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MSX2 (msh homeobox 2)

Gene

4488

Msh homeobox 2

MSX2

CRS2, FPP, HOX8, MSH, PFM, PFM1

5q35.2

This gene encodes a member of the muscle segment homeobox gene family. The encoded protein is a transcriptional repressor whose normal activity may establish a balance between survival and apoptosis of neural crest-derived cells required for proper cranio

Show/Hide all(6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104893895	C>A,T	Likely-pathogenic, pathogenic	3 prime UTR variant, coding sequence variant, missense variant
rs104893896	G>A	Pathogenic	3 prime UTR variant, coding sequence variant, missense variant
rs121912971	GC>TA	Pathogenic	Stop gained, coding sequence variant
rs121912972	G>-	Pathogenic	Stop gained, coding sequence variant
rs1561643029	->ATTG	Pathogenic	3 prime UTR variant, frameshift variant, coding sequence variant
rs1561643060	AGACCCAG>-	Pathogenic	3 prime UTR variant, frameshift variant, coding sequence variant

Show/Hide all(254)

miRTarBase ID	miRNA	Experiments	Reference
MIRT000728	hsa-miR-135b-5p	Review	19574400
MIRT724823	hsa-miR-4293	HITS-CLIP	19536157
MIRT724822	hsa-miR-148b-5p	HITS-CLIP	19536157
MIRT724821	hsa-miR-6874-3p	HITS-CLIP	19536157
MIRT724820	hsa-miR-4277	HITS-CLIP	19536157
MIRT724819	hsa-miR-181a-2-3p	HITS-CLIP	19536157
MIRT724818	hsa-miR-1273g-3p	HITS-CLIP	19536157
MIRT724817	hsa-miR-3660	HITS-CLIP	19536157
MIRT724816	hsa-miR-4526	HITS-CLIP	19536157
MIRT724815	hsa-miR-4742-3p	HITS-CLIP	19536157
MIRT724814	hsa-miR-2277-3p	HITS-CLIP	19536157
MIRT724813	hsa-miR-6509-3p	HITS-CLIP	19536157
MIRT724812	hsa-miR-4436b-5p	HITS-CLIP	19536157
MIRT724811	hsa-miR-3686	HITS-CLIP	19536157
MIRT724810	hsa-miR-3692-3p	HITS-CLIP	19536157
MIRT724809	hsa-miR-503-3p	HITS-CLIP	19536157
MIRT650547	hsa-miR-587	HITS-CLIP	23824327
MIRT641655	hsa-miR-6787-3p	HITS-CLIP	23824327
MIRT641654	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT641653	hsa-miR-6879-3p	HITS-CLIP	23824327
MIRT641652	hsa-miR-4691-5p	HITS-CLIP	23824327
MIRT641651	hsa-miR-6792-3p	HITS-CLIP	23824327
MIRT491440	hsa-miR-3928-5p	PAR-CLIP	23592263
MIRT491438	hsa-miR-6806-3p	PAR-CLIP	23592263
