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Aliases for MSX2 Gene

Aliases for MSX2 Gene

  • Msh Homeobox 2 2 3 5
  • Homeobox Protein Hox-8 3 4
  • HOX8 3 4
  • Msh (Drosophila) Homeo Box Homolog 2 2
  • Msh Homeobox Homolog 2 (Drosophila) 2
  • Craniosynostosis, Type 2 2
  • Homeobox Protein MSX-2 3
  • Msh Homeobox Homolog 2 3
  • Parietal Foramina 1 2
  • Msh Homeo Box 2 3
  • CRS2 3
  • PFM1 3
  • FPP 3
  • MSH 3
  • PFM 3

External Ids for MSX2 Gene

Previous HGNC Symbols for MSX2 Gene

  • PFM1

Previous GeneCards Identifiers for MSX2 Gene

  • GC05P174439
  • GC05P174884
  • GC05P174087
  • GC05P174132
  • GC05P174084
  • GC05P169247

Summaries for MSX2 Gene

Entrez Gene Summary for MSX2 Gene

  • 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 craniofacial morphogenesis. The encoded protein may also have a role in promoting cell growth under certain conditions and may be an important target for the RAS signaling pathways. Mutations in this gene are associated with parietal foramina 1 and craniosynostosis type 2. [provided by RefSeq, Jul 2008]

GeneCards Summary for MSX2 Gene

MSX2 (Msh Homeobox 2) is a Protein Coding gene. Diseases associated with MSX2 include Craniosynostosis 2 and Parietal Foramina With Cleidocranial Dysplasia. Among its related pathways are Neural Crest Differentiation and HTLV-I infection. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is MSX1.

UniProtKB/Swiss-Prot for MSX2 Gene

  • Acts as a transcriptional regulator in bone development. Represses the ALPL promoter activity and antogonizes the stimulatory effect of DLX5 on ALPL expression during osteoblast differentiation. Probable morphogenetic role. May play a role in limb-pattern formation. In osteoblasts, suppresses transcription driven by the osteocalcin FGF response element (OCFRE). Binds to the homeodomain-response element of the ALPL promoter.

Gene Wiki entry for MSX2 Gene

Additional gene information for MSX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MSX2 Gene

Genomics for MSX2 Gene

GeneHancer (GH) Regulatory Elements for MSX2 Gene

Promoters and enhancers for MSX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I174722 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 556 +1.3 1329 5.8 SIN3A FEZF1 GLI4 ZNF213 FOS ATF4 ZNF610 AEBP2 PRDM4 SP7 MSX2 LOC105377741 ENSG00000251670
GH05I174751 Promoter 1.1 Ensembl 11.3 +26.8 26768 0.6 KLF17 SIN3A ZNF2 ZBTB7B ZNF335 GLIS2 FOS EGR2 ZNF362 ZBTB11 MIR4634 ENSG00000251670 MSX2
GH05I174608 Enhancer 0.9 Ensembl ENCODE 10.4 -115.5 -115468 1.1 PKNOX1 KLF1 ZIC2 ZNF316 GLIS2 PATZ1 SCRT2 PRDM10 MAFK TCF7L2 GC05M174590 MSX2 SUMO2P6
GH05I174692 Enhancer 0.7 ENCODE 11.9 -31.3 -31335 1.3 KLF1 PKNOX1 USF1 MAX ZNF384 ZIC2 CTBP1 ZNF366 EZH2 ZNF362 MSX2 LOC105377741 HIGD1AP3
GH05I174717 Enhancer 1 FANTOM5 ENCODE 8 -4.5 -4520 4.5 ZBTB6 ZNF223 KLF17 SIN3A HIC1 ZNF335 ZFHX2 ZNF157 PRDM10 FOSL2 LOC105377741 MSX2 HIGD1AP3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around MSX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MSX2 gene promoter:

Genomic Locations for MSX2 Gene

Genomic Locations for MSX2 Gene
chr5:174,724,533-174,730,899
(GRCh38/hg38)
Size:
6,367 bases
Orientation:
Plus strand
chr5:174,151,536-174,157,902
(GRCh37/hg19)

Genomic View for MSX2 Gene

Genes around MSX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MSX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MSX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MSX2 Gene

Proteins for MSX2 Gene

  • Protein details for MSX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35548-MSX2_HUMAN
    Recommended name:
    Homeobox protein MSX-2
    Protein Accession:
    P35548
    Secondary Accessions:
    • D3DQN1
    • Q53XM4
    • Q9UD60

    Protein attributes for MSX2 Gene

    Size:
    267 amino acids
    Molecular mass:
    28897 Da
    Quaternary structure:
    • Interacts with MINT (By similarity). Interacts with XRCC6 (Ku70) and XRCC5 (Ku80).

