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 NBPF6 Gene

Aliases for NBPF6 Gene

  • NBPF Member 6 2 3 5
  • Neuroblastoma Breakpoint Family Member 6 3 4
  • Neuroblastoma Breakpoint Family, Member 6 2
  • NBPF6 5

External Ids for NBPF6 Gene

Previous GeneCards Identifiers for NBPF6 Gene

  • GC01U901190
  • GC01P108720
  • GC01P108794
  • GC01P108919
  • GC01P108376

Summaries for NBPF6 Gene

Entrez Gene Summary for NBPF6 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. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2013]

GeneCards Summary for NBPF6 Gene

NBPF6 (NBPF Member 6) is a Protein Coding gene. Diseases associated with NBPF6 include Hydrolethalus Syndrome 1 and Hydrolethalus Syndrome 2. An important paralog of this gene is NBPF4.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NBPF6 Gene

Genomics for NBPF6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NBPF6 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
GH01J108421 Promoter 0.3 Ensembl 250.7 -0.7 -695 6.8 ENSG00000224698 NBPF6 SLC25A24P2 lnc-NBPF4-2 HSALNG0005804 NBPF4
GH01J108450 Promoter 0.3 EPDnew 250.3 +28.8 28828 0.1 HSALNG0005804 piR-30795-003 piR-46858-003 piR-35882-003 piR-39270-003 piR-52369-003 NBPF6 FAM102B
GH01J108556 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 0.1 +137.7 137710 6.4 TBP SP1 NR2C1 DEK IKZF1 SMAD5 IRF2 HES1 MBD2 ZNF217 FAM102B lnc-HENMT1-4 PRPF38B SLC25A24 HSALNG0005815 NBPF6
GH01J108504 Enhancer 0.9 Ensembl 0.2 +84.0 84005 2.6 MNT IKZF1 HES1 BHLHE40 MCM7 MCM3 ARNT GABPA NFATC3 NBN SLC25A24 PRPF38B ENSG00000228665 FAM102B RPL17P7 HSALNG0005810 LOC100420170 lnc-NBPF6-7 NBPF6
GH01J108501 Enhancer 0.8 Ensembl ENCODE 0.2 +81.5 81479 2 BRCA1 CEBPB EP300 RXRA RAD21 RFX5 TEAD3 STAT3 TBP ZNF316 ENSG00000283354 HSALNG0005810 ST13P21 FAM102B SLC25A24 PRPF38B LOC100420170 lnc-NBPF6-7 NBPF6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NBPF6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NBPF6

Top Transcription factor binding sites by QIAGEN in the NBPF6 gene promoter:
  • AP-4

Genomic Locations for NBPF6 Gene

Latest Assembly
50,425 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
21,578 bases
Plus strand

(GRCh37/hg19 by Ensembl)
95,204 bases
Plus strand

Genomic View for NBPF6 Gene

Genes around NBPF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NBPF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NBPF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NBPF6 Gene

Proteins for NBPF6 Gene

  • Protein details for NBPF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuroblastoma breakpoint family member 6
    Protein Accession:
    Secondary Accessions:
    • A4QN25

    Protein attributes for NBPF6 Gene

    638 amino acids
    Molecular mass:
    72239 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.

    Alternative splice isoforms for NBPF6 Gene


neXtProt entry for NBPF6 Gene

Post-translational modifications for NBPF6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NBPF6 Gene

Domains & Families for NBPF6 Gene

Gene Families for NBPF6 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NBPF6 Gene


Suggested Antigen Peptide Sequences for NBPF6 Gene

GenScript: Design optimal peptide antigens:
  • Neuroblastoma breakpoint family member 6 (NBPF6_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 NBPF6: view

Function for NBPF6 Gene

Phenotypes From GWAS Catalog for NBPF6 Gene

Phenotypes for NBPF6 Gene

genes like me logo Genes that share phenotypes with NBPF6: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NBPF6

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for NBPF6 Gene

Localization for NBPF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NBPF6 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 NBPF6 gene
Compartment Confidence
nucleus 2
cytosol 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for NBPF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NBPF6: view

