This gene encodes a member of the NK family of homeobox-containing proteins. The encoded protein may play a role in skeletal development. [provided by RefSeq, Jul 2008] See more...

Aliases for NKX3-2 Gene

Aliases for NKX3-2 Gene

  • NK3 Homeobox 2 2 3 5
  • NKX3B 2 3 4
  • Bagpipe Homeobox Protein Homolog 1 3 4
  • Homeobox Protein NK-3 Homolog B 3 4
  • Homeobox Protein Nkx-3.2 3 4
  • NKX3.2 2 3
  • BAPX1 3 4
  • Bagpipe Homeobox Homolog 1 (Drosophila) 2
  • NKX3-2 5
  • SMMD 3

External Ids for NKX3-2 Gene

Previous HGNC Symbols for NKX3-2 Gene

  • BAPX1

Previous GeneCards Identifiers for NKX3-2 Gene

  • GC04M013152
  • GC04M012880

Summaries for NKX3-2 Gene

Entrez Gene Summary for NKX3-2 Gene

  • This gene encodes a member of the NK family of homeobox-containing proteins. The encoded protein may play a role in skeletal development. [provided by RefSeq, Jul 2008]

GeneCards Summary for NKX3-2 Gene

NKX3-2 (NK3 Homeobox 2) is a Protein Coding gene. Diseases associated with NKX3-2 include Spondylo-Megaepiphyseal-Metaphyseal Dysplasia and Metaphyseal Dysplasia. Among its related pathways are Endochondral Ossification. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific. An important paralog of this gene is NKX3-1.

UniProtKB/Swiss-Prot Summary for NKX3-2 Gene

  • Transcriptional repressor that acts as a negative regulator of chondrocyte maturation. PLays a role in distal stomach development; required for proper antral-pyloric morphogenesis and development of antral-type epithelium. In concert with GSC, defines the structural components of the middle ear; required for tympanic ring and gonium development and in the regulation of the width of the malleus (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NKX3-2 Gene

Genomics for NKX3-2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NKX3-2 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
GH04J013544 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 263.7 -0.1 -93 3.6 MYC ZNF592 ZIC2 ZNF341 MNT MAX SIN3A ELF1 KLF9 SP2 NKX3-2 BOD1L1 RAB28 HSALNG0033003 LINC01096
GH04J013542 Enhancer 0.3 ENCODE 250.7 +2.0 1969 0 CTCF EZH2 NKX3-2 RAB28 LINC01097
GH04J013482 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 5.4 +60.6 60605 3.4 ZNF207 JUND ATF2 BRCA1 POLR2A NFIC ZBTB10 YY1 NONO CTCF RAB28 HSALNG0032998 LOC105374495 lnc-CPEB2-17 NKX3-2 BOD1L1 lnc-CPEB2-13
GH04J013546 Promoter/Enhancer 1.1 Ensembl ENCODE 8 -3.4 -3393 1.8 KLF9 SP2 BHLHE40 CTCF ELF1 TAF1 ZBTB33 IKZF1 BACH1 HDAC2 LINC01096 HSALNG0033003 NKX3-2 BOD1L1
GH04J013548 Promoter/Enhancer 1.1 Ensembl ENCODE 7.5 -5.0 -4992 1 BCLAF1 ZNF207 ZNF654 ZNF600 CTCF REST ZNF592 TRIM22 FEZF1 RAD21 LINC01096 NKX3-2 piR-31534-518 BOD1L1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NKX3-2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NKX3-2

Top Transcription factor binding sites by QIAGEN in the NKX3-2 gene promoter:
  • Arnt
  • Sox9

Genomic Locations for NKX3-2 Gene

Latest Assembly
chr4:13,540,830-13,544,508
(GRCh38/hg38)
Size:
3,679 bases
Orientation:
Minus strand

Previous Assembly
chr4:13,542,454-13,546,132
(GRCh37/hg19 by Entrez Gene)
Size:
3,679 bases
Orientation:
Minus strand

chr4:13,542,454-13,546,674
(GRCh37/hg19 by Ensembl)
Size:
4,221 bases
Orientation:
Minus strand

Genomic View for NKX3-2 Gene

Genes around NKX3-2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NKX3-2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NKX3-2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NKX3-2 Gene

