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Aliases for GPNMB Gene

Aliases for GPNMB Gene

  • Glycoprotein Nmb 2 3 5
  • Hematopoietic Growth Factor Inducible Neurokinin-1 2 3
  • Glycoprotein Nonmetastatic Melanoma Protein B 2 3
  • Transmembrane Glycoprotein HGFIN 3 4
  • Glycoprotein (Transmembrane) Nmb 2 3
  • Glycoprotein Nmb-Like Protein 2 3
  • Osteoactivin 2 3
  • HGFIN 3 4
  • NMB 3 4
  • Transmembrane Glycoprotein NMB 3
  • Transmembrane Glycoprotein 2
  • Glycoprotein NMB 2
  • PLCA3 3

External Ids for GPNMB Gene

Previous GeneCards Identifiers for GPNMB Gene

  • GC07P022928
  • GC07P022994
  • GC07P023028
  • GC07P023059
  • GC07P023252
  • GC07P023170

Summaries for GPNMB Gene

Entrez Gene Summary for GPNMB Gene

  • The protein encoded by this gene is a type I transmembrane glycoprotein which shows homology to the pMEL17 precursor, a melanocyte-specific protein. GPNMB shows expression in the lowly metastatic human melanoma cell lines and xenografts but does not show expression in the highly metastatic cell lines. GPNMB may be involved in growth delay and reduction of metastatic potential. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for GPNMB Gene

GPNMB (Glycoprotein Nmb) is a Protein Coding gene. Diseases associated with GPNMB include Amyloidosis, Primary Localized Cutaneous, 3 and Melanoma. Among its related pathways are Signaling by PTK6 and Adhesion. Gene Ontology (GO) annotations related to this gene include heparin binding and integrin binding. An important paralog of this gene is PMEL.

UniProtKB/Swiss-Prot for GPNMB Gene

  • Could be a melanogenic enzyme.

Gene Wiki entry for GPNMB Gene

Additional gene information for GPNMB Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GPNMB Gene

Genomics for GPNMB Gene

GeneHancer (GH) Regulatory Elements for GPNMB Gene

Promoters and enhancers for GPNMB 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
GH07J023246 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 650.4 +11.5 11476 2.6 USF1 ZMYM3 ZNF507 ZNF316 POLR2A EED SCRT2 RCOR1 FOSL2 FOS GPNMB KLHL7-DT IGF2BP3 LOC389473 KLHL7 ENSG00000226816 MALSU1
GH07J023234 Enhancer 0.9 Ensembl ENCODE 650.7 -0.5 -493 2.6 CTCF PKNOX1 IRF2 ATF1 RB1 EBF1 KLF5 EED ZNF207 ATF7 GPNMB KLHL7-DT LOC101927890
GH07J023332 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10 +98.8 98834 4.9 PKNOX1 CLOCK FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF213 KLHL7-DT GPNMB IGF2BP3 ENSG00000232627 MALSU1 GC07M023312
GH07J023205 Promoter/Enhancer 1.2 Ensembl ENCODE 12.8 -29.4 -29367 1.9 ELF3 SOX13 FOXA2 SAP130 CEBPG ZNF48 POLR2A RCOR1 NR2F6 CHD2 ENSG00000226816 KLHL7-DT GPNMB NUPL2 LOC101927890
GH07J022671 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 9.8 -563.2 -563237 3.2 FOXA2 NFIB NEUROD1 SIN3A RARA FOS RCOR1 CEBPB NFYC MIER2 STEAP1B IL6 ENSG00000179428 GPNMB ENSG00000226329 LOC401312 GC07P022719 GC07P022403
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GPNMB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GPNMB gene promoter:
  • p53
  • ER-alpha
  • ARP-1
  • AP-4
  • Bach1

Genomic Locations for GPNMB Gene

Genomic Locations for GPNMB Gene
chr7:23,235,967-23,275,110
(GRCh38/hg38)
Size:
39,144 bases
Orientation:
Plus strand
chr7:23,275,586-23,314,729
(GRCh37/hg19)
Size:
39,144 bases
Orientation:
Plus strand

Genomic View for GPNMB Gene

Genes around GPNMB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for GPNMB Gene

Proteins for GPNMB Gene

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

    Protein Symbol:
    Q14956-GPNMB_HUMAN
    Recommended name:
    Transmembrane glycoprotein NMB
    Protein Accession:
    Q14956
    Secondary Accessions:
    • A4D155
    • Q6UVX1
    • Q8N1A1

    Protein attributes for GPNMB Gene

    Size:
    572 amino acids
    Molecular mass:
    63923 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for GPNMB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPNMB Gene

Post-translational modifications for GPNMB Gene

  • Glycosylation at isoforms=2467, isoforms=2459, Asn312, Asn306, isoforms=2300, isoforms=2296, isoforms=2275, isoforms=2249, Asn200, isoforms=2146, isoforms=2134, and Asn93
  • Modification sites at PhosphoSitePlus

Other Protein References for GPNMB Gene

Antibody Products

  • R&D Systems Antibodies for GPNMB (Osteoactivin/GPNMB)
  • Abcam antibodies for GPNMB
  • Boster Bio Antibodies for GPNMB

No data available for DME Specific Peptides for GPNMB Gene

Domains & Families for GPNMB Gene

Gene Families for GPNMB Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for GPNMB Gene

Graphical View of Domain Structure for InterPro Entry

Q14956

UniProtKB/Swiss-Prot:

GPNMB_HUMAN :
  • Belongs to the PMEL/NMB family.
Family:
  • Belongs to the PMEL/NMB family.
genes like me logo Genes that share domains with GPNMB: view

Function for GPNMB Gene

Molecular function for GPNMB Gene

UniProtKB/Swiss-Prot Function:
Could be a melanogenic enzyme.

