources:
Additional Orthologs for APOM

Paralogs for APOM Gene

No data available for Paralogs for APOM Gene

Variants for APOM Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for APOM Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for APOM Gene

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv1161370 CNV deletion 26073780
nsv462871 CNV loss 19166990
nsv601942 CNV loss 21841781
nsv830627 CNV loss 17160897

Variation tolerance for APOM Gene

Residual Variation Intolerance Score: 31% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.21; 24.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for APOM Gene

Human Gene Mutation Database (HGMD)
APOM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOM
Leiden Open Variation Database (LOVD)
APOM

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for APOM Gene

Disorders for APOM Gene

MalaCards: The human disease database

(5) MalaCards diseases for APOM Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search APOM in MalaCards View complete list of genes associated with diseases

Additional Disease Information for APOM

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with APOM: view

No data available for UniProtKB/Swiss-Prot and Genatlas for APOM Gene

Publications for APOM Gene

  1. Proposed lipocalin fold for apolipoprotein M based on bioinformatics and site-directed mutagenesis. (PMID: 11418126) Duan J … Villoutreix BO (FEBS letters 2001) 2 3 4 22
  2. A novel human apolipoprotein (apoM). (PMID: 10531326) Xu N … Dahlbäck B (The Journal of biological chemistry 1999) 2 3 4 22
  3. Apolipoprotein M promoter polymorphisms alter promoter activity and confer the susceptibility to the development of type 1 diabetes. (PMID: 19007767) Wu X … Liu Y (Clinical biochemistry 2009) 3 22 40
  4. Serendipitous fatty acid binding reveals the structural determinants for ligand recognition in apolipoprotein M. (PMID: 19733574) Sevvana M … Muller YA (Journal of molecular biology 2009) 3 4 22
  5. Apolipoprotein M associates to lipoproteins through its retained signal peptide. (PMID: 18279674) Axler O … Dahlbäck B (FEBS letters 2008) 3 4 22

Products for APOM Gene

Sources for APOM Gene