MSX1 (msh homeobox 1)

Gene

• Entrez ID: 4487
• Gene name: Msh homeobox 1
• Gene symbol: MSX1
• Synonyms (NCBI Gene): ECTD3, HOX7, HYD1, STHAG1
• Chromosome: 4
• Chromosome location: 4p16.2
• Summary: This gene encodes a member of the muscle segment homeobox gene family. The encoded protein functions as a transcriptional repressor during embryogenesis through interactions with components of the core transcription complex and other homeoproteins. It may

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs28928890	A>G,T	Pathogenic	Missense variant, coding sequence variant
rs28933081	G>A,T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs104893850	C>T	Pathogenic	Stop gained, coding sequence variant
rs104893852	C>A	Pathogenic	Stop gained, coding sequence variant
rs104893853	C>A,G	Pathogenic	Stop gained, missense variant, coding sequence variant
rs104893854	C>A,G,T	Pathogenic	Missense variant, coding sequence variant
rs121913129	G>C	Pathogenic	Missense variant, coding sequence variant
rs121913130	T>A,C	Pathogenic	Missense variant, coding sequence variant
rs515726227	->TA	Pathogenic	Frameshift variant, stop lost, terminator codon variant
rs1553877821	->A	Pathogenic	Coding sequence variant, frameshift variant
rs1553878162	C>T	Pathogenic	Stop gained, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1162001	hsa-miR-101	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT1162003	hsa-miR-144	CLIP-seq
MIRT1162004	hsa-miR-1909	CLIP-seq
MIRT1162005	hsa-miR-2052	CLIP-seq
MIRT1162006	hsa-miR-29a	CLIP-seq
MIRT1162007	hsa-miR-29b	CLIP-seq
MIRT1162008	hsa-miR-29c	CLIP-seq
MIRT1162009	hsa-miR-3065-3p	CLIP-seq
MIRT1162010	hsa-miR-3120-3p	CLIP-seq
MIRT1162011	hsa-miR-3135b	CLIP-seq
MIRT1162012	hsa-miR-3136-3p	CLIP-seq
MIRT1162013	hsa-miR-3159	CLIP-seq
MIRT1162014	hsa-miR-3163	CLIP-seq
MIRT1162015	hsa-miR-3185	CLIP-seq
MIRT1162016	hsa-miR-3545-3p	CLIP-seq
MIRT1162017	hsa-miR-3652	CLIP-seq
MIRT1162018	hsa-miR-3671	CLIP-seq
MIRT1162019	hsa-miR-4273	CLIP-seq
MIRT1162020	hsa-miR-4282	CLIP-seq
MIRT1162021	hsa-miR-4307	CLIP-seq
MIRT1162022	hsa-miR-4430	CLIP-seq
MIRT1162023	hsa-miR-4445	CLIP-seq
MIRT1162024	hsa-miR-4446-3p	CLIP-seq
MIRT1162025	hsa-miR-4492	CLIP-seq
MIRT1162026	hsa-miR-4498	CLIP-seq
MIRT1162027	hsa-miR-4677-5p	CLIP-seq
MIRT1162028	hsa-miR-4685-5p	CLIP-seq
MIRT1162029	hsa-miR-4733-3p	CLIP-seq
MIRT1162030	hsa-miR-4787-5p	CLIP-seq
MIRT1162031	hsa-miR-511	CLIP-seq
MIRT1162032	hsa-miR-513a-3p	CLIP-seq
MIRT1162033	hsa-miR-607	CLIP-seq
MIRT1162034	hsa-miR-653	CLIP-seq
MIRT1162035	hsa-miR-7	CLIP-seq
MIRT1162036	hsa-miR-762	CLIP-seq
MIRT1162037	hsa-miR-765	CLIP-seq
MIRT1162038	hsa-miR-939	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT1162019	hsa-miR-4273	CLIP-seq
MIRT1162023	hsa-miR-4445	CLIP-seq
MIRT1162027	hsa-miR-4677-5p	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT1162023	hsa-miR-4445	CLIP-seq
MIRT2046444	hsa-miR-383	CLIP-seq
MIRT2046445	hsa-miR-4494	CLIP-seq
MIRT2046446	hsa-miR-499a-5p	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT2275532	hsa-miR-1913	CLIP-seq
MIRT2275533	hsa-miR-324-3p	CLIP-seq
MIRT2275534	hsa-miR-361-3p	CLIP-seq
MIRT2275535	hsa-miR-4313	CLIP-seq
MIRT2275536	hsa-miR-4446-5p	CLIP-seq
MIRT2275537	hsa-miR-4753-3p	CLIP-seq
MIRT2275538	hsa-miR-4755-5p	CLIP-seq
MIRT2275539	hsa-miR-4768-5p	CLIP-seq
MIRT2275540	hsa-miR-670	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT1162019	hsa-miR-4273	CLIP-seq
MIRT1162023	hsa-miR-4445	CLIP-seq
MIRT1162027	hsa-miR-4677-5p	CLIP-seq
MIRT2275537	hsa-miR-4753-3p	CLIP-seq
MIRT2275539	hsa-miR-4768-5p	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT1162019	hsa-miR-4273	CLIP-seq
MIRT1162023	hsa-miR-4445	CLIP-seq
MIRT1162027	hsa-miR-4677-5p	CLIP-seq
MIRT2275537	hsa-miR-4753-3p	CLIP-seq
MIRT2275539	hsa-miR-4768-5p	CLIP-seq
MIRT1162002	hsa-miR-129-5p	CLIP-seq
MIRT1162023	hsa-miR-4445	CLIP-seq
MIRT2275537	hsa-miR-4753-3p	CLIP-seq
MIRT2275539	hsa-miR-4768-5p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
FOXE1	Activation	21177256
PHOX2B	Repression	18201699

