Free for academic non-profit institutions. Other users need a Commercial license

Aliases for NBPF12 Gene

Aliases for NBPF12 Gene

  • NBPF Member 12 2 3 5
  • KIAA1245 2 3 4
  • Chromosome 1 Amplified Sequence 1 3 4
  • COAS1 3 4
  • Chomosome One Amplified Sequence 1 Cyclophilin 3
  • Neuroblastoma Breakpoint Family, Member 12 2
  • Neuroblastoma Breakpoint Family Member 12 3

External Ids for NBPF12 Gene

Previous HGNC Symbols for NBPF12 Gene

  • KIAA1245

Previous GeneCards Identifiers for NBPF12 Gene

  • GC01P143685
  • GC01U901244
  • GC01M144746
  • GC01P144927
  • GC01M146617
  • GC01P146376

Summaries for NBPF12 Gene

Entrez Gene Summary for NBPF12 Gene

  • This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, May 2013]

GeneCards Summary for NBPF12 Gene

NBPF12 (NBPF Member 12) is a Protein Coding gene. Diseases associated with NBPF12 include Neuroblastoma. An important paralog of this gene is NBPF26.

Additional gene information for NBPF12 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NBPF12 Gene

Genomics for NBPF12 Gene

Regulatory Elements for NBPF12 Gene

Enhancers for NBPF12 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H146034 1.5 ENCODE dbSUPER 4.7 -901.0 -900994 5.6 MLX DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 ZFP41 MEF2D SSRP1 PIAS3 POLR3C NBPF20 GPR89A GNRHR2 NUDT17 ENSG00000213240 ANKRD35 TXNIP PEX11B
GH01H147578 1.1 Ensembl ENCODE 4.9 +642.3 642273 4.4 ZNF133 RAD21 ZNF366 ZNF391 RUNX3 TSHZ1 ZEB2 KAT8 ZFP69B NFIL3 BCL9 ACP6 NBPF12 PFN1P8 GC01P147574
GH01H147586 1.1 Ensembl ENCODE 4 +648.5 648458 1.9 ELF3 TBP PKNOX1 RARA FOS CREM MIXL1 EGR2 KLF11 SP5 BCL9 NBPF12 GC01P147574 ACP6
GH01H146933 1.1 Ensembl ENCODE 0.7 -4.0 -3989 1.3 HDAC1 LEF1 PKNOX1 NFRKB TAL1 ETV1 TCF12 CTBP1 POLR2A FOXK2 NBPF12 ENSG00000274450
GH01H146938 1 ENCODE 0.7 -0.1 -119 0.3 HDGF ARID4B SIN3A ZNF2 GLIS2 ELK1 ZNF143 ZNF207 ATF7 SP3 BCL9 NBPF12 ENSG00000274450
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NBPF12 on UCSC Golden Path with GeneCards custom track

Promoters for NBPF12 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000013065 355 2201 HDGF ARID4B SIN3A ZNF2 GLIS2 ELK1 ZNF143 ZNF207 ATF7 SP3

Genomic Locations for NBPF12 Gene

Genomic Locations for NBPF12 Gene
57,658 bases
Plus strand

Genomic View for NBPF12 Gene

Genes around NBPF12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NBPF12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NBPF12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NBPF12 Gene

Proteins for NBPF12 Gene

  • Protein details for NBPF12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuroblastoma breakpoint family member 12
    Protein Accession:
    Secondary Accessions:
    • O95877

    Protein attributes for NBPF12 Gene

    269 amino acids
    Molecular mass:
    31307 Da
    Quaternary structure:
    No Data Available
    • Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the chromosome 1.
    • Sequence=CAI22485.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for NBPF12 Gene

Post-translational modifications for NBPF12 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NBPF12 Gene

Domains & Families for NBPF12 Gene

Gene Families for NBPF12 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NBPF12 Gene


Suggested Antigen Peptide Sequences for NBPF12 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NBPF family.
  • Belongs to the NBPF family.
genes like me logo Genes that share domains with NBPF12: view

Function for NBPF12 Gene

Phenotypes From GWAS Catalog for NBPF12 Gene

Phenotypes for NBPF12 Gene

genes like me logo Genes that share phenotypes with NBPF12: view

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NBPF12 Gene

Localization for NBPF12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NBPF12 Gene


Subcellular locations from

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 NBPF12 gene
Compartment Confidence
nucleus 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NBPF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NBPF12: view

Pathways & Interactions for NBPF12 Gene

SuperPathways for NBPF12 Gene

No Data Available

Interacting Proteins for NBPF12 Gene

Selected Interacting proteins: Q5TAG4-NBPFC_HUMAN for NBPF12 Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for NBPF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with NBPF12: view