neXtProt entry for MSX2 Gene

Post-translational modifications for MSX2 Gene

No Post-translational modifications

Other Protein References for MSX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for MSX2 Gene

Domains & Families for MSX2 Gene

Gene Families for MSX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for MSX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P35548

UniProtKB/Swiss-Prot:

MSX2_HUMAN :
  • Belongs to the Msh homeobox family.
Family:
  • Belongs to the Msh homeobox family.
genes like me logo Genes that share domains with MSX2: view

Function for MSX2 Gene

Molecular function for MSX2 Gene

GENATLAS Biochemistry:
Drosophila,muscle segment (msh) homolog 2,homeo domain encoding gene,expressed in developing teeth and various tumors of mesenchymal origin,also expressed in extra-embryonic tissues such as placenta,involved in epithelial-mesenchymal signaling in many organs,interacting with MSX1 in mouse limb bud patterning through BMP4 regulation,involved in the enhancing of parietal bone growth
UniProtKB/Swiss-Prot Function:
Acts as a transcriptional regulator in bone development. Represses the ALPL promoter activity and antogonizes the stimulatory effect of DLX5 on ALPL expression during osteoblast differentiation. Probable morphogenetic role. May play a role in limb-pattern formation. In osteoblasts, suppresses transcription driven by the osteocalcin FGF response element (OCFRE). Binds to the homeodomain-response element of the ALPL promoter.

Phenotypes From GWAS Catalog for MSX2 Gene

Gene Ontology (GO) - Molecular Function for MSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0000989 transcription factor activity, transcription factor binding IEA --
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003712 transcription cofactor activity IEA,ISS --
genes like me logo Genes that share ontologies with MSX2: view
genes like me logo Genes that share phenotypes with MSX2: view

Human Phenotype Ontology for MSX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MSX2 Gene

MGI Knock Outs for MSX2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for MSX2 Gene

Localization for MSX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MSX2 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 MSX2 gene
Compartment Confidence
nucleus 5
cytosol 4
extracellular 2
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005829 cytosol IDA --
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with MSX2: view

Pathways & Interactions for MSX2 Gene

genes like me logo Genes that share pathways with MSX2: view

Pathways by source for MSX2 Gene

1 BioSystems pathway for MSX2 Gene
1 KEGG pathway for MSX2 Gene

SIGNOR curated interactions for MSX2 Gene

Activates:

Gene Ontology (GO) - Biological Process for MSX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II ISS --
GO:0001503 ossification IEA --
GO:0001649 osteoblast differentiation ISS,IEA --
GO:0002063 chondrocyte development IEA --
GO:0002076 osteoblast development IEA --
genes like me logo Genes that share ontologies with MSX2: view

Drugs & Compounds for MSX2 Gene

(2) Drugs for MSX2 Gene - From: ApexBio and Novoseek

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

(2) Additional Compounds for MSX2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(1) ApexBio Compounds for MSX2 Gene

Compound Action Cas Number
a-MSH, amide Melanocyte-stimulating hormones
genes like me logo Genes that share compounds with MSX2: view

Drug Products

Transcripts for MSX2 Gene

mRNA/cDNA for MSX2 Gene

Unigene Clusters for MSX2 Gene

Msh homeobox 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for MSX2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b
SP1: -
SP2:

Relevant External Links for MSX2 Gene

GeneLoc Exon Structure for
MSX2
ECgene alternative splicing isoforms for
MSX2

Expression for MSX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MSX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MSX2 Gene

This gene is overexpressed in Bladder (x8.1), Artery - Tibial (x5.4), and Skin - Not Sun Exposed (Suprapubic) (x5.0).

Protein differential expression in normal tissues from HIPED for MSX2 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for MSX2 Gene



Protein tissue co-expression partners for MSX2 Gene

NURSA nuclear receptor signaling pathways regulating expression of MSX2 Gene:

MSX2

SOURCE GeneReport for Unigene cluster for MSX2 Gene:

Hs.89404

Evidence on tissue expression from TISSUES for MSX2 Gene

  • Bone(4.5)
  • Bone marrow(4.2)
  • Pancreas(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for MSX2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • scalp
  • skull
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
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with MSX2: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for MSX2 Gene

