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Aliases for MSX1 Gene

Aliases for MSX1 Gene

  • Msh Homeobox 1 2 3 5
  • Msh Homeobox 1-Like Protein 3 4
  • Homeobox Protein Hox-7 3 4
  • HOX7 3 4
  • Msh (Drosophila) Homeo Box Homolog 1 (Formerly Homeo Box 7) 2
  • Msh Homeobox Homolog 1 (Drosophila) 2
  • Homeobox Protein MSX-1 3
  • Msh Homeobox Homolog 1 3
  • Msh Homeo Box 1 3
  • Homeobox 7 3
  • STHAG1 3
  • ECTD3 3
  • HYD1 3

External Ids for MSX1 Gene

Previous HGNC Symbols for MSX1 Gene

  • HOX7

Previous GeneCards Identifiers for MSX1 Gene

  • GC04P004739
  • GC04P004907
  • GC04P004925
  • GC04P004979

Summaries for MSX1 Gene

Entrez Gene Summary for MSX1 Gene

  • 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 also have roles in limb-pattern formation, craniofacial development, particularly odontogenesis, and tumor growth inhibition. Mutations in this gene, which was once known as homeobox 7, have been associated with nonsyndromic cleft lip with or without cleft palate 5, Witkop syndrome, Wolf-Hirschom syndrome, and autosomoal dominant hypodontia. [provided by RefSeq, Jul 2008]

GeneCards Summary for MSX1 Gene

MSX1 (Msh Homeobox 1) is a Protein Coding gene. Diseases associated with MSX1 include Ectodermal Dysplasia 3, Witkop Type and Orofacial Cleft 5. Among its related pathways are HTLV-I infection and Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers. GO annotations related to this gene include sequence-specific DNA binding and p53 binding. An important paralog of this gene is MSX2.

UniProtKB/Swiss-Prot for MSX1 Gene

  • Acts as a transcriptional repressor. May play a role in limb-pattern formation. Acts in cranofacial development and specifically in odontogenesis. Expression in the developing nail bed mesenchyme is important for nail plate thickness and integrity.

Gene Wiki entry for MSX1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MSX1 Gene

Genomics for MSX1 Gene

Regulatory Elements for MSX1 Gene

Enhancers for MSX1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G004752 0.7 ENCODE 10.5 -106.1 -106122 2.3 CTCF PKNOX1 KLF1 FEZF1 ZBTB40 CTBP1 NCOR1 PRDM10 KLF7 ZBTB20 MSX1 LOC101928279 GC04M004686
GH04G004859 1 ENCODE 5.4 +0.8 795 2.7 CREB3L1 ARID4B SIN3A ZNF48 GLIS2 FOS ZNF263 SP3 SP5 NFYC MSX1 GC04P004888
GH04G004864 0.7 Ensembl 5 +6.5 6538 3.4 CTCF RNF2 SUZ12 CBX2 MNT RBBP5 CBX8 ZFHX2 NBN CREB1 MSX1 GC04P004888
GH04G004968 0.6 ENCODE 5.4 +108.7 108734 0.1 CTBP1 GATA3 NFIB CREB1 FOS DPF2 MSX1 GC04P004939 GC04M005011
GH04G004856 0.6 ENCODE 0.7 -3.1 -3117 0.2 CTCF RNF2 SUZ12 CBX2 TCF7L2 EZH2 MSX1 LINC01396
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around MSX1 on UCSC Golden Path with GeneCards custom track

Promoters for MSX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000165273 535 1601 ARID4B SIN3A ZNF48 GLIS2 FOS ZNF263 SP3 SP5 NFYC KAT8
ENSR00000308557 1635 201 CTCF SAP130 SUZ12 BMI1 ZIC2 GLIS2 ZNF316 PRDM10 MAFK EZH2

Genomic Location for MSX1 Gene

Chromosome:
4
Start:
4,859,665 bp from pter
End:
4,863,936 bp from pter
Size:
4,272 bases
Orientation:
Plus strand

Genomic View for MSX1 Gene

Genes around MSX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MSX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MSX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MSX1 Gene

Proteins for MSX1 Gene

  • Protein details for MSX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P28360-MSX1_HUMAN
    Recommended name:
    Homeobox protein MSX-1
    Protein Accession:
    P28360
    Secondary Accessions:
    • A0SZU5
    • A8K3M1
    • Q96NY4

    Protein attributes for MSX1 Gene

    Size:
    303 amino acids
    Molecular mass:
    31496 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAA52683.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAA58665.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH67353.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAL17870.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=ABK81117.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAF83325.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for MSX1 Gene

Post-translational modifications for MSX1 Gene

Other Protein References for MSX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for MSX1 Gene

Domains & Families for MSX1 Gene

Gene Families for MSX1 Gene

Graphical View of Domain Structure for InterPro Entry

P28360

UniProtKB/Swiss-Prot:

MSX1_HUMAN :
  • Belongs to the Msh homeobox family.
Family:
  • Belongs to the Msh homeobox family.
genes like me logo Genes that share domains with MSX1: view

Function for MSX1 Gene

Molecular function for MSX1 Gene

GENATLAS Biochemistry:
Drosophila,muscle segment (msh) homolog 1,homeo domain encoding gene,inhibiting MYOD1 expression,highly expressed in dental mesenchyme during critical bud stage,involved in epithelial-mesenchymal signaling in many organs,and in the pathogenesis of cleft lip and palate,interacting with MSX2 in mouse limb bud patterning
UniProtKB/Swiss-Prot Function:
Acts as a transcriptional repressor. May play a role in limb-pattern formation. Acts in cranofacial development and specifically in odontogenesis. Expression in the developing nail bed mesenchyme is important for nail plate thickness and integrity.

