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... See more...

Aliases for NBPF3 Gene

Aliases for NBPF3 Gene

  • NBPF Member 3 2 3 5
  • Neuroblastoma Breakpoint Family Member 3 3 4
  • Protein SHIIIa4 3 4
  • Neuroblastoma Breakpoint Family, Member 3 2
  • Protein AE2 4
  • AE2 3

External Ids for NBPF3 Gene

Previous GeneCards Identifiers for NBPF3 Gene

  • GC01P021512
  • GC01P021639
  • GC01P021766
  • GC01P020010

Summaries for NBPF3 Gene

Entrez Gene Summary for NBPF3 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. DUF1220 copy number variations in 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, Feb 2013]

GeneCards Summary for NBPF3 Gene

NBPF3 (NBPF Member 3) is a Protein Coding gene. Diseases associated with NBPF3 include Neuroblastoma and Schizophrenia. An important paralog of this gene is NBPF12.

Gene Wiki entry for NBPF3 Gene

Additional gene information for NBPF3 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NBPF3 Gene

Genomics for NBPF3 Gene

GeneHancer (GH) Regulatory Elements for NBPF3 Gene

Promoters and enhancers for NBPF3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J021439 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 586.5 +5.1 5083 2.8 NRF1 POLR2G ZFX POLR2A ZBTB26 REST RFX1 TOE1 CTBP1 SKI NBPF3 lnc-ALPL-3 NBPF2P ZBTB40 CDC42-IT1 DDOST ENSG00000271428 HP1BP3 piR-61534-002
GH01J021435 Promoter 0.6 EPDnew 500.7 +1.1 1092 0.1 ZFP36 RBM39 EZH2 NBPF3 piR-32214-018 CROCCP5 lnc-NBPF3-5
GH01J021336 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 61.5 -93.6 -93553 10.1 EP300 FOXK2 HNRNPK ZSCAN5C TCF12 NRF1 POLR2G SP1 NCOR1 RBAK ECE1 HP1BP3 NBPF3 NBPF2P USP48 LDLRAD2 ENSG00000236936 HSPG2 MUL1 CDC42-IT1
GH01J021449 Enhancer 1.1 Ensembl ENCODE 77.3 +17.6 17559 6.2 ZSCAN5C PHB2 ZBTB5 ZIC2 ZNF623 AFF1 TARDBP CTBP1 HINFP ZEB1 piR-61534-002 NBPF3 NBPF2P lnc-ALPL-2 lnc-ALPL-3
GH01J021468 Enhancer 0.8 Ensembl ENCODE 82.1 +33.3 33283 2.8 ZNF217 CTCF REST SMC3 CTBP1 LEF1 FOXA1 DPF2 FOXK2 RCOR1 piR-48801 NBPF3 NBPF2P ALPL RAP1GAP piR-37972-014
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NBPF3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NBPF3

Top Transcription factor binding sites by QIAGEN in the NBPF3 gene promoter:
  • AP-4
  • AREB6
  • CREB
  • deltaCREB
  • GR-alpha
  • HEN1
  • Max1
  • p53

Genomic Locations for NBPF3 Gene

Genomic Locations for NBPF3 Gene
49,688 bases
Plus strand
44,878 bases
Plus strand

Genomic View for NBPF3 Gene

Genes around NBPF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NBPF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NBPF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NBPF3 Gene

Proteins for NBPF3 Gene

  • Protein details for NBPF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuroblastoma breakpoint family member 3
    Protein Accession:
    Secondary Accessions:
    • A8K965
    • B4DSP2
    • I3L0I8
    • Q3BBW1
    • Q5VTG2
    • Q5VTG3
    • Q5VTG4
    • Q8IX78
    • Q8ND86
    • Q8TC96

    Protein attributes for NBPF3 Gene

    633 amino acids
    Molecular mass:
    72951 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=AAH24011.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for NBPF3 Gene


neXtProt entry for NBPF3 Gene

Post-translational modifications for NBPF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NBPF3 Gene

Domains & Families for NBPF3 Gene

Gene Families for NBPF3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NBPF3 Gene


Suggested Antigen Peptide Sequences for NBPF3 Gene

GenScript: Design optimal peptide antigens:
  • Protein SHIIIa4 (NBPF3_HUMAN)

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 NBPF3: view

Function for NBPF3 Gene

Phenotypes From GWAS Catalog for NBPF3 Gene

genes like me logo Genes that share phenotypes with NBPF3: view

Animal Model Products

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 NBPF3 Gene

Localization for NBPF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NBPF3 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 NBPF3 gene
Compartment Confidence
nucleus 2
cytosol 1
extracellular 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NBPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NBPF3: view

Pathways & Interactions for NBPF3 Gene

PathCards logo

SuperPathways for NBPF3 Gene

No Data Available

Interacting Proteins for NBPF3 Gene


Gene Ontology (GO) - Biological Process for NBPF3 Gene


No data available for Pathways by source and SIGNOR curated interactions for NBPF3 Gene

