MSX1 (msh homeobox 1)

Gene

• Entrez ID: 4487
• Gene name: Msh homeobox 1
• Gene symbol: MSX1
• Synonyms: 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: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: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:0002039	Function	P53 binding	IPI	15705871
GO:0003198	Process	Epithelial to mesenchymal transition involved in endocardial cushion formation	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	IDA	15705871
GO:0005654	Component	Nucleoplasm	IDA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007517	Process	Muscle organ development	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0010463	Process	Mesenchymal cell proliferation	IEA
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:0030513	Process	Positive regulation of BMP signaling pathway	IEA
GO:0030901	Process	Midbrain development	IEA
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	IMP	11369996
GO:0042474	Process	Middle ear morphogenesis	IEA
GO:0042475	Process	Odontogenesis of dentin-containing tooth	IMP	8696335, 10742093, 11369996
GO:0042481	Process	Regulation of odontogenesis	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:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048598	Process	Embryonic morphogenesis	IBA	21873635
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:0060021	Process	Roof of mouth development	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:0061312	Process	BMP signaling pathway involved in heart development	IEA
GO:0071316	Process	Cellular response to nicotine	IEA
GO:0090427	Process	Activation of meiosis	IEA
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:2000678	Process	Negative regulation of transcription regulatory region DNA binding	IEA
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
Disease name	Disease term	dbSNP ID	References
Gastric cancer	Hereditary Diffuse Gastric Cancer	rs137854571, rs63751108, rs34612342, rs121908383, rs121909144, rs121909775, rs121909219, rs121909223, rs63750871, rs80359530, rs121964873, rs121913530, rs606231203, rs121918505, rs587776802, rs28933369, rs121912469, rs80358011, rs397507262, rs80359439, rs397507333, rs80359543, rs80358831, rs80359596, rs80358920, rs80358972, rs80359659, rs397507404, rs397514661, rs80359516, rs200495564, rs80358419, rs80359274, rs80359283, rs80358427, rs80358428, rs80358435, rs81002805, rs397507660, rs397507663, rs80359391, rs80359443, rs81002797, rs80359466, rs397507752, rs80359484, rs80359603, rs397507954, rs80359058, rs80359071, rs397507981, rs80359121, rs80357086, rs80357064, rs397508936, rs80357695, rs80357661, rs397509035, rs80357544, rs80357577, rs80357881, rs80357296, rs80356923, rs80356866, rs80357504, rs80357390, rs80357239, rs80358099, rs397509284, rs80357258, rs199474738, rs199474747, rs587779204, rs63750439, rs267608076, rs587779246, rs63749999, rs267608078, rs63751327, rs267607719, rs267607734, rs63750706, rs63751711, rs587779047, rs587779075, rs267607949, rs63750633, rs63750803, rs63751618, rs267608154, rs200640585, rs80358018, rs80357857, rs80357882, rs180177103, rs587779815, rs587779865, rs587779872, rs587780059, rs121912666, rs587780088, rs587780104, rs200432447, rs180177100, rs587780226, rs587780784, rs587776416, rs587781276, rs587781629, rs587781694, rs587781727, rs587781730, rs587781807, rs587781894, rs587781948, rs121913344, rs587782292, rs587782350, rs587782558, rs587782719, rs587782885, rs587783057, rs730881833, rs730881411, rs730881336, rs139770721, rs730881869, rs730881633, rs730882007, rs786203115, rs765123255, rs1553333738, rs762083530, rs786202800, rs17174393, rs55996097, rs750621215, rs786203451, rs747604569, rs764389018, rs786204433, rs786204862, rs772821016, rs779582317, rs863225406, rs193922343, rs759965045, rs63749919, rs760228510, rs746481984, rs762307622, rs876659736, rs876660933, rs747727055, rs1450394308, rs876658348, rs876658431, rs876659326, rs876660444, rs730881369, rs878853865, rs753862052, rs587780024, rs138941496, rs886040739, rs886040744, rs886040347, rs878854957, rs886040123, rs398122662, rs886040942, rs1057517104, rs1057516320, rs1057516683, rs879254046, rs1057517253, rs587781927, rs985033810, rs1057519989, rs775464903, rs374230313, rs758304323, rs1060501599, rs758081262, rs1060500126, rs1060502734, rs587776408, rs1060501695, rs1114167816, rs1114167596, rs1114167667, rs1555460315, rs1135402788, rs1554086196, rs730881919, rs773356478, rs769237459, rs1553653158, rs587782087, rs1555107263, rs1555119940, rs1403784434, rs1342519012, rs751710099, rs1553616361, rs1553619721, rs1270783041, rs775036118, rs1555288557, rs1555460548, rs1555461154, rs1298667185, rs1553622218, rs63751101, rs1349928568, rs771936821, rs1021662947, rs1555921011, rs81002831, rs1555124506, rs1555574803, rs1060502716, rs1555605362, rs747057367, rs1565385010, rs1567554500, rs1567516230, rs1558644995, rs1555591308, rs778306619, rs1566231194, rs1603328466, rs1570406302, rs1586108714, rs768362387, rs1597713777, rs1060502926, rs1597867185, rs1591517571, rs1591663236, rs1593903006, rs1555284779, rs1597096243, rs45459799, rs1597360340, rs587781905, rs864622481, rs1601753141, rs1966858562, rs1966967065, rs1967016153, rs1967113484, rs2080473458, rs1591387978, rs1224428422, rs1597747184, rs2082309297, rs2051929740, rs147542208	16367923
Hearing loss	Conductive hearing loss	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359, rs180177151, rs180177154, rs180177153, rs35689081, rs35887622, rs80338944, rs104894396, rs104894398, rs80338947, rs80338948, rs80338942, rs104894402, rs104894403, rs80338945, rs28931594, rs80338940, rs80338941, rs80356590, rs80338950, rs387906706, rs387906707, rs387906708, rs398122848, rs387907016, rs587776894, rs387907088, rs397515411, rs370965183, rs398122930, rs199897298, rs111033187, rs111033448, rs199606180, rs111033284, rs397516413, rs111033305, rs111033220, rs111033256, rs111033297, rs111033253, rs104894408, rs111033295, rs397516874, rs76434661, rs111033335, rs397517323, rs111033247, rs367928692, rs374793617, rs143939430, rs397515605, rs80338939, rs200656442, rs779748859, rs587781261, rs587781262, rs143343083, rs200147906, rs730880338, rs797044491, rs146281367, rs756484720, rs869025593, rs201306709, rs540895576, rs777777359, rs879255246, rs1554358720, rs142498437, rs377145777, rs1057517519, rs779077039, rs952741388, rs1060499797, rs764139009, rs1060499590, rs1064794012, rs1064797115, rs756790858, rs775633137, rs1554952443, rs1554952193, rs782063761, rs1199012623, rs756147087, rs1555648043, rs1555661490, rs1553196233, rs781546107, rs111033190, rs775428246, rs782539587, rs537227442, rs148695069, rs1554835827, rs953422571, rs1554834186, rs1554834161, rs1554835103, rs1554577339, rs1554577402, rs768471577, rs782279338, rs781951909, rs998045226, rs375759781, rs755804651, rs1557458426, rs767797828, rs538027448, rs1559366084, rs367688416, rs1558480402, rs1558490542, rs1559870857, rs1560690591, rs1561299289, rs1562817224, rs1562817529, rs1562822565, rs1562835391, rs1564113368, rs1564554255, rs773851192, rs1564555240, rs761261855, rs1564805114, rs1565522273, rs1565127413, rs781790246, rs1565430886, rs1565469959, rs746667217, rs1565819402, rs1565855932, rs150529554, rs1567939793, rs201866631, rs754472294, rs1559372512, rs1558464965, rs1558488902, rs775062249, rs1226171550, rs1561590396, rs765574676, rs762876554, rs757327146, rs1564949059, rs1565519673, rs368050948, rs1565541888, rs781989117, rs1565402473, rs750358148, rs1386887007, rs1209665716, rs1567641234, rs1237955948, rs1569042782, rs752672077, rs146689036, rs1560070780, rs149712664, rs1564556995, rs762226905, rs773573968, rs1568528171, rs1198256157, rs377267777, rs370564476, rs1577876794, rs747787770, rs759432278, rs1043716893, rs1581138934, rs2033773650, rs1421964916, rs771766431, rs780917129, rs1895773215, rs1895769400, rs761543680, rs1565920060
Hypoplastic enamel-onycholysis-hypohidrosis syndrome	Hypoplastic enamel-onycholysis-hypohidrosis syndrome	rs104893853, rs1553878162, rs1737950187	11369996
Nonsyndromic deafness	Nonsyndromic Deafness	rs606231410, rs794729665, rs730880338, rs1566538321	27356075
Oligodontia	Oligodontia	rs1591901585
Orofacial cleft	OROFACIAL CLEFT 5	rs28933081, rs387906597, rs1560277554	15354328, 12807959, 25565750
Situs inversus	Situs inversus totalis	rs528302390, rs1596264554
Tooth agenesis	Tooth Agenesis, Familial	rs121908119, rs121908121, rs1881345182, rs104894467, rs28933970, rs2139108031, rs28933971, rs28933972, rs1594475481, rs2139106532, rs2139108874, rs121917720, rs121913129, rs104893852, rs104893850, rs121913130, rs1553877821, rs782540538, rs318240759, rs515726227, rs587776350, rs864309647, rs864309649, rs869320640, rs869320636, rs866789963, rs869320639, rs869320637, rs779326570, rs766021478, rs372993798, rs1057519288, rs1555316697, rs1131692057, rs1565611848, rs745522921, rs773036759	8696335, 25565750, 12097313
Wolf-hirschhorn syndrome	Wolf-Hirschhorn Syndrome	rs1560602800, rs1560635105, rs1560696317	14630905