Proteins for NKX3-2 Gene

  • Protein details for NKX3-2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78367-NKX32_HUMAN
    Recommended name:
    Homeobox protein Nkx-3.2
    Protein Accession:
    P78367
    Secondary Accessions:
    • Q2M2I7

    Protein attributes for NKX3-2 Gene

    Size:
    333 amino acids
    Molecular mass:
    34814 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NKX3-2 Gene

Post-translational modifications for NKX3-2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NKX3-2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for NKX3-2
  • Boster Bio Antibodies for NKX3-2
  • Santa Cruz Biotechnology (SCBT) Antibodies for NKX3-2

No data available for DME Specific Peptides for NKX3-2 Gene

Domains & Families for NKX3-2 Gene

Gene Families for NKX3-2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for NKX3-2 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature

Suggested Antigen Peptide Sequences for NKX3-2 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein NK-3 homolog B (NKX32_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P78367

UniProtKB/Swiss-Prot:

NKX32_HUMAN :
  • Belongs to the NK-3 homeobox family.
Family:
  • Belongs to the NK-3 homeobox family.
genes like me logo Genes that share domains with NKX3-2: view

Function for NKX3-2 Gene

Molecular function for NKX3-2 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional repressor that acts as a negative regulator of chondrocyte maturation. PLays a role in distal stomach development; required for proper antral-pyloric morphogenesis and development of antral-type epithelium. In concert with GSC, defines the structural components of the middle ear; required for tympanic ring and gonium development and in the regulation of the width of the malleus (By similarity).

Phenotypes From GWAS Catalog for NKX3-2 Gene

Gene Ontology (GO) - Molecular Function for NKX3-2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA,IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with NKX3-2: view
genes like me logo Genes that share phenotypes with NKX3-2: view

Human Phenotype Ontology for NKX3-2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NKX3-2 Gene

MGI Knock Outs for NKX3-2:
Targeted motifs for NKX3-2 Gene
HOMER Transcription Factor Regulatory Elements motif NKX3-2
  • Consensus sequence: TTRAGTGSYK Submotif: canonical Cell Type: VertebralCol GEO ID: GSE36672

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NKX3-2

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for NKX3-2 Gene

Localization for NKX3-2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NKX3-2 Gene

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 NKX3-2 gene
Compartment Confidence
nucleus 5
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NKX3-2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with NKX3-2: view

Pathways & Interactions for NKX3-2 Gene

PathCards logo

SuperPathways for NKX3-2 Gene

SuperPathway Contained pathways
1 Endochondral Ossification
genes like me logo Genes that share pathways with NKX3-2: view

Pathways by source for NKX3-2 Gene

1 BioSystems pathway for NKX3-2 Gene

Gene Ontology (GO) - Biological Process for NKX3-2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001501 skeletal system development IEA,TAS 9344671
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0006366 transcription by RNA polymerase II TAS 9344671
genes like me logo Genes that share ontologies with NKX3-2: view

No data available for SIGNOR curated interactions for NKX3-2 Gene

Drugs & Compounds for NKX3-2 Gene

No Compound Related Data Available

Transcripts for NKX3-2 Gene

mRNA/cDNA for NKX3-2 Gene

1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
1 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 NKX3-2

Alternative Splicing Database (ASD) splice patterns (SP) for NKX3-2 Gene

No ASD Table

Relevant External Links for NKX3-2 Gene

GeneLoc Exon Structure for
NKX3-2

Expression for NKX3-2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NKX3-2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NKX3-2 Gene

This gene is overexpressed in Colon - Sigmoid (x19.2), Colon - Transverse (x8.4), and Stomach (x4.2).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NKX3-2

SOURCE GeneReport for Unigene cluster for NKX3-2 Gene:

Hs.590927

mRNA Expression by UniProt/SwissProt for NKX3-2 Gene:

P78367-NKX32_HUMAN
Tissue specificity: Expressed at highest levels in cartilage, bone (osteosarcoma) and gut (small intestine and colon), whereas moderate expression is seen in trachea and brain. Expressed in visceral mesoderm and embryonic skeleton.

Evidence on tissue expression from TISSUES for NKX3-2 Gene

  • Muscle(2.3)
  • Heart(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NKX3-2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • eye
  • head
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
Pelvis:
  • pelvis
  • testicle
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with NKX3-2: view

Primer products for research

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for NKX3-2 Gene

Orthologs for NKX3-2 Gene

This gene was present in the common ancestor of animals.