Gene Ontology (GO) - Molecular Function for MSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0000982 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding IEA --
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IEA --
GO:0002039 p53 binding IPI 15705871
genes like me logo Genes that share ontologies with MSX1: view
genes like me logo Genes that share phenotypes with MSX1: view

Human Phenotype Ontology for MSX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MSX1 Gene

MGI Knock Outs for MSX1:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for MSX1 Gene

Localization for MSX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MSX1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MSX1 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for MSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 15705871
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with MSX1: view

Pathways & Interactions for MSX1 Gene

genes like me logo Genes that share pathways with MSX1: view

Pathways by source for MSX1 Gene

2 Cell Signaling Technology pathways for MSX1 Gene
2 BioSystems pathways for MSX1 Gene

SIGNOR curated interactions for MSX1 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for MSX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0000902 cell morphogenesis IDA 15705871
GO:0001701 in utero embryonic development IEA --
GO:0001837 epithelial to mesenchymal transition IEA --
GO:0003007 heart morphogenesis IEA --
genes like me logo Genes that share ontologies with MSX1: view

Drugs & Compounds for MSX1 Gene

(1) Drugs for MSX1 Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
a-MSH, amide Pharma Melanocyte-stimulating hormones 0

(1) Additional Compounds for MSX1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(1) ApexBio Compounds for MSX1 Gene

Compound Action Cas Number
a-MSH, amide Melanocyte-stimulating hormones
genes like me logo Genes that share compounds with MSX1: view

Drug Products

Transcripts for MSX1 Gene

mRNA/cDNA for MSX1 Gene

Unigene Clusters for MSX1 Gene

Msh homeobox 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MSX1 Gene

No ASD Table

Relevant External Links for MSX1 Gene

GeneLoc Exon Structure for
MSX1
ECgene alternative splicing isoforms for
MSX1

Expression for MSX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MSX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MSX1 Gene

This gene is overexpressed in Cervix - Endocervix (x7.7) and Cervix - Ectocervix (x4.8).

Protein differential expression in normal tissues from HIPED for MSX1 Gene

This gene is overexpressed in Breast (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for MSX1 Gene



Protein tissue co-expression partners for MSX1 Gene

NURSA nuclear receptor signaling pathways regulating expression of MSX1 Gene:

MSX1

SOURCE GeneReport for Unigene cluster for MSX1 Gene:

Hs.424414

mRNA Expression by UniProt/SwissProt for MSX1 Gene:

P28360-MSX1_HUMAN
Tissue specificity: Expressed in the developing nail bed mesenchyme.

Evidence on tissue expression from TISSUES for MSX1 Gene

  • Blood(4.2)
  • Nervous system(2.3)
  • Bone(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MSX1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • skeleton
Organs:
Head and neck:
  • chin
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with MSX1: view

Primer Products

Orthologs for MSX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for MSX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia MSX1 34 35
  • 99.67 (n)
cow
(Bos Taurus)
Mammalia MSX1 34 35
  • 90.68 (n)
dog
(Canis familiaris)
Mammalia MSX1 34 35
  • 89.55 (n)
mouse
(Mus musculus)
Mammalia Msx1 34 16 35
  • 88.12 (n)
rat
(Rattus norvegicus)
Mammalia Msx1 34
  • 87.77 (n)
oppossum
(Monodelphis domestica)
Mammalia MSX1 35
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia MSX1 35
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves GHOX-7 35
  • 81 (a)
OneToOne
MSX1 34
  • 78.17 (n)
lizard
(Anolis carolinensis)
Reptilia MSX1 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia msx1 34
  • 68.73 (n)
LOC394692 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.16449 34
zebrafish
(Danio rerio)
Actinopterygii msxe 34 35
  • 71.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dr 36 35
  • 47 (a)
worm
(Caenorhabditis elegans)
Secernentea vab-15 35 36
  • 39 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 30 (a)
OneToMany
Species where no ortholog for MSX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for MSX1 Gene

ENSEMBL:
Gene Tree for MSX1 (if available)
TreeFam:
Gene Tree for MSX1 (if available)

