Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	579
Gene name	NK3 homeobox 2
Gene symbol	NKX3-2
Synonyms (NCBI Gene)	BAPX1NKX3.2NKX3BSMMD
Chromosome	4
Chromosome location	4p15.33
Summary	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]

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs371597026	A>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs606231352	C>-,CC	Pathogenic	Frameshift variant, coding sequence variant
rs606231353	CC>A	Pathogenic	Frameshift variant, coding sequence variant
rs606231354	GGGCGCC>-	Pathogenic	Frameshift variant, coding sequence variant
rs921673580	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs1560165127	TG>-	Pathogenic-likely-pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (59)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018824	hsa-miR-335-5p	Microarray	18185580
MIRT025136	hsa-miR-181a-5p	Microarray	17612493
MIRT030139	hsa-miR-26b-5p	Microarray	19088304
MIRT644805	hsa-miR-4762-5p	HITS-CLIP	23824327
MIRT644804	hsa-miR-4719	HITS-CLIP	23824327
MIRT644803	hsa-miR-101-3p	HITS-CLIP	23824327
MIRT644802	hsa-miR-582-5p	HITS-CLIP	23824327
MIRT644801	hsa-miR-513b-5p	HITS-CLIP	23824327
MIRT644800	hsa-miR-2681-5p	HITS-CLIP	23824327
MIRT644805	hsa-miR-4762-5p	HITS-CLIP	23824327
MIRT644804	hsa-miR-4719	HITS-CLIP	23824327
MIRT644803	hsa-miR-101-3p	HITS-CLIP	23824327
MIRT644802	hsa-miR-582-5p	HITS-CLIP	23824327
MIRT644801	hsa-miR-513b-5p	HITS-CLIP	23824327
MIRT644800	hsa-miR-2681-5p	HITS-CLIP	23824327
MIRT1186608	hsa-miR-3135b	CLIP-seq
MIRT1186609	hsa-miR-4300	CLIP-seq
MIRT1186610	hsa-miR-4487	CLIP-seq
MIRT1186611	hsa-miR-4633-3p	CLIP-seq
MIRT1186612	hsa-miR-5096	CLIP-seq
MIRT1186613	hsa-miR-629	CLIP-seq
MIRT1186614	hsa-miR-920	CLIP-seq
MIRT2054088	hsa-miR-1254	CLIP-seq
MIRT2054089	hsa-miR-2467-3p	CLIP-seq
MIRT2054090	hsa-miR-3116	CLIP-seq
MIRT2054091	hsa-miR-4446-3p	CLIP-seq
MIRT2054092	hsa-miR-4455	CLIP-seq
MIRT2054093	hsa-miR-4514	CLIP-seq
MIRT2054094	hsa-miR-4645-5p	CLIP-seq
MIRT2054095	hsa-miR-4673	CLIP-seq
MIRT2054096	hsa-miR-4692	CLIP-seq
MIRT2054097	hsa-miR-4721	CLIP-seq
MIRT2054098	hsa-miR-609	CLIP-seq
MIRT2054099	hsa-miR-661	CLIP-seq
MIRT2283235	hsa-miR-1252	CLIP-seq
MIRT2054088	hsa-miR-1254	CLIP-seq
MIRT2054089	hsa-miR-2467-3p	CLIP-seq
MIRT2054090	hsa-miR-3116	CLIP-seq
MIRT2283236	hsa-miR-378	CLIP-seq
MIRT2283237	hsa-miR-378b	CLIP-seq
MIRT2283238	hsa-miR-378c	CLIP-seq
MIRT2283239	hsa-miR-378d	CLIP-seq
MIRT2283240	hsa-miR-378e	CLIP-seq
MIRT2283241	hsa-miR-378f	CLIP-seq
MIRT2283242	hsa-miR-378h	CLIP-seq
MIRT2283243	hsa-miR-378i	CLIP-seq
MIRT2283244	hsa-miR-3919	CLIP-seq
MIRT2283245	hsa-miR-422a	CLIP-seq
MIRT2054091	hsa-miR-4446-3p	CLIP-seq
MIRT2054092	hsa-miR-4455	CLIP-seq
MIRT2283246	hsa-miR-4491	CLIP-seq
MIRT2283247	hsa-miR-4657	CLIP-seq
MIRT2054097	hsa-miR-4721	CLIP-seq
MIRT2283248	hsa-miR-4755-3p	CLIP-seq
MIRT2283249	hsa-miR-4756-3p	CLIP-seq
MIRT2283250	hsa-miR-576-3p	CLIP-seq
MIRT2054098	hsa-miR-609	CLIP-seq
MIRT2054099	hsa-miR-661	CLIP-seq
MIRT2283251	hsa-miR-933	CLIP-seq