Orthologs for MSX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for MSX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia MSX2 33 34
  • 99.88 (n)
cow
(Bos Taurus)
Mammalia MSX2 33 34
  • 92.76 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia MSX2 34
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia MSX2 33 34
  • 90.39 (n)
rat
(Rattus norvegicus)
Mammalia Msx2 33
  • 88.51 (n)
mouse
(Mus musculus)
Mammalia Msx2 33 16 34
  • 88.01 (n)
oppossum
(Monodelphis domestica)
Mammalia MSX2 34
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves MSX2 33 34
  • 79.27 (n)
lizard
(Anolis carolinensis)
Reptilia MSX2 34
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia msx2 33
  • 71.5 (n)
LOC394987 33
African clawed frog
(Xenopus laevis)
Amphibia msx2-A 33
zebrafish
(Danio rerio)
Actinopterygii msxd 33 34
  • 63.46 (n)
msxa 34
  • 50 (a)
OneToMany
-- 33
fruit fly
(Drosophila melanogaster)
Insecta Dr 35 34
  • 50 (a)
worm
(Caenorhabditis elegans)
Secernentea vab-15 34
  • 39 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9618 33
Species where no ortholog for MSX2 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 MSX2 Gene

ENSEMBL:
Gene Tree for MSX2 (if available)
TreeFam:
Gene Tree for MSX2 (if available)

Paralogs for MSX2 Gene

Paralogs for MSX2 Gene

(1) SIMAP similar genes for MSX2 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for MSX2 Gene

genes like me logo Genes that share paralogs with MSX2: view

Variants for MSX2 Gene

Sequence variations from dbSNP and Humsavar for MSX2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs10038500 likely-benign, Craniosynostosis, Enlarged parietal foramina 174,729,999(+) A/C 3_prime_UTR_variant
rs10044147 likely-benign, Enlarged parietal foramina, Craniosynostosis 174,730,241(+) C/T 3_prime_UTR_variant
rs104893895 pathogenic, Craniosynostosis 2, Craniosynostosis 2 (CRS2) [MIM:604757], Craniosynostosis 2 (CRS2) [MIM:604757] 174,729,222(+) C/A/T 3_prime_UTR_variant, coding_sequence_variant, missense_variant
rs104893896 pathogenic, Parietal foramina 1, Parietal foramina 1 (PFM1) [MIM:168500] 174,729,294(+) G/A 3_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1050348474 uncertain-significance, Craniosynostosis, Enlarged parietal foramina 174,730,895(+) A/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant

Variation tolerance for MSX2 Gene

Residual Variation Intolerance Score: 26.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MSX2 Gene

Human Gene Mutation Database (HGMD)
MSX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MSX2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for MSX2 Gene

Disorders for MSX2 Gene

MalaCards: The human disease database

(20) MalaCards diseases for MSX2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search MSX2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

MSX2_HUMAN
  • Craniosynostosis 2 (CRS2) [MIM:604757]: A primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. CRS2 is characterized by either fronto-orbital recession, or frontal bossing, or turribrachycephaly, or cloverleaf skull. Associated features include severe headache, high incidence of visual problems (myopia or hyperopia), and short first metatarsals. Intelligence is normal. {ECO:0000269 PubMed:23918290, ECO:0000269 PubMed:23949913, ECO:0000269 PubMed:8106171}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Parietal foramina 1 (PFM1) [MIM:168500]: Autosomal dominant disease characterized by oval defects of the parietal bones caused by deficient ossification around the parietal notch, which is normally obliterated during the fifth fetal month. {ECO:0000269 PubMed:10742103, ECO:0000269 PubMed:10767351}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Parietal foramina with cleidocranial dysplasia (PFMCCD) [MIM:168550]: Combines skull defects in the form of enlarged parietal foramina and deficient ossification of the clavicles. {ECO:0000269 PubMed:14571277}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for MSX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MSX2: view

No data available for Genatlas for MSX2 Gene

Publications for MSX2 Gene

  1. Association of the MSX2 gene polymorphisms with ankylosing spondylitis in Japanese. (PMID: 18299954) Furuichi T … Ikegawa S (Journal of human genetics 2008) 3 22 44 58
  2. Parietal foramina with cleidocranial dysplasia is caused by mutation in MSX2. (PMID: 14571277) Garcia-Miñaur S … Wilkie AO (European journal of human genetics : EJHG 2003) 3 4 22 58
  3. Regulation of osteocalcin gene expression by a novel Ku antigen transcription factor complex. (PMID: 12145306) Willis DM … Towler DA (The Journal of biological chemistry 2002) 3 4 22 58
  4. Functional haploinsufficiency of the human homeobox gene MSX2 causes defects in skull ossification. (PMID: 10742103) Wilkie AO … Maxson RE (Nature genetics 2000) 3 4 22 58
  5. Identification of mutations in the MSX2 homeobox gene in families affected with foramina parietalia permagna. (PMID: 10767351) Wuyts W … Van Hul W (Human molecular genetics 2000) 3 4 22 58

Products for MSX2 Gene

Sources for MSX2 Gene

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