No data available for Pathways by source and SIGNOR curated interactions for NBPF12 Gene

Drugs & Compounds for NBPF12 Gene

No Compound Related Data Available

Transcripts for NBPF12 Gene

mRNA/cDNA for NBPF12 Gene

(1) REFSEQ mRNAs :
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NBPF12 Gene

No ASD Table

Relevant External Links for NBPF12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NBPF12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NBPF12 Gene

mRNA differential expression in normal tissues according to GTEx for NBPF12 Gene

This gene is overexpressed in Stomach (x5.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NBPF12 Gene

Protein tissue co-expression partners for NBPF12 Gene

NURSA nuclear receptor signaling pathways regulating expression of NBPF12 Gene:


mRNA Expression by UniProt/SwissProt for NBPF12 Gene:

Tissue specificity: Widely expressed with highest levels in brain, ovary, mammary gland, skin and adipose tissue. Also expressed in testis. Detected in a number of tumors including osteosarcoma, mammary carcinoma and hepatocellular carcinoma.

Evidence on tissue expression from TISSUES for NBPF12 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with NBPF12: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NBPF12 Gene

Orthologs for NBPF12 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for NBPF12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC458021 33
  • 81.22 (n)
Species where no ortholog for NBPF12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for NBPF12 Gene

Gene Tree for NBPF12 (if available)
Gene Tree for NBPF12 (if available)

Paralogs for NBPF12 Gene Pseudogenes for NBPF12 Gene

genes like me logo Genes that share paralogs with NBPF12: view

Variants for NBPF12 Gene

Sequence variations from dbSNP and Humsavar for NBPF12 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1043477 -- 146,994,545(+) CTGGT(C/G)TTCCA reference, synonymous-codon
rs1043489 -- 146,994,714(+) TCTCA(A/G)AGCAT utr-variant-3-prime
rs1043491 -- 146,994,716(+) TCAGA(C/G)CATGC utr-variant-3-prime
rs1043508 -- 146,994,816(+) CAGCC(A/G)GACAT utr-variant-3-prime
rs10900302 -- 146,941,420(-) AAAGA(C/T)TGATA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NBPF12 Gene

Variant ID Type Subtype PubMed ID
nsv1132304 CNV duplication 24896259
nsv1139499 CNV duplication 24896259
nsv1143458 CNV deletion 24896259
nsv1148365 CNV duplication 26484159
nsv2732 CNV insertion 18451855
nsv509457 CNV insertion 20534489
nsv510962 OTHER complex 20534489
nsv820542 CNV duplication 20802225
nsv946295 CNV duplication 23825009
nsv1130969 CNV deletion 24896259
nsv1121774 CNV deletion 24896259
nsv1078188 CNV deletion 25765185
nsv1005055 CNV loss 25217958
nsv1003688 CNV gain 25217958
esv3447305 CNV duplication 20981092
esv2761299 CNV gain+loss 21179565
esv24069 CNV gain 19812545
dgv66e199 CNV deletion 23128226
dgv327n100 CNV gain 25217958
dgv203e59 CNV duplication 20981092
dgv181n106 CNV duplication 24896259
nsv951828 CNV duplication 24416366
nsv951826 CNV deletion 24416366
nsv946831 CNV duplication 23825009
nsv946830 CNV duplication 23825009
nsv946829 CNV duplication 23825009
nsv946828 CNV duplication 23825009
nsv946827 CNV duplication 23825009

Variation tolerance for NBPF12 Gene

Gene Damage Index Score: 8.60; 86.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NBPF12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NBPF12 Gene

Disorders for NBPF12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NBPF12 Gene - From: GeneCards

Disorder Aliases PubMed IDs
  • neuroblastoma 1
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for NBPF12

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with NBPF12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NBPF12 Gene

Publications for NBPF12 Gene

  1. Positional cloning identifies a novel cyclophilin as a candidate amplified oncogene in 1q21. (PMID: 11948409) Meza-Zepeda LA … Myklebost O (Oncogene 2002) 2 3 4 60
  2. A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. (PMID: 16079250) Vandepoele K … van Roy F (Molecular biology and evolution 2005) 3 4 60
  3. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PMID: 23314748) Nathan JA … Goldberg AL (The EMBO journal 2013) 3 60
  4. Evolutionary history and genome organization of DUF1220 protein domains. (PMID: 22973535) O'Bleness MS … Sikela JM (G3 (Bethesda, Md.) 2012) 3 60
  5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PMID: 21906983) Kim W … Gygi SP (Molecular cell 2011) 3 60

Products for NBPF12 Gene

Sources for NBPF12 Gene

Loading form....