MIRT491439	hsa-miR-1252-5p	PAR-CLIP	23592263
MIRT491437	hsa-miR-3195	PAR-CLIP	23592263
MIRT491436	hsa-miR-4533	PAR-CLIP	23592263
MIRT491435	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT491434	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT491439	hsa-miR-1252-5p	PAR-CLIP	26701625
MIRT491439	hsa-miR-1252-5p	PAR-CLIP	26701625
MIRT491439	hsa-miR-1252-5p	PAR-CLIP	26701625
MIRT491439	hsa-miR-1252-5p	PAR-CLIP	26701625
MIRT491437	hsa-miR-3195	PAR-CLIP	26701625
MIRT491437	hsa-miR-3195	PAR-CLIP	26701625
MIRT491437	hsa-miR-3195	PAR-CLIP	26701625
MIRT491437	hsa-miR-3195	PAR-CLIP	26701625
MIRT491440	hsa-miR-3928-5p	PAR-CLIP	26701625
MIRT491436	hsa-miR-4533	PAR-CLIP	26701625
MIRT491436	hsa-miR-4533	PAR-CLIP	26701625
MIRT491436	hsa-miR-4533	PAR-CLIP	26701625
MIRT491435	hsa-miR-4747-5p	PAR-CLIP	26701625
MIRT491435	hsa-miR-4747-5p	PAR-CLIP	26701625
MIRT491435	hsa-miR-4747-5p	PAR-CLIP	26701625
MIRT491435	hsa-miR-4747-5p	PAR-CLIP	26701625
MIRT491434	hsa-miR-5196-5p	PAR-CLIP	26701625
MIRT491434	hsa-miR-5196-5p	PAR-CLIP	26701625
MIRT491434	hsa-miR-5196-5p	PAR-CLIP	26701625
MIRT491434	hsa-miR-5196-5p	PAR-CLIP	26701625
MIRT491438	hsa-miR-6806-3p	PAR-CLIP	26701625
MIRT736458	hsa-miR-410-3p	Luciferase reporter assay, Western blotting, Immunohistochemistry (IHC), qRT-PCR	33209671
MIRT724823	hsa-miR-4293	HITS-CLIP	19536157
MIRT724822	hsa-miR-148b-5p	HITS-CLIP	19536157
MIRT724821	hsa-miR-6874-3p	HITS-CLIP	19536157
MIRT724820	hsa-miR-4277	HITS-CLIP	19536157
MIRT724819	hsa-miR-181a-2-3p	HITS-CLIP	19536157
MIRT724818	hsa-miR-1273g-3p	HITS-CLIP	19536157
MIRT724817	hsa-miR-3660	HITS-CLIP	19536157
MIRT724816	hsa-miR-4526	HITS-CLIP	19536157
MIRT724815	hsa-miR-4742-3p	HITS-CLIP	19536157
MIRT724814	hsa-miR-2277-3p	HITS-CLIP	19536157
MIRT724813	hsa-miR-6509-3p	HITS-CLIP	19536157
MIRT724812	hsa-miR-4436b-5p	HITS-CLIP	19536157
MIRT724811	hsa-miR-3686	HITS-CLIP	19536157
MIRT724810	hsa-miR-3692-3p	HITS-CLIP	19536157
MIRT724809	hsa-miR-503-3p	HITS-CLIP	19536157
MIRT650547	hsa-miR-587	HITS-CLIP	23824327
MIRT641655	hsa-miR-6787-3p	HITS-CLIP	23824327
MIRT641654	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT641653	hsa-miR-6879-3p	HITS-CLIP	23824327