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0001501	Process	Skeletal system development	IEA
GO:0001501	Process	Skeletal system development	IEA
GO:0001501	Process	Skeletal system development	TAS	9344671
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006366	Process	Transcription by RNA polymerase II	TAS	9344671
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0030154	Process	Cell differentiation	IBA
GO:0031016	Process	Pancreas development	IEA
GO:0032331	Process	Negative regulation of chondrocyte differentiation	IEA
GO:0032331	Process	Negative regulation of chondrocyte differentiation	ISS
GO:0042474	Process	Middle ear morphogenesis	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0048513	Process	Animal organ development	IEA
GO:0048536	Process	Spleen development	IEA
GO:0048645	Process	Animal organ formation	IEA
GO:0048705	Process	Skeletal system morphogenesis	IEA
GO:0048706	Process	Embryonic skeletal system development	IEA
GO:0055123	Process	Digestive system development	IEA
GO:0060576	Process	Intestinal epithelial cell development	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

MIM	HGNC	e!Ensembl
602183	951	ENSG00000109705

P78367

Protein name

Homeobox protein Nkx-3.2 (Bagpipe homeobox protein homolog 1) (Homeobox protein NK-3 homolog B)

Protein 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, d

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00046	Homeodomain	207 → 263	Homeodomain	Domain

Tissue specificity

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. {ECO:0000269|PubMed:200

Sequence

MAVRGANTLTSFSIQAILNKKEERGGLAAPEGRPAPGGTAASVAAAPAVCCWRLFGERDA
GALGGAEDSLLASPAGTRTAAGRTAESPEGWDSDSALSEENESRRRCADARGASGAGLAG
GSLSLGQPVCELAASKDLEEEAAGRSDSEMSASVSGDRSPRTEDDGVGPRGAHVSALCSG
AGGGGGSGPAGVAEEEEEPAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLA
ASLKLTETQVKIWFQNRRYKTKRRQMAADLLASAPAAKKVAVKVLVRDDQRQYLPGEVLR
PPSLLPLQPSYYYPYYCLPGWALSTCAAAAGTQ

Sequence length

333

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Connective tissue disorder	Likely pathogenic	rs2109005842	RCV002278789	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylo-megaepiphyseal-metaphyseal dysplasia	Pathogenic; Likely pathogenic	rs606231352, rs606231353, rs606231354, rs1560165127	RCV000007920 RCV000007921 RCV000007922 RCV000684827	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CONNECTIVE TISSUE DISEASES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NKX3-2-related disorder	Uncertain significance; Likely benign; Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (15)

Disease Name	Disease (Merged)	Source	PMID	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Congenital small ears	Microtia	GENOMICS_ENGLAND_DG	9426254	★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	28315334	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28315334, 29746601	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteochondrodysplasias	Osteochondrodysplasia	BEFREE	9344671	★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	Lymphoblastic Leukemia	BEFREE	29746601	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pyle metaphyseal dysplasia	Pyle Metaphyseal Dysplasia	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
Skeletal dysplasia	Skeletal Dysplasia	BEFREE	9344671	★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	BEFREE	20004766, 29704686	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	ORPHANET_DG	20004766	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylo-megaepiphyseal-metaphyseal dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	Orphanet		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	CLINVAR_DG	29704686	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	GENOMICS_ENGLAND_DG	9426254	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	CTD_human_DG		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Stomach Carcinoma	Stomach Carcinoma	BEFREE	28315334	★★★★★ ★☆☆☆☆ Found in Text Mining only

NKX3-2 (NK3 homeobox 2)