Orthologs for NKX3-2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NKX3-2 29 30
  • 99.38 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia NKX3-2 29 30
  • 89.7 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NKX3-2 29 30
  • 87.71 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Nkx3-2 29 16 30
  • 83.98 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia NKX3-2 30
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nkx3-2 29
  • 66.67 (n)
African clawed frog
(Xenopus laevis)
Amphibia bapx1-A 29
Zebrafish
(Danio rerio)
Actinopterygii nkx3.2 29 30
  • 67.49 (n)
OneToOne
bapx1 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6919 29
Fruit Fly
(Drosophila melanogaster)
Insecta bap 30
  • 25 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ceh-27 30
  • 19 (a)
ManyToMany
Species where no ortholog for NKX3-2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • 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)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • 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)
  • Wheat (Triticum aestivum)

Evolution for NKX3-2 Gene

ENSEMBL:
Gene Tree for NKX3-2 (if available)
TreeFam:
Gene Tree for NKX3-2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NKX3-2: view image
Alliance of Genome Resources:
Additional Orthologs for NKX3-2

Paralogs for NKX3-2 Gene

genes like me logo Genes that share paralogs with NKX3-2: view

Variants for NKX3-2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NKX3-2 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
1024320 Uncertain Significance: not provided 13,543,942(-) AG/A
NM_001189.4(NKX3-2):c.466+6del
INTRON
1031215 Uncertain Significance: Spondylo-megaepiphyseal-metaphyseal dysplasia 13,544,120(-) C/T
NM_001189.4(NKX3-2):c.295G>A (p.Glu99Lys)
MISSENSE
1043487 Uncertain Significance: not provided 13,544,279(-) CC/AT
NM_001189.4(NKX3-2):c.135_136delinsAT (p.Ala46Ser)
MISSENSE
1047713 Uncertain Significance: not provided 13,542,361(-) C/A
NM_001189.4(NKX3-2):c.634G>T (p.Ala212Ser)
MISSENSE
999293 Uncertain Significance: not provided 13,544,216(-) C/T
NM_001189.4(NKX3-2):c.199G>A (p.Glu67Lys)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NKX3-2 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 NKX3-2 Gene

Variant ID Type Subtype PubMed ID
nsv1014473 CNV gain 25217958
nsv593750 CNV gain 21841781

Variation tolerance for NKX3-2 Gene

Gene Damage Index Score: 1.68; 32.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NKX3-2 Gene

Human Gene Mutation Database (HGMD)
NKX3-2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NKX3-2
Leiden Open Variation Database (LOVD)
NKX3-2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NKX3-2 Gene

Disorders for NKX3-2 Gene

MalaCards: The human disease database

(13) MalaCards diseases for NKX3-2 Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

NKX32_HUMAN
  • Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD) [MIM:613330]: A skeletal dysplasia characterized by disproportionate short stature with a short and stiff neck and trunk, relatively long limbs that may show flexion contractures of the distal joints, delayed and impaired ossification of the vertebral bodies, the presence of large epiphyseal ossification centers and wide growth plates in the long tubular bones, and numerous pseudoepiphyses of the short tubular bones in hands and feet. {ECO:0000269 PubMed:20004766}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for NKX3-2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with NKX3-2: view

No data available for Genatlas for NKX3-2 Gene

Publications for NKX3-2 Gene

  1. Homozygous inactivating mutations in the NKX3-2 gene result in spondylo-megaepiphyseal-metaphyseal dysplasia. (PMID: 20004766) Hellemans J … Mortier G (American journal of human genetics 2009) 3 4 72
  2. Sequence and chromosomal assignment of human BAPX1, a bagpipe-related gene, to 4p16.1: a candidate gene for skeletal dysplasia. (PMID: 9344671) Yoshiura KI … Murray JC (Genomics 1997) 2 3 4
  3. Bapx1: an evolutionary conserved homologue of the Drosophila bagpipe homeobox gene is expressed in splanchnic mesoderm and the embryonic skeleton. (PMID: 9256352) Tribioli C … Lufkin T (Mechanisms of development 1997) 3 4 22
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Molecular cloning, chromosomal mapping and developmental expression of BAPX1, a novel human homeobox-containing gene homologous to Drosophila bagpipe. (PMID: 9426254) Tribioli C … Lufkin T (Gene 1997) 3 4

Products for NKX3-2 Gene

Sources for NKX3-2 Gene