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A form of syndromic craniosynostosis, characterized by a highly variable craniosynostosis with frontal bossing, turribrachycephaly and cloverleaf skull anomaly. Hypoplasia of the supraorbital ridges, cleft palate, extra teeth and limb anomalies (triphalangeal thumb, 3-4 syndactyly of the hands, a short first metatarsal, middle phalangeal agenesis in the feet) have also been described. Associated problems include headache, poor vision, and seizures. Intelligence is normal.
Features include always present findings: Craniosynostosis; and sometimes findings: Triphalangeal thumb, Brachydactyly, Hypermetropia, and Trigonocephaly and others. 20 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 3 | Seizure, Headache, Intellectual disability |
MSX2 encodes msh homeobox 2 (267 aa). Acts as a transcriptional regulator in bone development. Represses the ALPL promoter activity and antagonizes the stimulatory effect of DLX5 on ALPL expression during osteoblast differentiation. Highest expression in Bladder (17.6 TPM) and Artery Tibial (11.3 TPM).
Craniosynostosis 2 is caused by mutations in the MSX2 gene on chromosome 5.
The MSX2 protein participates in RUNX2 gene expression from distal (P1) promoter is inhibited by NKX3-2, MSX2 and RUNX2-P1, and stimulated by DLX5,(DLX6), KLF4 stimulates CDH1 gene transcription, and Expression of MSX1 in the neural plate border pathways.
MSX2 is classified as a druggable target (Transcription Factor Complex category) with score 0.0.
Genetic testing for MSX2 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for craniosynostosis 2 has been reported in the published literature.
Phenotype severity distribution: 1 always present feature.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for craniosynostosis 2.
4 publications have been identified in PubMed for craniosynostosis 2. Research spans Other (25%), Diagnostic / Biomarker (25%), and Case Report / Case Series (25%).
Alter NE (2026). [PMID: 41483067](https://pubmed.ncbi.nlm.nih.gov/41483067/). *Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery*. [Diagnostic / Biomarker]
McGivern B (2025). [PMID: 39600096](https://pubmed.ncbi.nlm.nih.gov/39600096/). *HGG advances*. [Other]
Bambakidis E (2025). [PMID: 40146214](https://pubmed.ncbi.nlm.nih.gov/40146214/). *The Journal of craniofacial surgery*. [Case Report / Case Series]
Scagnet M (2025). [PMID: 38953669](https://pubmed.ncbi.nlm.nih.gov/38953669/). *Operative neurosurgery (Hagerstown, Md.)*. [Clinical Trial Publication]
Data assembled from 7 of 12 sources · Last updated Sep 19, 2026, 12:59 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
2 |
Craniosynostosis, Cleft soft palate |
Bones and joints | 1 | Wormian bones |