Phenotypes From GWAS Catalog for GPNMB Gene

Gene Ontology (GO) - Molecular Function for GPNMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding IEA,IBA --
GO:0005515 protein binding IPI 12609765
GO:0008201 heparin binding IDA 19350579
GO:0042056 chemoattractant activity NAS 20711474
GO:0045545 syndecan binding IPI 19350579
genes like me logo Genes that share ontologies with GPNMB: view
genes like me logo Genes that share phenotypes with GPNMB: view

Animal Models for GPNMB Gene

MGI Knock Outs for GPNMB:
  • Gpnmb Gpnmb<tm1.1(KOMP)Vlcg>
  • Gpnmb Gpnmb<tm1Ari>

Animal Model Products

CRISPR Products

miRNA for GPNMB Gene

miRTarBase miRNAs that target GPNMB

Inhibitory RNA Products

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

Clone Products

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

Localization for GPNMB Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPNMB Gene

Cell membrane; Single-pass type I membrane protein. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV. Detected at the cell surface in different types of cancers cells, including glioblastoma multiforme cells and most melanoma cell lines.

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 GPNMB gene
Compartment Confidence
plasma membrane 5
extracellular 2
lysosome 2
mitochondrion 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for GPNMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IEA,IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IDA,IEA 12609765
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with GPNMB: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GPNMB Gene

Pathways & Interactions for GPNMB Gene

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

Pathways by source for GPNMB Gene

1 Cell Signaling Technology pathway for GPNMB Gene

Gene Ontology (GO) - Biological Process for GPNMB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001649 osteoblast differentiation IEA --
GO:0001818 negative regulation of cytokine production IDA 19350579
GO:0001934 positive regulation of protein phosphorylation IDA,IEA 22891158
GO:0007155 cell adhesion IEA --
GO:0007165 signal transduction IMP 19350579
genes like me logo Genes that share ontologies with GPNMB: view

No data available for SIGNOR curated interactions for GPNMB Gene

Drugs & Compounds for GPNMB Gene

(15) Drugs for GPNMB Gene - From: DrugBank, ClinicalTrials, and DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Capecitabine Approved, Investigational Pharma RNA processing inhibitor and thymidylate synthase inhibitor, F-pyrimidines 1402
Docetaxel Approved, Investigational Pharma Microtubulin disassembly inhibitor, Tubulin and VEGF inhibitor, Taxanes 2040
Doxil Approved June 1999 Pharma DNA intercalator and TOPO II inhibitor, Topoisomerase 2 Inhibitors 1828
Doxorubicin Approved, Investigational Pharma Topo II inhibitor,immunosuppresive antineoplastic antibiotic 1828
Gemcitabine Approved Pharma Ribonucleotide reductase and DNA synthesis inhibitor, Nucleoside Analogs 2100
genes like me logo Genes that share compounds with GPNMB: view

Transcripts for GPNMB Gene

Unigene Clusters for GPNMB Gene

Glycoprotein (transmembrane) nmb:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d ^
SP1: - - - - -
SP2: - - - -
SP3: -
SP4: - - - - - - - - -
SP5: - - - - - - -
SP6: - -
SP7:
SP8: - - - - - - - -
SP9: - - - - -
SP10: - - - -
SP11:
SP12:
SP13:

ExUns: 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d · 15e
SP1: - - -
SP2: - - -
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -

Relevant External Links for GPNMB Gene

GeneLoc Exon Structure for
GPNMB
ECgene alternative splicing isoforms for
GPNMB

Expression for GPNMB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x4.4).

Protein differential expression in normal tissues from HIPED for GPNMB Gene

This gene is overexpressed in Hair follicle (20.1), Nasal epithelium (13.2), and Amniocyte (10.6).

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



NURSA nuclear receptor signaling pathways regulating expression of GPNMB Gene:

GPNMB

SOURCE GeneReport for Unigene cluster for GPNMB Gene:

Hs.190495

mRNA Expression by UniProt/SwissProt for GPNMB Gene:

Q14956-GPNMB_HUMAN
Tissue specificity: Up-regulated in various cancer cells, including in glioblastoma multiforme. Expressed in many melanoma cells, as well as in tissue macrophages, including liver Kuppfer cells and lung alveolar macrophages, in podocytes and in some cells of the ciliary body of the eye (at protein level). Hardly detectable in healthy brain.