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:0000902	Process	Cell morphogenesis	IDA	15705871
GO:0000976	Function	Transcription cis-regulatory region binding	IEA
GO:0000976	Function	Transcription cis-regulatory region binding	ISS
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA
GO:0000977	Function	RNA polymerase II transcription 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:0000987	Function	Cis-regulatory region sequence-specific DNA binding	IEA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001701	Process	In utero embryonic development	IEA
GO:0001837	Process	Epithelial to mesenchymal transition	IEA
GO:0002039	Function	P53 binding	IPI	15705871
GO:0003007	Process	Heart morphogenesis	IEA
GO:0003161	Process	Cardiac conduction system development	NAS	26786210
GO:0003198	Process	Epithelial to mesenchymal transition involved in endocardial cushion formation	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	15705871
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005667	Component	Transcription regulator complex	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	IEA
GO:0007507	Process	Heart development	IEA
GO:0007517	Process	Muscle organ development	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0009887	Process	Animal organ morphogenesis	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0010463	Process	Mesenchymal cell proliferation	IEA
GO:0010629	Process	Negative regulation of gene expression	IEA
GO:0010629	Process	Negative regulation of gene expression	ISS
GO:0021983	Process	Pituitary gland development	IEA
GO:0023019	Process	Signal transduction involved in regulation of gene expression	IEA
GO:0030308	Process	Negative regulation of cell growth	IDA	15705871
GO:0030326	Process	Embryonic limb morphogenesis	IEA
GO:0030509	Process	BMP signaling pathway	IEA
GO:0030513	Process	Positive regulation of BMP signaling pathway	IEA
GO:0030900	Process	Forebrain development	IEA
GO:0030901	Process	Midbrain development	IEA
GO:0034399	Component	Nuclear periphery	IEA
GO:0034399	Component	Nuclear periphery	ISS
GO:0034504	Process	Protein localization to nucleus	IDA	15705871
GO:0035115	Process	Embryonic forelimb morphogenesis	IEA
GO:0035116	Process	Embryonic hindlimb morphogenesis	IEA
GO:0035880	Process	Embryonic nail plate morphogenesis	IEA
GO:0035880	Process	Embryonic nail plate morphogenesis	IMP	11369996
GO:0042474	Process	Middle ear morphogenesis	IEA
GO:0042475	Process	Odontogenesis of dentin-containing tooth	IEA
GO:0042475	Process	Odontogenesis of dentin-containing tooth	IMP	8696335, 10742093, 11369996
GO:0042476	Process	Odontogenesis	IEA
GO:0042481	Process	Regulation of odontogenesis	IEA
GO:0042481	Process	Regulation of odontogenesis	ISS
GO:0042482	Process	Positive regulation of odontogenesis	IEA
GO:0042482	Process	Positive regulation of odontogenesis	ISS
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0043517	Process	Positive regulation of DNA damage response, signal transduction by p53 class mediator	IC	15705871
GO:0043565	Function	Sequence-specific DNA binding	IEA
GO:0043584	Process	Nose development	IEA
GO:0043584	Process	Nose development	ISS
GO:0045787	Process	Positive regulation of cell cycle	IEA
GO:0045787	Process	Positive regulation of cell cycle	ISS
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048598	Process	Embryonic morphogenesis	IBA
GO:0048839	Process	Inner ear development	IEA
GO:0048839	Process	Inner ear development	ISS
GO:0048863	Process	Stem cell differentiation	IEA
GO:0050821	Process	Protein stabilization	IDA	15705871
GO:0051154	Process	Negative regulation of striated muscle cell differentiation	IEA
GO:0051216	Process	Cartilage development	IEA
GO:0060021	Process	Roof of mouth development	IEA
GO:0060021	Process	Roof of mouth development	ISS
GO:0060325	Process	Face morphogenesis	IEA
GO:0060325	Process	Face morphogenesis	IMP	10742093, 11332647, 12651933
GO:0060349	Process	Bone morphogenesis	IEA
GO:0060536	Process	Cartilage morphogenesis	IEA
GO:0061180	Process	Mammary gland epithelium development	IEA
GO:0061311	Process	Cell surface receptor signaling pathway involved in heart development	IEA
GO:0071316	Process	Cellular response to nicotine	IEA
GO:0090427	Process	Activation of meiosis	IEA
GO:0097152	Process	Mesenchymal cell apoptotic process	IEA
GO:1901330	Process	Negative regulation of odontoblast differentiation	IEA
GO:1901330	Process	Negative regulation of odontoblast differentiation	ISS
GO:1902255	Process	Positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator	IDA	15705871
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:2001055	Process	Positive regulation of mesenchymal cell apoptotic process	IEA