Paralogs for MSX1 Gene

genes like me logo Genes that share paralogs with MSX1: view

Variants for MSX1 Gene

Sequence variations from dbSNP and Humsavar for MSX1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs121913129 Pathogenic, Tooth agenesis, selective, 1 (STHAG1) [MIM:106600] 4,862,836(+) CGAGC(C/G)CGCGG reference, missense
rs121913130 Pathogenic, Tooth agenesis, selective, 1 (STHAG1) [MIM:106600] 4,860,099(+) GCTCA(A/T)GGCCG reference, missense
rs150284621 Non-syndromic orofacial cleft 5 (OFC5) [MIM:608874] 4,862,702(+) TCAGG(A/G/T)CGGCT reference, synonymous-codon, missense
rs28928890 Pathogenic, Non-syndromic orofacial cleft 5 (OFC5) [MIM:608874] 4,860,150(+) CTCCG(A/T)GGGCG reference, missense
rs28933081 Pathogenic, Non-syndromic orofacial cleft 5 (OFC5) [MIM:608874] 4,860,264(+) GGGGG(A/G/T)ACTCC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for MSX1 Gene

Variant ID Type Subtype PubMed ID
dgv1451e212 CNV loss 25503493
dgv1452e212 CNV loss 25503493
esv34196 OTHER inversion 12058347
esv3569251 CNV loss 25503493
esv3569255 CNV loss 25503493
esv3569256 CNV loss 25503493
nsv1074677 CNV deletion 25765185
nsv997889 CNV gain 25217958

Variation tolerance for MSX1 Gene

Residual Variation Intolerance Score: 63.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.93; 67.85% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for MSX1 Gene

Human Gene Mutation Database (HGMD)
MSX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MSX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MSX1 Gene

Disorders for MSX1 Gene

MalaCards: The human disease database

(20) MalaCards diseases for MSX1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ectodermal dysplasia 3, witkop type
  • witkop syndrome
orofacial cleft 5
  • nonsyndromic cleft lip with or without cleft palate 5
tooth agenesis, selective, 1, with or without orofacial cleft
  • tooth agenesis, selective, 1
tooth agenesis
  • familial tooth agenesis
cleft lip
  • cheiloschisis
- elite association - COSMIC cancer census association via MalaCards
Search MSX1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

MSX1_HUMAN
  • Ectodermal dysplasia 3, Witkop type (ECTD3) [MIM:189500]: A form of ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures such as hair, teeth, nails and sweat glands, with or without any additional clinical sign. Each combination of clinical features represents a different type of ectodermal dysplasia. ECTD3 is characterized by abnormalities largely limited largely to teeth (some of which are missing) and nails (which are poorly formed early in life, especially toenails). This condition is distinguished from anhidrotic ectodermal dysplasia by autosomal dominant inheritance and little involvement of hair and sweat glands. The teeth are not as severely affected. {ECO:0000269 PubMed:11369996}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Non-syndromic orofacial cleft 5 (OFC5) [MIM:608874]: A birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. {ECO:0000269 PubMed:12807959}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=MSX1 is deleted in some patients with Wolf-Hirschhorn syndrome (WHS). WHS results from sub-telomeric deletions in the short arm of chromosome 4. {ECO:0000305 PubMed:1969845}.
  • Tooth agenesis, selective, 1 (STHAG1) [MIM:106600]: A form of selective tooth agenesis, a common anomaly characterized by the congenital absence of one or more teeth. Selective tooth agenesis without associated systemic disorders has sometimes been divided into 2 types: oligodontia, defined as agenesis of 6 or more permanent teeth, and hypodontia, defined as agenesis of less than 6 teeth. The number in both cases does not include absence of third molars (wisdom teeth). STHAG1 can be associated with orofacial cleft in some patients. {ECO:0000269 PubMed:12097313, ECO:0000269 PubMed:8696335}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for MSX1

Genetic Association Database (GAD)
MSX1
Human Genome Epidemiology (HuGE) Navigator
MSX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MSX1
genes like me logo Genes that share disorders with MSX1: view

No data available for Genatlas for MSX1 Gene

Publications for MSX1 Gene

  1. [Association of muscle segment homeobox gene 1 polymorphisms with nonsyndromic cleft lip with or without cleft palate]. (PMID: 18705505) Zhang L. … Liang S.Z. (Hua Xi Kou Qiang Yi Xue Za Zhi 2008) 3 22 46 64
  2. The MSX1 allele 4 homozygous child exposed to smoking at periconception is most sensitive in developing nonsyndromic orofacial clefts. (PMID: 18932005) van den Boogaard M.J. … Steegers-Theunissen R.P. (Hum. Genet. 2008) 3 22 46 64
  3. [Association study on microsatellite polymorphisms of MSX1 gene and nonsyndromic cleft lip and palate]. (PMID: 17557248) Wu P.A. … Wang K. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2007) 3 22 46 64
  4. MSX1 mutations contribute to nonsyndromic cleft lip in a Thai population. (PMID: 16868654) Tongkobpetch S. … Shotelersuk V. (J. Hum. Genet. 2006) 3 22 46 64
  5. Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. (PMID: 12807959) Jezewski P.A. … Murray J.C. (J. Med. Genet. 2003) 3 4 22 64

Products for MSX1 Gene

Sources for MSX1 Gene

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