NKX3-2 NK3 homeobox 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NKX3-2provided by HGNC
Official Full Name: NK3 homeobox 2provided by HGNC
Primary source: HGNC:HGNC:951
See related: Ensembl:ENSG00000109705 MIM:602183; AllianceGenome:HGNC:951
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SMMD; BAPX1; NKX3B; NKX3.2
Summary: Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; negative regulation of chondrocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including intestinal epithelial cell development; middle ear morphogenesis; and skeletal system development. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in spleen (RPKM 1.5), ovary (RPKM 0.7) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p15.33

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (13540830..13547744, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (13520522..13527516, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (13542454..13546132, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

BMP7 increases protein synthesis in SW1353 cells and determines rRNA levels in a NKX3-2-dependent manner.
Title: BMP7 increases protein synthesis in SW1353 cells and determines rRNA levels in a NKX3-2-dependent manner.
A novel NKX3-2 mutation causes perinatal lethal spondylo-megaepiphyseal-metaphyseal dysplasia.
Title: A novel NKX3-2 mutation associated with perinatal lethal phenotype of spondylo-megaepiphyseal-metaphyseal dysplasia in a neonate.
NKL homeobox gene NKX2-5 was activated by NKX3-2 in CCRF-CEM and by FOXG1 in PEER, representing mutually inhibitory activators of this translocated oncogene.
Title: Aberrant activity of NKL homeobox gene NKX3-2 in a T-ALL subset.
post-translational modification of Nkx3.2 employing HDAC9-PIASy-RNF4 axis plays a crucial role in controlling chondrocyte viability and hypertrophic maturation during skeletal development in vertebrates.
Title: A post-translational modification cascade employing HDAC9-PIASy-RNF4 axis regulates chondrocyte hypertrophy by modulating Nkx3.2 protein stability.
Bapx1 indicates poor prognosis for gastric cancer patients by promoting tumor migration and invasion via TGF-beta-induced epithelial-mesenchymal transition.
Title: Bapx1 mediates transforming growth factor-β- induced epithelial-mesenchymal transition and promotes a malignancy phenotype of gastric cancer cells.
PI3K-mediated suppression of Nkx3.2 in chondrocytes plays a role in the control of cartilage hypertrophy during skeletal development in vertebrates.
Title: Suppression of Nkx3.2 by phosphatidylinositol-3-kinase signaling regulates cartilage development by modulating chondrocyte hypertrophy.
Our findings indicate that BAPX-1/NKX-3.2 is a molecular switch that is involved in controlling the hypertrophic phenotype of the postdevelopmental (OA) articular chondrocyte.
Title: BAPX-1/NKX-3.2 acts as a chondrocyte hypertrophy molecular switch in osteoarthritis.
Ihh-induced Nkx3.2 degradation requires Wnt5a, which is capable of triggering Nkx3.2 degradation
Title: Indian Hedgehog signalling triggers Nkx3.2 protein degradation during chondrocyte maturation.
Data show that IkappaB kinase beta (IKKbeta) can be activated in the nucleus by Nkx3.2 in the absence of exogenous IKK-activating signals, allowing constitutive nuclear degradation of IkappaB-alpha.
Title: Exogenous signal-independent nuclear IkappaB kinase activation triggered by Nkx3.2 enables constitutive nuclear degradation of IkappaB-alpha in chondrocytes.
NKX3-2 plays an important role in endochondral ossification of both the axial and appendicular skeleton in humans
Title: Homozygous inactivating mutations in the NKX3-2 gene result in spondylo-megaepiphyseal-metaphyseal dysplasia.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spondylo-megaepiphyseal-metaphyseal dysplasia MedGen: C2750066 OMIM: 613330 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-67264 (e-PCR)
- UniSTS:49694

NoName (e-PCR)
- UniSTS:481599

NoName (e-PCR)
- UniSTS:490189

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ formation	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in determination of left/right symmetry	IEA Inferred from Electronic Annotation more info
involved_in embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
involved_in intestinal epithelial cell development	IEA Inferred from Electronic Annotation more info
involved_in middle ear morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of chondrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in pancreas development	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	TAS Traceable Author Statement more info	PubMed
involved_in skeletal system morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in spleen development	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein Nkx-3.2

Names: bagpipe homeobox protein homolog 1; homeobox protein NK-3 homolog B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023192.1 RefSeqGene

Range

4983..8661

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001189.4 → NP_001180.1 homeobox protein Nkx-3.2

See identical proteins and their annotated locations for NP_001180.1

Status: REVIEWED

Source sequence(s)

AC006445, BC111966

Consensus CDS

CCDS3410.1

UniProtKB/Swiss-Prot

P78367, Q2M2I7

Related

ENSP00000371875.5, ENST00000382438.6

Conserved Domains (1) summary

pfam00046
Location:209 → 262

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

13540830..13547744 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416050.1 → XP_047272006.1 homeobox protein Nkx-3.2 isoform X1

UniProtKB/Swiss-Prot

P78367, Q2M2I7
XM_047416049.1 → XP_047272005.1 homeobox protein Nkx-3.2 isoform X1

UniProtKB/Swiss-Prot

P78367, Q2M2I7