MIRT641652	hsa-miR-4691-5p	HITS-CLIP	23824327
MIRT641651	hsa-miR-6792-3p	HITS-CLIP	23824327
MIRT491440	hsa-miR-3928-5p	PAR-CLIP	23592263
MIRT491438	hsa-miR-6806-3p	PAR-CLIP	23592263
MIRT491439	hsa-miR-1252-5p	PAR-CLIP	23592263
MIRT491437	hsa-miR-3195	PAR-CLIP	23592263
MIRT491436	hsa-miR-4533	PAR-CLIP	23592263
MIRT491435	hsa-miR-4747-5p	PAR-CLIP	23592263
MIRT491434	hsa-miR-5196-5p	PAR-CLIP	23592263
MIRT1162039	hsa-miR-1185	CLIP-seq
MIRT1162040	hsa-miR-1197	CLIP-seq
MIRT1162041	hsa-miR-1237	CLIP-seq
MIRT1162042	hsa-miR-1253	CLIP-seq
MIRT1162043	hsa-miR-1294	CLIP-seq
MIRT1162044	hsa-miR-1323	CLIP-seq
MIRT1162045	hsa-miR-135a	CLIP-seq
MIRT1162046	hsa-miR-135b	CLIP-seq
MIRT1162047	hsa-miR-142-5p	CLIP-seq
MIRT1162048	hsa-miR-1908	CLIP-seq
MIRT1162049	hsa-miR-1913	CLIP-seq
MIRT1162050	hsa-miR-197	CLIP-seq
MIRT1162051	hsa-miR-3117-3p	CLIP-seq
MIRT1162052	hsa-miR-3119	CLIP-seq
MIRT1162053	hsa-miR-3121-5p	CLIP-seq
MIRT1162054	hsa-miR-3151	CLIP-seq
MIRT1162055	hsa-miR-3163	CLIP-seq
MIRT1162056	hsa-miR-3180	CLIP-seq
MIRT1162057	hsa-miR-3180-3p	CLIP-seq
MIRT1162058	hsa-miR-3196	CLIP-seq
MIRT1162059	hsa-miR-324-3p	CLIP-seq
MIRT1162060	hsa-miR-329	CLIP-seq
MIRT1162061	hsa-miR-3605-5p	CLIP-seq
MIRT1162062	hsa-miR-362-3p	CLIP-seq
MIRT1162063	hsa-miR-3647-3p	CLIP-seq
MIRT1162064	hsa-miR-3653	CLIP-seq
MIRT1162065	hsa-miR-3658	CLIP-seq
MIRT1162066	hsa-miR-3679-5p	CLIP-seq
MIRT1162067	hsa-miR-3691-3p	CLIP-seq
MIRT1162068	hsa-miR-3919	CLIP-seq
MIRT1162069	hsa-miR-3941	CLIP-seq
MIRT1162070	hsa-miR-409-5p	CLIP-seq
MIRT1162071	hsa-miR-410	CLIP-seq
MIRT1162072	hsa-miR-4263	CLIP-seq
MIRT1162073	hsa-miR-4282	CLIP-seq
MIRT1162074	hsa-miR-4287	CLIP-seq
MIRT1162075	hsa-miR-4313	CLIP-seq
MIRT1162076	hsa-miR-4316	CLIP-seq
MIRT1162077	hsa-miR-4422	CLIP-seq
MIRT1162078	hsa-miR-4447	CLIP-seq
MIRT1162079	hsa-miR-4469	CLIP-seq
MIRT1162080	hsa-miR-4472	CLIP-seq
MIRT1162081	hsa-miR-4476	CLIP-seq
MIRT1162082	hsa-miR-4488	CLIP-seq
MIRT1162083	hsa-miR-4495	CLIP-seq
MIRT1162084	hsa-miR-450b-5p	CLIP-seq
MIRT1162085	hsa-miR-4520a-3p	CLIP-seq
MIRT1162086	hsa-miR-4677-3p	CLIP-seq
MIRT1162087	hsa-miR-4679	CLIP-seq
MIRT1162088	hsa-miR-4685-3p	CLIP-seq