Unknown
Disease name	Disease term	dbSNP ID	References
Anodontia	Developmental absence of tooth, Anodontia of Permanent Dentition
Congenital abnormality of eustachian tube	Congenital abnormality of Eustachian tube
Congenital clubfoot	Congenital clubfoot
Congenital exomphalos	Congenital exomphalos
Dysphagia	Deglutition Disorders
Hypodontia	Hypodontia		8696335, 24914010
Hypodontia and nail dysgenesis	Hypodontia and nail dysgenesis, Hypodontia-dysplasia of nails syndrome		11369996
Hypoplasia of the maxilla	Hypoplasia of the maxilla
Macrodontia	Macrodontia
Malnutrition	Malnutrition
Microdontia	Microdontia (disorder)
Micrognathism	Micrognathism
Odontome	Odontome		14630905
Oropharyngeal dysphagia	Oropharyngeal Dysphagia
Otitis media	Chronic otitis media, Recurrent otitis media	rs601338, rs1047781, rs1800028
Peg-shaped teeth	Peg-shaped teeth
Pitt-rogers-danks syndrome	Pitt-Rogers-Danks Syndrome		14630905
Polycystic ovary syndrome	Polycystic Ovary Syndrome
Specific learning disorder	Specific learning disability	rs1057519497
Stomach neoplasms	Malignant neoplasm of stomach, Stomach Neoplasms		16367923
Velopharyngeal insufficiency	Velopharyngeal Insufficiency