Other IDs

• MIM: 142983
• HGNC: 7391
• e!Ensembl: ENSG00000163132

Protein

• UniProt ID: P28360
• Protein name: Homeobox protein MSX-1 (Homeobox protein Hox-7) (Msh homeobox 1-like protein)
• Protein function: Acts as a transcriptional repressor (By similarity). Capable of transcription autoinactivation (By similarity). Binds to the consensus sequence 5'-C/GTAAT-3' in downstream activin regulatory elements (DARE) in the gene promoter, thereby repressi
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00046	Homeodomain	173 → 229	Homeodomain	Domain

• Sequence:

  MAPAADMTSLPLGVKVEDSAFGKPAGGGAGQAPSAAAATAAAMGADEEGAKPKVSPSLLP
  FSVEALMADHRKPGAKESALAPSEGVQAAGGSAQPLGVPPGSLGAPDAPSSPRPLGHFSV
  GGLLKLPEDALVKAESPEKPERTPWMQSPRFSPPPARRLSPPACTLRKHKTNRKPRTPFT
  TAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRLQEAELEKLKM
  AAKPMLPPAAFGLSFPLGGPAAVAAAAGASLYGASGPFQRAALPVAPVGLYTAHVGYSMY
  HLT

• Sequence length: 303

Pathways

KEGG:

Human T-cell leukemia virus 1 infection

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Hypoplastic enamel-onycholysis-hypohidrosis syndrome	Pathogenic	rs2108777701, rs1737950636, rs2474113860, rs104893853, rs1553878162, rs1737950187	RCV001934405 RCV001898322 RCV002829092 RCV000016011 RCV000544581 RCV001048347
MSX1-related disorder	Likely pathogenic; Pathogenic	rs1464389153, rs104893853, rs2474113971	RCV003123243 RCV004532364 RCV004542694
Oligodontia	Pathogenic	rs2108778623	RCV001374733
Orofacial cleft 5	Pathogenic	rs2108778592, rs28933081	RCV001771824 RCV000016013
Tooth agenesis, selective, 1	Pathogenic	rs515726227, rs121913129, rs104893852, rs104893850, rs121913130, rs1553877821, rs761710147, rs2474111547	RCV000157079 RCV000016008 RCV000016009 RCV000016010 RCV000016015 RCV000016016 RCV004577939 RCV004577940

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Craniosynostosis syndrome	Conflicting classifications of pathogenicity	rs184700656	RCV000985272