MIRT1162089	hsa-miR-4697-5p	CLIP-seq
MIRT1162090	hsa-miR-4724-3p	CLIP-seq
MIRT1162091	hsa-miR-4727-5p	CLIP-seq
MIRT1162092	hsa-miR-4735-5p	CLIP-seq
MIRT1162093	hsa-miR-507	CLIP-seq
MIRT1162094	hsa-miR-5096	CLIP-seq
MIRT1162095	hsa-miR-518a-5p	CLIP-seq
MIRT1162096	hsa-miR-527	CLIP-seq
MIRT1162097	hsa-miR-541	CLIP-seq
MIRT1162098	hsa-miR-548c-3p	CLIP-seq
MIRT1162099	hsa-miR-548l	CLIP-seq
MIRT1162100	hsa-miR-548n	CLIP-seq
MIRT1162101	hsa-miR-548o	CLIP-seq
MIRT1162102	hsa-miR-557	CLIP-seq
MIRT1162103	hsa-miR-561	CLIP-seq
MIRT1162104	hsa-miR-576-5p	CLIP-seq
MIRT1162105	hsa-miR-580	CLIP-seq
MIRT1162106	hsa-miR-603	CLIP-seq
MIRT1162107	hsa-miR-642a	CLIP-seq
MIRT1162108	hsa-miR-651	CLIP-seq
MIRT1162109	hsa-miR-654-5p	CLIP-seq
MIRT1162110	hsa-miR-663	CLIP-seq
MIRT2046447	hsa-miR-1291	CLIP-seq
MIRT2046448	hsa-miR-1293	CLIP-seq
MIRT2046449	hsa-miR-146b-3p	CLIP-seq
MIRT2046450	hsa-miR-185	CLIP-seq
MIRT1162048	hsa-miR-1908	CLIP-seq
MIRT2046451	hsa-miR-3158-3p	CLIP-seq
MIRT2046452	hsa-miR-3175	CLIP-seq
MIRT1162056	hsa-miR-3180	CLIP-seq
MIRT1162057	hsa-miR-3180-3p	CLIP-seq
MIRT1162058	hsa-miR-3196	CLIP-seq
MIRT2046453	hsa-miR-328	CLIP-seq
MIRT2046454	hsa-miR-339-5p	CLIP-seq
MIRT2046455	hsa-miR-4306	CLIP-seq
MIRT2046456	hsa-miR-4440	CLIP-seq
MIRT1162078	hsa-miR-4447	CLIP-seq
MIRT1162080	hsa-miR-4472	CLIP-seq
MIRT2046457	hsa-miR-4483	CLIP-seq
MIRT1162082	hsa-miR-4488	CLIP-seq
MIRT2046458	hsa-miR-4644	CLIP-seq
MIRT1162089	hsa-miR-4697-5p	CLIP-seq
MIRT2046459	hsa-miR-4723-5p	CLIP-seq
MIRT2046460	hsa-miR-513a-3p	CLIP-seq
MIRT2046461	hsa-miR-644	CLIP-seq
MIRT1162110	hsa-miR-663	CLIP-seq
MIRT2046462	hsa-miR-663b	CLIP-seq
MIRT2275541	hsa-miR-1266	CLIP-seq
MIRT2275542	hsa-miR-1278	CLIP-seq
MIRT2046447	hsa-miR-1291	CLIP-seq
MIRT2046448	hsa-miR-1293	CLIP-seq
MIRT2046449	hsa-miR-146b-3p	CLIP-seq
MIRT2046450	hsa-miR-185	CLIP-seq
MIRT1162048	hsa-miR-1908	CLIP-seq
MIRT2275543	hsa-miR-1915	CLIP-seq
MIRT2275544	hsa-miR-193a-3p	CLIP-seq
MIRT2275545	hsa-miR-193b	CLIP-seq
MIRT2275546	hsa-miR-2278	CLIP-seq
MIRT2275547	hsa-miR-2682	CLIP-seq
MIRT2275548	hsa-miR-3064-5p	CLIP-seq
MIRT2046452	hsa-miR-3175	CLIP-seq
MIRT1162056	hsa-miR-3180	CLIP-seq
MIRT1162057	hsa-miR-3180-3p	CLIP-seq
