NBPF1 Gene (Protein Coding)

NBPF Member 1

GC01M016562
GIFtS:
31
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 NBPF1 Gene

Aliases for NBPF1 Gene

  • NBPF Member 1 2 3 5
  • Neuroblastoma Breakpoint Family Member 1 3 4
  • Neuroblastoma Breakpoint Family, Member 1 2
  • KIAA1693 4
  • AB13 3
  • AB14 3
  • AB23 3
  • NBPF 3
  • AD2 3
  • NBG 3

External Ids for NBPF1 Gene

Previous GeneCards Identifiers for NBPF1 Gene

  • GC01M016666
  • GC01M016764
  • GC01M016888
  • GC01M015383

Summaries for NBPF1 Gene

Entrez Gene Summary for NBPF1 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, Apr 2013]

GeneCards Summary for NBPF1 Gene

NBPF1 (NBPF Member 1) is a Protein Coding gene. Diseases associated with NBPF1 include Astrocytoma and Neuroblastoma. An important paralog of this gene is NBPF12.

Additional gene information for NBPF1 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NBPF1 Gene

Genomics for NBPF1 Gene

GeneHancer (GH) Regulatory Elements for NBPF1 Gene

Promoters and enhancers for NBPF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NBPF1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NBPF1

Top Transcription factor binding sites by QIAGEN in the NBPF1 gene promoter:
  • LUN-1
  • MyoD
  • NF-E2
  • NF-E2 p45
  • Olf-1
  • Pax-5
  • SRF
  • SRF (504 AA)
  • XBP-1
  • ZID

Genomic Locations for NBPF1 Gene

Genomic Locations for NBPF1 Gene
chr1:16,562,319-16,613,605
(GRCh38/hg38)
Size:
51,287 bases
Orientation:
Minus strand
chr1:16,888,814-16,940,057
(GRCh37/hg19)
Size:
51,244 bases
Orientation:
Minus strand

Genomic View for NBPF1 Gene

Genes around NBPF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NBPF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NBPF1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for NBPF1 Gene

Proteins for NBPF1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for NBPF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q3BBV0-NBPF1_HUMAN
    Recommended name:
    Neuroblastoma breakpoint family member 1
    Protein Accession:
    Q3BBV0
    Secondary Accessions:
    • Q8N4E8
    • Q9C0H0
    • S4R3K2

    Protein attributes for NBPF1 Gene

    Size:
    1214 amino acids
    Molecular mass:
    139258 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the chromosome 1.

    Alternative splice isoforms for NBPF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NBPF1 Gene

Protein Expression for NBPF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for NBPF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NBPF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NBPF1 Gene

Domains & Families for NBPF1 Gene

Gene Families for NBPF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for NBPF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NBPF1 Gene

GenScript: Design optimal peptide antigens:
  • Neuroblastoma breakpoint family member 1 (NBPF1_HUMAN)
  • NBPF1 protein (Q4VC10_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q3BBV0

UniProtKB/Swiss-Prot:

NBPF1_HUMAN :
  • Belongs to the NBPF family.
Family:
  • Belongs to the NBPF family.
genes like me logo Genes that share domains with NBPF1: view

Function for NBPF1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for NBPF1 Gene

genes like me logo Genes that share phenotypes with NBPF1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NBPF1

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 NBPF1 Gene

Localization for NBPF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NBPF1 Gene

Cytoplasm.

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 NBPF1 gene
Compartment Confidence
plasma membrane 1
nucleus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for NBPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NBPF1: view

Pathways & Interactions for NBPF1 Gene

PathCards logo

SuperPathways for NBPF1 Gene

No Data Available

Interacting Proteins for NBPF1 Gene

STRING Interaction Network Preview (showing top 3 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000474456 Q3BBV0-NBPF1_HUMAN for NBPF1 Gene via STRING IID

GPS-Prot Interaction Network for NBPF1
;

Gene Ontology (GO) - Biological Process for NBPF1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for NBPF1 Gene

Drugs & Compounds for NBPF1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for NBPF1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for NBPF1 Gene