Pathways & Interactions for NBPF6 Gene

PathCards logo

SuperPathways for NBPF6 Gene

No Data Available

Interacting Proteins for NBPF6 Gene

Gene Ontology (GO) - Biological Process for NBPF6 Gene


No data available for Pathways by source and SIGNOR curated interactions for NBPF6 Gene

Drugs & Compounds for NBPF6 Gene

No Compound Related Data Available

Transcripts for NBPF6 Gene

mRNA/cDNA for NBPF6 Gene

1 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 NBPF6

Alternative Splicing Database (ASD) splice patterns (SP) for NBPF6 Gene

No ASD Table

Relevant External Links for NBPF6 Gene

GeneLoc Exon Structure for

Expression for NBPF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NBPF6 Gene

mRNA differential expression in normal tissues according to GTEx for NBPF6 Gene

This gene is overexpressed in Testis (x21.2), Small Intestine - Terminal Ileum (x6.0), and Brain - Putamen (basal ganglia) (x5.2).

Protein differential expression in normal tissues from HIPED for NBPF6 Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NBPF6 Gene

Protein tissue co-expression partners for NBPF6 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NBPF6

SOURCE GeneReport for Unigene cluster for NBPF6 Gene:


Evidence on tissue expression from TISSUES for NBPF6 Gene

  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with NBPF6: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NBPF6 Gene

Orthologs for NBPF6 Gene

This gene was present in the common ancestor of mammals.

Orthologs for NBPF6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LOC740049 30
  • 98.1 (n)
-- 31
  • 94 (a)
(Bos Taurus)
Mammalia LOC101903302 30
  • 63.35 (n)
-- 31
  • 40 (a)
-- 31
  • 35 (a)
(Canis familiaris)
Mammalia -- 31
  • 40 (a)
Species where no ortholog for NBPF6 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)
  • 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 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for NBPF6 Gene

Gene Tree for NBPF6 (if available)
Gene Tree for NBPF6 (if available)

Paralogs for NBPF6 Gene

(17) SIMAP similar genes for NBPF6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with NBPF6: view

Variants for NBPF6 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NBPF6 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 NBPF6 Gene

Variant ID Type Subtype PubMed ID
dgv250n100 CNV gain 25217958
dgv481n54 CNV loss 21841781
dgv486n54 CNV loss 21841781
dgv75e212 CNV gain 25503493
dgv76e212 CNV loss 25503493
esv23343 CNV gain+loss 19812545
esv2758958 CNV gain+loss 17122850
esv3391223 CNV duplication 20981092
nsv10606 CNV loss 18304495
nsv1128597 CNV duplication 24896259
nsv1148137 CNV duplication 26484159
nsv1161257 CNV deletion 26073780
nsv2276 CNV deletion 18451855
nsv428179 CNV gain 18775914
nsv498679 CNV loss 21111241
nsv547410 CNV gain 21841781
nsv821488 CNV deletion 20802225
nsv823886 CNV gain 20364138
nsv946124 CNV duplication 23825009
nsv951369 CNV deletion 24416366

Variation tolerance for NBPF6 Gene

Gene Damage Index Score: 12.04; 93.75% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NBPF6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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 NBPF6 Gene

Disorders for NBPF6 Gene

MalaCards: The human disease database

(4) MalaCards diseases for NBPF6 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
hydrolethalus syndrome 1
  • hls1
hydrolethalus syndrome 2
  • hls2
  • nb
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards
Search NBPF6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NBPF6

genes like me logo Genes that share disorders with NBPF6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NBPF6 Gene

Publications for NBPF6 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
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. (PMID: 28986522) Antoniali G … Tell G (Nature communications 2017) 3
  4. Evolutionary history and genome organization of DUF1220 protein domains. (PMID: 22973535) O'Bleness MS … Sikela JM (G3 (Bethesda, Md.) 2012) 3
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 4

Products for NBPF6 Gene

Sources for NBPF6 Gene