Associations from Text Mining
Disease Name	Relationship Type	References
Achondroplasia	Associate	8661097
Adenocarcinoma	Associate	29134539
Alzheimer Disease	Associate	30124448, 34697589, 37549144
Anodontia	Associate	12097313, 12733956, 16498076, 16723652, 18790474, 19346736, 19776500, 21111400, 22581971, 23227268, 23549991, 23718693, 24631698, 25101640, 26030286, 27665865, 28910570, 29034883, 29893310, 30134957, 30192788, 31781599, 31914153, 33419968, 35247841, 36017684, 36672972
Anodontia of Permanent Dentition	Associate	19346736
Anonychia congenita	Associate	34099859
Anophthalmia plus syndrome	Associate	21740177
Atelosteogenesis type 1	Associate	15029481
Barrett Esophagus	Associate	29134539
Carcinogenesis	Associate	24631698, 30696738
Carcinoma Endometrioid	Stimulate	32630554
Carcinoma Squamous Cell	Associate	22143938
Cleft Lip	Associate	12733956, 16327884, 17326252, 20087401, 23580168, 24748298, 29034883, 9683588
Cleft Palate	Associate	16723652, 17326252, 21740177, 23580168, 24738728, 27369588, 31262291, 35110662, 9683588
Colonic Neoplasms	Associate	28537673
Colorectal Neoplasms	Associate	35169223
Conversion Disorder	Associate	36017684
Deafness oligodontia syndrome	Associate	16498076, 19346736, 24222224, 25101640, 26629556, 30134957, 30192788, 31914153, 33419968, 38069551
Double Outlet Right Ventricle	Associate	26556783
Duane Retraction Syndrome	Associate	21980133
Ectodermal Dysplasia	Associate	29034883
Ectodermal Dysplasia 1 Anhidrotic	Associate	26759063
Ellis Van Creveld Syndrome	Associate	8661097
Endometrial Neoplasms	Associate	32630554, 36575819, 37101223, 38115305
Epilepsy	Associate	34697589
Epstein Barr Virus Infections	Associate	21792887
Glioblastoma	Inhibit	26271668
Heart Defects Congenital	Associate	25587870, 26556783, 33463545
Heart Septal Defects Atrial	Associate	31712678
Hereditary renal agenesis	Associate	31781599
Hodgkin Disease	Associate	26406991, 26473286
Huntington Disease	Associate	15029481
Infertility	Associate	27312535
Jaw Edentulous	Associate	35647187
Keloid	Associate	35047146
Leukemia	Associate	19430199
Lymphoma B Cell	Associate	26406991
Lymphoma Primary Effusion	Associate	21792887
Melanoma	Associate	29273143
Multiple Myeloma	Inhibit	21980133
Muscular Dystrophy Congenital Megaconial Type	Associate	36017684
Nail dysplasia isolated congenital	Associate	35247841
Necrosis	Stimulate	21980133
Neoplasm Metastasis	Inhibit	21980133
Neoplasm Metastasis	Stimulate	29273143
Neoplasms	Associate	19430199, 29134539, 32630554, 36575819, 37101223
Neoplasms	Inhibit	21980133
Neural crest tumor	Associate	29434243
Neuraminidase 1 deficiency	Associate	25115389
Neuroblastoma	Associate	31480262
Nonsyndromic Deafness	Associate	27356075
Nonsyndromic sensorineural hearing loss	Associate	27356075
Odontogenic Tumors	Associate	36344906
Orofacial Cleft 1	Associate	16687911, 16723652, 17326252, 23718693, 23903689, 24748298, 27369588, 27456059, 28232668, 35247841, 9683588
Osteoarthritis	Associate	20060954
Osteonecrosis	Associate	20942943
Ovarian Neoplasms	Associate	26763252
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	19430199
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	28151996
Single upper central incisor	Associate	23718693, 36672972
Stomach Neoplasms	Associate	16367923, 25982683
Tooth Abnormalities	Associate	29034883
Tooth Agenesis Selective 4	Associate	36672972
Tooth Diseases	Associate	19346736
Tooth Impacted	Associate	33923458
Tooth Injuries	Associate	26030286
Tooth Loss	Associate	33419968
Urinary Bladder Neoplasms	Stimulate	37988196
Uterine Cervicitis	Associate	30696738
Varicose Veins	Associate	39341975