MIRT1162058	hsa-miR-3196	CLIP-seq
MIRT2046453	hsa-miR-328	CLIP-seq
MIRT2046454	hsa-miR-339-5p	CLIP-seq
MIRT2275549	hsa-miR-3652	CLIP-seq
MIRT2275550	hsa-miR-3664-3p	CLIP-seq
MIRT2275551	hsa-miR-3677-3p	CLIP-seq
MIRT2275552	hsa-miR-4297	CLIP-seq
MIRT2046455	hsa-miR-4306	CLIP-seq
MIRT2275553	hsa-miR-4320	CLIP-seq
MIRT2275554	hsa-miR-4419a	CLIP-seq
MIRT2275555	hsa-miR-4430	CLIP-seq
MIRT2275556	hsa-miR-4433	CLIP-seq
MIRT2046456	hsa-miR-4440	CLIP-seq
MIRT1162078	hsa-miR-4447	CLIP-seq
MIRT1162080	hsa-miR-4472	CLIP-seq
MIRT2046457	hsa-miR-4483	CLIP-seq
MIRT1162082	hsa-miR-4488	CLIP-seq
MIRT2275557	hsa-miR-449c	CLIP-seq
MIRT2275558	hsa-miR-4505	CLIP-seq
MIRT2275559	hsa-miR-4510	CLIP-seq
MIRT2275560	hsa-miR-4514	CLIP-seq
MIRT2275561	hsa-miR-4518	CLIP-seq
MIRT2275562	hsa-miR-4524	CLIP-seq
MIRT2046458	hsa-miR-4644	CLIP-seq
MIRT2275563	hsa-miR-4645-5p	CLIP-seq
MIRT2275564	hsa-miR-4659a-3p	CLIP-seq
MIRT2275565	hsa-miR-4659b-3p	CLIP-seq
MIRT2275566	hsa-miR-4673	CLIP-seq
MIRT2275567	hsa-miR-4678	CLIP-seq
MIRT2275568	hsa-miR-4692	CLIP-seq
MIRT1162089	hsa-miR-4697-5p	CLIP-seq
MIRT2275569	hsa-miR-4722-5p	CLIP-seq
MIRT2046459	hsa-miR-4723-5p	CLIP-seq
MIRT2275570	hsa-miR-4726-3p	CLIP-seq
MIRT1162104	hsa-miR-576-5p	CLIP-seq
MIRT2046461	hsa-miR-644	CLIP-seq
MIRT1162110	hsa-miR-663	CLIP-seq
MIRT2046462	hsa-miR-663b	CLIP-seq
MIRT2275571	hsa-miR-892b	CLIP-seq
MIRT2275572	hsa-miR-942	CLIP-seq
MIRT2046450	hsa-miR-185	CLIP-seq
MIRT1162048	hsa-miR-1908	CLIP-seq
MIRT2046452	hsa-miR-3175	CLIP-seq
MIRT1162056	hsa-miR-3180	CLIP-seq
MIRT1162057	hsa-miR-3180-3p	CLIP-seq
MIRT1162058	hsa-miR-3196	CLIP-seq
MIRT2046455	hsa-miR-4306	CLIP-seq
MIRT1162078	hsa-miR-4447	CLIP-seq
MIRT1162080	hsa-miR-4472	CLIP-seq
MIRT1162082	hsa-miR-4488	CLIP-seq
MIRT2046458	hsa-miR-4644	CLIP-seq
MIRT1162089	hsa-miR-4697-5p	CLIP-seq
MIRT2046459	hsa-miR-4723-5p	CLIP-seq
MIRT1162110	hsa-miR-663	CLIP-seq
MIRT2046450	hsa-miR-185	CLIP-seq
MIRT2431271	hsa-miR-3125	CLIP-seq
MIRT2431272	hsa-miR-3916	CLIP-seq
MIRT2046455	hsa-miR-4306	CLIP-seq
MIRT2275554	hsa-miR-4419a	CLIP-seq
MIRT2431273	hsa-miR-4496	CLIP-seq
MIRT2275559	hsa-miR-4510	CLIP-seq
MIRT2046458	hsa-miR-4644	CLIP-seq