1 REFSEQ mRNAs :
33 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NBPF1

Alternative Splicing Database (ASD) splice patterns (SP) for NBPF1 Gene

No ASD Table

Relevant External Links for NBPF1 Gene

GeneLoc Exon Structure for
NBPF1

Expression for NBPF1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NBPF1 Gene

mRNA expression in normal human tissues for NBPF1 Gene
mRNA expression by GTEx for NBPF1 GenemRNA expression by BioGPS for NBPF1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NBPF1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NBPF1

SOURCE GeneReport for Unigene cluster for NBPF1 Gene:

Hs.467587

mRNA Expression by UniProt/SwissProt for NBPF1 Gene:

Q3BBV0-NBPF1_HUMAN
Tissue specificity: Widely expressed. The only tissue which shows a weak expression is kidney.
genes like me logo Genes that share expression patterns with NBPF1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NBPF1 Gene

Orthologs for NBPF1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for NBPF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia -- 31
  • 99 (a)
 ManyToMany
-- 31
  • 99 (a)
 ManyToMany
-- 31
  • 99 (a)
 ManyToMany
-- 31
  • 99 (a)
 ManyToMany
LOC458021 30
  • 90.11 (n)
-- 31
  • 83 (a)
 ManyToMany
-- 31
  • 81 (a)
 ManyToMany
-- 31
  • 79 (a)
 ManyToMany
dog
(Canis familiaris)
 Mammalia -- 31
  • 35 (a)
 OneToMany
cow
(Bos Taurus)
 Mammalia -- 31
  • 31 (a)
 ManyToMany
-- 31
  • 28 (a)
 ManyToMany
Species where no ortholog for NBPF1 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 NBPF1 Gene

ENSEMBL:
Gene Tree for NBPF1 (if available)
TreeFam:
Gene Tree for NBPF1 (if available)

Paralogs for NBPF1 Gene

Paralogs for NBPF1 Gene

(17) SIMAP similar genes for NBPF1 Gene using alignment to 7 proteins:

  • NBPF1_HUMAN
  • Q4VC10_HUMAN
  • S4R2X0_HUMAN
  • S4R2Z6_HUMAN
  • S4R3H5_HUMAN
  • S4R3K2_HUMAN
  • S4R3W5_HUMAN

Pseudogenes.org Pseudogenes for NBPF1 Gene

genes like me logo Genes that share paralogs with NBPF1: view

Variants for NBPF1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NBPF1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs1553179810 Uncertain Significance: not specified 16,565,804(-) G/A MISSENSE_VARIANT
rs3896430 Uncertain Significance: not specified 16,576,487(-) G/T INTRON_VARIANT
rs763081531 Uncertain Significance: not specified 16,567,977(-) A/G SPLICE_DONOR_VARIANT
rs28453011 - p.Cys663Arg
rs3738661 - p.Cys591Gly

