MSX2 msh homeobox 2 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 5q35.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (174724582..174730896)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (175263949..175271855)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (174151585..174157899)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells.
Title: Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells.
Expression of VEGFA-mRNA in classical and MSX2-mRNA in non-classical monocytes in patients with spondyloarthritis is associated with peripheral arthritis.
Title: Expression of VEGFA-mRNA in classical and MSX2-mRNA in non-classical monocytes in patients with spondyloarthritis is associated with peripheral arthritis.
MSX2 suppression through inhibition of TGFbeta signaling enhances hematopoietic differentiation of human embryonic stem cells.
Title: MSX2 suppression through inhibition of TGFβ signaling enhances hematopoietic differentiation of human embryonic stem cells.
A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma.
Title: A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma.
Induced pluripotent stem cell-derived mesenchymal stromal cells (iMSCs) are functionally and genetically different from bone marrow-derived mesenchymal stromal cells (BM-MSCs): iMSCs express very high levels of both KDR and MSX2 compared with BM-MSCs, while BM-MSCs had significantly higher levels of PDGFRalpha.
Title: Induced Pluripotent Stem Cell-Derived Mesenchymal Stromal Cells Are Functionally and Genetically Different From Bone Marrow-Derived Mesenchymal Stromal Cells.
Low MSX2 expression is associated with drug resistance in lung cancer.
Title: The FBXW2-MSX2-SOX2 axis regulates stem cell property and drug resistance of cancer cells.
The extent of calcification correlated positively with the flow velocity, as did the mRNA and protein levels of TGF-beta1, BMP2, and MSX2. These findings indicate that TGF-beta1/BMP2 signaling is involved in valve calcification induced by abnormal mechanical stimulation.
Title: Role of TGF-β1 Signaling in Heart Valve Calcification Induced by Abnormal Mechanical Stimulation in a Tissue Engineering Model.
p19(INK4d) plays an active role during human tooth development along with MSX1 and MSX2
Title: Regulation of proliferation in developing human tooth germs by MSX homeodomain proteins and cyclin-dependent kinase inhibitor p19(INK4d).
MSX2 might be a new drug resistance related gene in pancreatic cancer cells by up-regulation of MRP2 expression.
Title: [A novel chemo-resistant gene MSX2 discovered by establishment of two pancreatic cancer drug resistant cell lines JF305/CDDP and PANC-1/GEM].
MSX2 played a crucial role in the progression of colorectal cancer and may be a potential novel prognostic factor
Title: Prognostic Relevance and Function of MSX2 in Colorectal Cancer.

Submit: New GeneRIF Correction See all GeneRIFs (47)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MSX2_1676 (e-PCR)
- UniSTS:277511

Msx2 (e-PCR), detects polymorphism
- UniSTS:516407

Msx2 (e-PCR), detects polymorphism
- UniSTS:531526

RH79930 (e-PCR)
- UniSTS:85864

STS-X69295 (e-PCR)
- UniSTS:54909

PMC164857P2 (e-PCR)
- UniSTS:271526

GDB:266598 (e-PCR)
- UniSTS:156336

Msx2 (e-PCR), detects polymorphism
- UniSTS:498394

SHGC-11995 (e-PCR)
- UniSTS:63973

RH119225 (e-PCR)
- UniSTS:138734

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within BMP signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within activation of meiosis	IEA Inferred from Electronic Annotation more info
involved_in animal organ morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within bone trabecula formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within 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
acts_upstream_of_or_within cartilage development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to estradiol stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to growth factor stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chondrocyte development	IEA Inferred from Electronic Annotation more info
involved_in cranial suture morphogenesis	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within embryonic digit morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic limb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic nail plate morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within enamel mineralization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within endochondral bone growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epithelial to mesenchymal transition involved in endocardial cushion formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within frontal suture morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mammary gland epithelium development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of fat cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	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
acts_upstream_of_or_within odontogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ossification	IEA Inferred from Electronic Annotation more info
involved_in ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within osteoblast development	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within outflow tract morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within outflow tract septum morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of BMP signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of mesenchymal cell apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of osteoblast differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of timing of catagen	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of apoptotic process	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
acts_upstream_of_or_within signal transduction involved in regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within stem cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within wound healing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within wound healing, spreading of epidermal cells	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment 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
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein MSX-2

Names: homeobox protein Hox-8; msh homeo box 2; msh homeobox homolog 2

NCBI Reference Sequences (RefSeq)

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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

NG_008124.1 RefSeqGene

Range

5011..11325

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001363626.2 → NP_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
NM_002449.5 → NP_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:145 → 199

Homeobox; Homeobox domain