NKX3-2 (NK3 homeobox 2)

Gene

• Entrez ID: 579
• Gene name: NK3 homeobox 2
• Gene symbol: NKX3-2
• Synonyms: BAPX1, NKX3.2, NKX3B, SMMD
• 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]

SNPs

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

miRNA

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

Gene ontology (GO)

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	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
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	TAS	9344671
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA	21873635
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
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	21873635
GO:0031016	Process	Pancreas development	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: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:0060576	Process	Intestinal epithelial cell development	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 602183
• HGNC: 951
• e!Ensembl: ENSG00000109705

Protein

• UniProt ID: 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

• Sequence:

  MAVRGANTLTSFSIQAILNKKEERGGLAAPEGRPAPGGTAASVAAAPAVCCWRLFGERDA
  GALGGAEDSLLASPAGTRTAAGRTAESPEGWDSDSALSEENESRRRCADARGASGAGLAG
  GSLSLGQPVCELAASKDLEEEAAGRSDSEMSASVSGDRSPRTEDDGVGPRGAHVSALCSG
  AGGGGGSGPAGVAEEEEEPAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLA
  ASLKLTETQVKIWFQNRRYKTKRRQMAADLLASAPAAKKVAVKVLVRDDQRQYLPGEVLR
  PPSLLPLQPSYYYPYYCLPGWALSTCAAAAGTQ

• Sequence length: 333

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Macrocephaly	Macrocephaly	rs786204854, rs764333096, rs1557739557
Pyle metaphyseal dysplasia	Pyle metaphyseal dysplasia	rs879255603, rs755007671, rs879253778
Spondylo-megaepiphyseal-metaphyseal dysplasia	Spondylo-Megaepiphyseal-Metaphyseal Dysplasia	rs606231352, rs606231353, rs606231354, rs1560165127	20004766, 29704686, 9426254

Unknown
Disease name	Disease term	dbSNP ID	References
Microtia	Congenital small ears		9426254