Additional dbSNP identifiers (rs#s) for NBPF1 Gene

Structural Variations from Database of Genomic Variants (DGV) for NBPF1 Gene

Variant ID Type Subtype PubMed ID
dgv10e201 CNV deletion 23290073
dgv1e203 CNV gain+loss 21179565
dgv1n16 CNV deletion 17901297
dgv1n68 CNV loss 17160897
dgv20n67 CNV gain 20364138
dgv21e199 CNV deletion 23128226
dgv39n100 CNV gain 25217958
dgv40n100 CNV gain 25217958
dgv41n100 CNV gain 25217958
dgv42n100 CNV loss 25217958
dgv43n100 CNV loss 25217958
dgv44n100 CNV gain+loss 25217958
dgv45n100 CNV gain 25217958
dgv46n100 CNV gain 25217958
dgv47n100 CNV gain+loss 25217958
dgv48n100 CNV gain+loss 25217958
dgv49e59 CNV duplication 20981092
dgv49n100 CNV loss 25217958
dgv49n106 CNV duplication 24896259
dgv50n100 CNV gain 25217958
dgv51n100 CNV loss 25217958
dgv52n100 CNV gain+loss 25217958
dgv53n100 CNV loss 25217958
dgv54n100 CNV gain 25217958
dgv55n100 CNV gain+loss 25217958
dgv56n100 CNV loss 25217958
dgv57n100 CNV loss 25217958
dgv58n100 CNV gain+loss 25217958
dgv59n100 CNV gain 25217958
dgv60n100 CNV loss 25217958
dgv61n100 CNV gain+loss 25217958
dgv62n100 CNV gain 25217958
dgv63n100 CNV gain 25217958
dgv64n100 CNV loss 25217958
dgv65n100 CNV gain 25217958
dgv66n100 CNV gain 25217958
dgv67n100 CNV gain+loss 25217958
dgv68n100 CNV gain 25217958
esv2597795 CNV gain 19546169
esv2678817 CNV deletion 23128226
esv2744463 CNV deletion 23290073
esv2750816 CNV gain 17911159
esv2758925 CNV gain+loss 17122850
esv29642 CNV gain+loss 19812545
esv33046 CNV loss 17666407
esv3419518 CNV insertion 20981092
esv3429389 CNV duplication 20981092
esv3444386 CNV duplication 20981092
esv34697 CNV gain 17911159
esv3549677 CNV deletion 23714750
esv3577752 CNV loss 25503493
nsv1001952 CNV gain+loss 25217958
nsv1003019 CNV loss 25217958
nsv1004807 CNV gain+loss 25217958
nsv1008129 CNV gain+loss 25217958
nsv1077283 CNV duplication 25765185
nsv1113083 CNV deletion 24896259
nsv1116446 OTHER inversion 24896259
nsv1145322 CNV deletion 24896259
nsv1152149 CNV duplication 26484159
nsv1161242 CNV duplication 26073780
nsv1161246 CNV duplication 26073780
nsv159149 CNV deletion 16902084
nsv160674 CNV deletion 16902084
nsv221 CNV insertion 15895083
nsv3632 CNV insertion 18451855
nsv3743 CNV deletion 18451855
nsv428421 CNV gain+loss 18775914
nsv435932 CNV insertion 17901297
nsv436039 CNV insertion 17901297
nsv436814 CNV insertion 17901297
nsv469795 CNV gain+loss 16826518
nsv471343 CNV gain 19718026
nsv471344 CNV gain 19718026
nsv471655 CNV gain+loss 15918152
nsv482190 CNV gain 20164927
nsv499577 OTHER inversion 21111241
nsv514916 CNV gain 21397061
nsv545643 CNV loss 21841781
nsv7173 OTHER inversion 18451855
nsv821511 CNV duplication 20802225
nsv829625 CNV gain 20364138
nsv834203 CNV loss 17160897
nsv834247 CNV gain+loss 17160897
nsv9324 CNV gain+loss 18304495
nsv945569 CNV duplication 23825009
nsv945570 CNV duplication 23825009
nsv945571 CNV duplication 23825009
nsv945572 CNV duplication 23825009
nsv945793 CNV duplication 23825009
nsv954847 CNV duplication 24416366
nsv954848 CNV duplication 24416366
nsv957837 CNV deletion 24416366
nsv998073 CNV gain+loss 25217958
nsv999755 CNV gain 25217958

Variation tolerance for NBPF1 Gene

Gene Damage Index Score: 22.83; 99.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NBPF1 Gene

Human Gene Mutation Database (HGMD)
NBPF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NBPF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NBPF1 Gene

Disorders for NBPF1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NBPF1 Gene - From: LncRNADisease, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
astrocytoma
  • astrocytic tumor
neuroblastoma
  • nb
chronic cervicitis
- elite association - COSMIC cancer census association via MalaCards
Search NBPF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NBPF1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NBPF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NBPF1 Gene

Publications for NBPF1 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. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 54
  3. Effects of neuroblastoma breakpoint family member 1 (NBPF1) gene on growth and Akt-p53-Cyclin D pathway in cutaneous squamous carcinoma cells. (PMID: 31058534) Gao Y … Mao Q (Neoplasma 2019) 3 54
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  5. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3 54

ExternalLinks

View latest publications for NBPF1 gene in Mastermind

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