Show/Hide all(20)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IMP	14671321
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	ISS
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription regulatory region sequence-specific DNA binding	ISS
GO:0000977	Function	RNA polymerase II transcription 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:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISS
GO:0001649	Process	Osteoblast differentiation	ISS
GO:0005515	Function	Protein binding	IPI	12145306, 32296183, 32814053
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005829	Component	Cytosol	IDA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0016607	Component	Nuclear speck	IDA
GO:0043565	Function	Sequence-specific DNA binding	IDA	9073066
GO:0045892	Process	Negative regulation of transcription, DNA-templated	ISS
GO:0048598	Process	Embryonic morphogenesis	IBA	21873635
GO:0060363	Process	Cranial suture morphogenesis	TAS	8968743
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:2000678	Process	Negative regulation of transcription regulatory region DNA binding	ISS

MIM	HGNC	e!Ensembl
123101	7392	ENSG00000120149

Protein

UniProt ID

P35548

Protein name

Homeobox protein MSX-2 (Homeobox protein Hox-8)

Protein function

Acts as a transcriptional regulator in bone development. Represses the ALPL promoter activity and antagonizes the stimulatory effect of DLX5 on ALPL expression during osteoblast differentiation. Probable morphogenetic role. May play a role in li

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00046	Homeodomain	143 → 199	Homeodomain	Domain

Sequence

MASPSKGNDLFSPDEEGPAVVAGPGPGPGGAEGAAEERRVKVSSLPFSVEALMSDKKPPK
EASPLPAESASAGATLRPLLLSGHGAREAHSPGPLVKPFETASVKSENSEDGAAWMQEPG
RYSPPPRHMSPTTCTLRKHKTNRKPRTPFTTSQLLALERKFRQKQYLSIAERAEFSSSLN
LTETQVKIWFQNRRAKAKRLQEAELEKLKMAAKPMLPSSFSLPFPISSPLQAASIYGASY
PFHRPVLPIPPVGLYATPVGYGMYHLS

Sequence length

267

Interactions

View interactions

	KEGG
	Human T-cell leukemia virus 1 infection

Associated diseases

Show/Hide Causal Diseases (6)

Causal
Disease name	Disease term	dbSNP ID	References
Aplasia cutis congenita	Aplasia cutis congenita of scalp	rs587777706
Craniosynostosis	Craniosynostosis, CRANIOSYNOSTOSIS, TYPE 2	rs104893895, rs587777006, rs587777007, rs587777008, rs587777010, rs281865153, rs281865154, rs864321680, rs864321681, rs1057517670, rs1085307122, rs1064794325, rs1884302, rs1555750816, rs1599823350	23918290, 23949913, 23918290, 14571277, 8106171
Craniosynostosis syndrome	Craniosynostosis, Boston type	rs121918487, rs121918491, rs28931615, rs4647924, rs139494583, rs1057519046, rs1597730335, rs1597816045
Macrocephaly	Macrocephaly	rs786204854, rs764333096, rs1557739557
Parietal foramina	PARIETAL FORAMINA, PARIETAL FORAMINA 1	rs104894191, rs104894192, rs104894193, rs587776614, rs104894196, rs104894197, rs387906325, rs2113498725, rs104893896, rs121912971, rs121912972, rs1561643060, rs587777700, rs587777702	16319823, 10742103, 10767351, 23918290
Parietal foramina with cleidocranial dysplasia	Parietal Foramina With Cleidocranial Dysplasia	rs1561643029	14571277, 23918290

Show/Hide Unknown Diseases (9)

Unknown
Disease name	Disease term	dbSNP ID	References
Congenital cerebral hernia	Congenital cerebral hernia
Short clavicles	Congenital hypoplasia of clavicle
Dermoid cyst	Dermoid Cyst
Enlarged parietal foramina	Enlarged parietal foramina
Female urogenital diseases	Female Urogenital Diseases		16513791
Frontal bossing	Frontal bossing
Microtia	Congenital small ears
Parietal foramina with clavicular hypoplasia	Parietal foramina with clavicular hypoplasia
Trigonocephaly	Trigonocephaly	rs281875280, rs184394424, rs200650442, rs762799389, rs556974765

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