Drugs & Compounds for NBPF3 Gene

No Compound Related Data Available

Transcripts for NBPF3 Gene

mRNA/cDNA for NBPF3 Gene

13 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NBPF3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^
SP1: - - - - -
SP2: - -
SP4: - -
SP5: - -
SP6: - - - - - - - - - - -
SP7: - - - - - - - - - - - - - -
SP8: - - - - - -
SP9: - - - - - - - - -
SP10: - - - - - - - - - - -
SP11: - -
SP14: - - - - - - - - -

ExUns: 12 ^ 13a · 13b · 13c ^ 14 ^ 15

Relevant External Links for NBPF3 Gene

GeneLoc Exon Structure for

Expression for NBPF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NBPF3 Gene

Protein differential expression in normal tissues from HIPED for NBPF3 Gene

This gene is overexpressed in Adipocyte (45.0), Breast (16.7), and Urine (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NBPF3 Gene

Protein tissue co-expression partners for NBPF3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NBPF3

SOURCE GeneReport for Unigene cluster for NBPF3 Gene:


mRNA Expression by UniProt/SwissProt for NBPF3 Gene:

Tissue specificity: Expressed in testis and fetal heart, as well as in non small cell lung carcinoma and neuroblastoma cell line.

Evidence on tissue expression from TISSUES for NBPF3 Gene

  • Nervous system(4.4)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with NBPF3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NBPF3 Gene

Orthologs for NBPF3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for NBPF3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NBPF3 31 30
  • 98.63 (n)
(Canis familiaris)
Mammalia -- 31
  • 33 (a)
(Bos Taurus)
Mammalia -- 31
  • 30 (a)
-- 31
  • 28 (a)
Species where no ortholog for NBPF3 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)
  • 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 NBPF3 Gene

Gene Tree for NBPF3 (if available)
Gene Tree for NBPF3 (if available)
Evolutionary constrained regions (ECRs) for NBPF3: view image

Paralogs for NBPF3 Gene

(17) SIMAP similar genes for NBPF3 Gene using alignment to 1 proteins:

  • NBPF3_HUMAN Pseudogenes for NBPF3 Gene

genes like me logo Genes that share paralogs with NBPF3: view

Variants for NBPF3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NBPF3 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
789913 Benign: not provided 21,472,920(+) C/T INTRON_VARIANT
789914 Benign: not provided 21,480,934(+) G/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs12034222 - p.Leu459Val
rs12043777 - p.Asp444Glu
rs16825377 - p.Arg198Gln

Additional dbSNP identifiers (rs#s) for NBPF3 Gene

Structural Variations from Database of Genomic Variants (DGV) for NBPF3 Gene

Variant ID Type Subtype PubMed ID
dgv56n106 CNV deletion 24896259
esv1213372 CNV deletion 17803354
esv1311289 CNV deletion 17803354
esv2195718 CNV deletion 18987734
esv2456631 CNV deletion 19546169
esv26055 CNV gain 19812545
esv2661318 CNV deletion 23128226
esv2745042 CNV deletion 23290073
esv2745053 CNV deletion 23290073
esv2745064 CNV deletion 23290073
esv2758926 CNV gain+loss 17122850
esv2990456 CNV deletion 24192839
esv3350627 CNV duplication 20981092
esv34155 CNV loss 18971310
esv3555455 CNV deletion 23714750
esv3585443 CNV loss 21293372
esv3585446 CNV loss 21293372
esv7069 OTHER inversion 19470904
esv989724 CNV deletion 20482838
nsv1012251 CNV gain 25217958
nsv1069038 CNV deletion 25765185
nsv1122308 CNV deletion 24896259
nsv1124565 CNV duplication 24896259
nsv1152841 CNV duplication 26484159
nsv1152902 CNV deletion 26484159
nsv160214 CNV deletion 16902084
nsv428432 CNV gain 18775914
nsv820559 CNV duplication 20802225
nsv9435 CNV gain+loss 18304495
nsv945575 CNV duplication 23825009
nsv945576 CNV duplication 23825009
nsv945813 CNV duplication 23825009

Variation tolerance for NBPF3 Gene

Residual Variation Intolerance Score: 89.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.53; 82.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NBPF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NBPF3 Gene

Disorders for NBPF3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for NBPF3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
  • nb
  • sczd
- elite association - COSMIC cancer census association via MalaCards
Search NBPF3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NBPF3

genes like me logo Genes that share disorders with NBPF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NBPF3 Gene

Publications for NBPF3 Gene

  1. 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) 2 3 4 54
  2. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 54
  3. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. (PMID: 22001757) Chambers JC … Kooner JS (Nature genetics 2011) 3 41 54
  4. Common genetic variants associate with serum phosphorus concentration. (PMID: 20558539) Kestenbaum B … Fox CS (Journal of the American Society of Nephrology : JASN 2010) 3 41 54
  5. Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations. (PMID: 19303062) Tanaka T … Ferrucci L (American journal of human genetics 2009) 3 41 54

Products for NBPF3 Gene

Sources for NBPF3 Gene