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    MSX2 msh homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 4488, updated on 17-Jun-2024

    Summary

    Official Symbol
    MSX2provided by HGNC
    Official Full Name
    msh homeobox 2provided by HGNC
    Primary source
    HGNC:HGNC:7392
    See related
    Ensembl:ENSG00000120149 MIM:123101; AllianceGenome:HGNC:7392
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FPP; MSH; PFM; CRS2; HOX8; PFM1
    Summary
    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]
    Expression
    Biased expression in placenta (RPKM 16.6), urinary bladder (RPKM 6.4) and 5 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See MSX2 in Genome Data Viewer
    Location:
    5q35.2
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (174724582..174730896)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (175263949..175271855)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (174151585..174157899)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377740 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:174056950-174057177 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174099129-174099629 Neighboring gene NANOG hESC enhancer GRCh37_chr5:174108078-174108601 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:174119538-174120038 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:174120039-174120539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174135192-174135692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174135693-174136193 Neighboring gene NANOG hESC enhancer GRCh37_chr5:174147650-174148179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174158556-174159119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:174159120-174159682 Neighboring gene VISTA enhancer hs1256 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:174162201-174163131 Neighboring gene microRNA 4634 Neighboring gene uncharacterized LOC105377742

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Craniosynostosis 2
    MedGen: C1858160 OMIM: 604757 GeneReviews: Not available
    Compare labs
    Parietal foramina 1
    MedGen: C1868599 OMIM: 168500 GeneReviews: Enlarged Parietal Foramina
    Compare labs
    Parietal foramina with cleidocranial dysplasia
    MedGen: C1868597 OMIM: 168550 GeneReviews: Enlarged Parietal Foramina
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2023-06-28)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2023-06-28)

    ClinGen Genome Curation Page

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in activation of meiosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone trabecula formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in branching involved in mammary gland duct morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiac conduction system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cell surface receptor signaling pathway involved in heart development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to estradiol stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cranial suture morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic nail plate morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in enamel mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endochondral bone growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial to mesenchymal transition involved in endocardial cushion formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in frontal suture morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchymal cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of fat cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of keratinocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in osteoblast development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in outflow tract septum morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of mesenchymal cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of timing of catagen IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in signal transduction involved in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in wound healing, spreading of epidermal cells IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    homeobox protein MSX-2
    Names
    homeobox protein Hox-8
    msh homeo box 2
    msh homeobox homolog 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008124.1 RefSeqGene

      Range
      5011..11325
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001363626.2NP_001350555.1  homeobox protein MSX-2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC117531
      Consensus CDS
      CCDS87348.1
      UniProtKB/TrEMBL
      D6RIS4
      Related
      ENSP00000427425.1, ENST00000507785.2
    2. NM_002449.5NP_002440.2  homeobox protein MSX-2 isoform 1

      See identical proteins and their annotated locations for NP_002440.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC117531, AL552909, D89377, W38629
      Consensus CDS
      CCDS4392.1
      UniProtKB/Swiss-Prot
      D3DQN1, P35548, Q53XM4, Q9UD60
      Related
      ENSP00000239243.5, ENST00000239243.7
      Conserved Domains (1) summary
      pfam00046
      Location:145199
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      174724582..174730896
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      175263949..175271855
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352655.1XP_054208630.1  homeobox protein MSX-2 isoform X1