Evidence on tissue expression from TISSUES for GPNMB Gene

  • Blood(5)
  • Nervous system(5)
  • Skin(4.5)
  • Liver(4.4)
  • Heart(3.6)
  • Lung(3.6)
  • Intestine(3.4)
  • Eye(2.8)
  • Kidney(2.7)
  • Lymph node(2.6)
  • Muscle(2.6)
  • Gall bladder(2.3)
  • Pancreas(2.2)
  • Spleen(2.2)
  • Bone(2.1)
genes like me logo Genes that share expression patterns with GPNMB: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for GPNMB Gene

Orthologs for GPNMB Gene

This gene was present in the common ancestor of chordates.

Orthologs for GPNMB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPNMB 34 33
  • 99.42 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GPNMB 34 33
  • 85.31 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GPNMB 34 33
  • 82.97 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gpnmb 16 34 33
  • 76.85 (n)
rat
(Rattus norvegicus)
Mammalia Gpnmb 33
  • 76.55 (n)
oppossum
(Monodelphis domestica)
Mammalia GPNMB 34
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GPNMB 34
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves GPNMB 34 33
  • 61.92 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GPNMB 34
  • 50 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gpnmb 33
  • 59.8 (n)
Str.6500 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.6913 33
zebrafish
(Danio rerio)
Actinopterygii gpnmb 34 33
  • 48.8 (n)
OneToOne
Species where no ortholog for GPNMB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 squirt (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 GPNMB Gene

ENSEMBL:
Gene Tree for GPNMB (if available)
TreeFam:
Gene Tree for GPNMB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPNMB: view image

Paralogs for GPNMB Gene

Paralogs for GPNMB Gene

(1) SIMAP similar genes for GPNMB Gene using alignment to 5 proteins:

  • GPNMB_HUMAN
  • F5GY20_HUMAN
  • F6SKP1_HUMAN
  • Q8IXJ5_HUMAN
  • Q96F58_HUMAN
genes like me logo Genes that share paralogs with GPNMB: view

Variants for GPNMB Gene

Sequence variations from dbSNP and Humsavar for GPNMB Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs755767733 A breast cancer sample 23,254,274(+) C/A coding_sequence_variant, missense_variant
VAR_036263 A breast cancer sample p.Ser531Ile
rs1000155455 -- 23,265,651(+) G/T intron_variant
rs1000257382 -- 23,272,100(+) C/T intron_variant
rs1000308499 -- 23,259,564(+) G/A intron_variant

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

Variant ID Type Subtype PubMed ID
esv3612541 CNV gain 21293372
nsv1016316 CNV gain 25217958
nsv1027363 CNV gain 25217958
nsv520600 CNV loss 19592680
nsv5661 CNV insertion 18451855
nsv7393 OTHER inversion 18451855

Variation tolerance for GPNMB Gene

Residual Variation Intolerance Score: 87.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.36; 63.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPNMB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPNMB

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPNMB Gene

Disorders for GPNMB Gene

MalaCards: The human disease database

(4) MalaCards diseases for GPNMB Gene - From: OMIM, ClinVar, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
amyloidosis, primary localized cutaneous, 3
  • plca3
melanoma
  • malignant melanoma
glioblastoma multiforme
  • adult glioblastoma multiforme
glioblastoma
  • glioblastoma multiforme
- elite association - COSMIC cancer census association via MalaCards
Search GPNMB in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GPNMB_HUMAN
  • Note=Glioblastoma multiforme patients that exhibit increased mRNA and protein levels (>3-fold over normal brain) in biopsy samples have a significantly higher risk of death (PubMed:16609006). In the context of cancer immunotherapy, including that of melanoma, has been proposed to be used as a cell surface protein antigen targeted by antibodies coupled to cytotoxic drugs (PubMed:16489096). {ECO:0000269 PubMed:16489096, ECO:0000269 PubMed:16609006}.

Additional Disease Information for GPNMB

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GPNMB: view

No data available for Genatlas for GPNMB Gene

Publications for GPNMB Gene

  1. nmb, a novel gene, is expressed in low-metastatic human melanoma cell lines and xenografts. (PMID: 7814155) Weterman MA … Bloemers HP (International journal of cancer 1995) 2 3 4 22 58
  2. Hematopoietic growth factor inducible neurokinin-1 type: a transmembrane protein that is similar to neurokinin 1 interacts with substance P. (PMID: 12609765) Bandari PS … Rameshwar P (Regulatory peptides 2003) 3 4 22 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Glycoprotein nonmetastatic melanoma protein b, a melanocytic cell marker, is a melanosome-specific and proteolytically released protein. (PMID: 20056711) Hoashi T … Hearing VJ (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2010) 3 22 58
  5. Glycoprotein nonmetastatic B is an independent prognostic indicator of recurrence and a novel therapeutic target in breast cancer. (PMID: 20215530) Rose AA … Siegel PM (Clinical cancer research : an official journal of the American Association for Cancer Research 2010) 3 22 58

Products for GPNMB Gene

Sources for GPNMB Gene

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