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Features include always present findings: Progressive microcephaly; and very common findings: Dystonia, Difficulty swallowing (dysphagia), Chorea, and Visual impairment. 23 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 10 | Dystonia, Seizure, Cerebral cortical atrophy |
Muscles | 3 | Cerebral cortical atrophy, Congenital contracture, Damage to the optic nerve (optic atrophy) |
Digestive system | 2 | Feeding difficulties in infancy, Difficulty swallowing (dysphagia) |
Head and neck | 2 | Progressive microcephaly, Microcephaly |
Eyes | 2 | Visual impairment, Damage to the optic nerve (optic atrophy) |
Bones and joints | 1 | Severe backward arching of the body (opisthotonus) |
Pregnancy and birth | 1 | Congenital contracture |
Age of onset: at birth.
To date, at least 131 individuals have been identified with TSEN54 pontocerebellar hypoplasia (TSEN54-PCH) . The phenotypic spectrum of TSEN54-PCH comprises the three PCH phenotypes (PCH 2, 4, and 5) thought to be distinct entities before their molecular basis was known. The main difference between the three PCH phenotypes is life expectancy: individuals with PCH2 usually survive into childhood, whereas those with PCH4 and PCH5 usually die as neonates. Pontocerebellar Hypoplasia Type 2 The following description of the phenotypic features associated with TSEN54-PCH type 2 is based on . Table 2. Select Features of TSEN54 Pontocerebellar Hypoplasia Type 2
Feature | % of Personswith Feature | Comment |
|---|---|---|
Severe developmental delay | 100% | — |
Neurologic |
TSEN54 function has not been fully characterized.
Pontocerebellar hypoplasia type 2A is associated with mutations in the TSEN54 gene on chromosome 17.
The following clinical data, supported by pathogenic data, strongly suggest a genotype-phenotype correlation. The common missense variant is strongly associated with a dragonfly-like cerebellar pattern on MRI. In general, infants with the PCH4 phenotype who are compound heterozygotes for a pathogenic nonsense or splice site variant and a pathogenic missense variant have poorer survival than children with the PCH2 phenotype who are homozygous for a missense variant .
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
The phenotypic spectrum of TSEN54 pontocerebellar hypoplasia (TSEN54-PCH) includes three PCH phenotypes (thought to be distinct entities before the molecular basis of PCH was known) based on neuroradiologic and neurologic findings: PCH type 2 (PCH2), PCH type 4 (PCH4), and PCH type 5 (PCH5).
TSEN54-PCH should be suspected in children with severe neurologic impairment and the following findings on brain imaging .
Brain MRI Findings
Common findings
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
Table 3. Genes of Interest in the Differential Diagnosis of TSEN54 Pontocerebellar Hypoplasia
Gene(s) | Phenotype/Disorder | MOI | Brain MRI Findings | Clinical Characteristics |
|---|---|---|---|---|
B3GALNT2B4GAT1DAG1FKRPFKTNGMPPBISPDLARGE1POMGNT1POMGNT2POMKPOMT1POMT2RXYLT11 | Alpha-dystroglycanopathies | AR | Wide spectrum of brain malformations incl cobblestone lissencephaly hydrocephalus | Muscle weakness ophthalmologic abnormalities |
Genetic testing for TSEN54 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for pontocerebellar hypoplasia type 2A has been reported in the published literature.
No approved treatments are currently available for pontocerebellar hypoplasia type 2A. The disease remains an area of unmet medical need.
Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with TSEN54 pontocerebellar hypoplasia (TSEN54-PCH), the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Note that recommendations are based only on PCH2 caused by homozygosity for theTSEN54 pathogenic variant , as all other subtypes are very rare. Table 4. Recommended Evaluations Following Initial Diagnosis of TSEN54 Pontocerebellar Hypoplasia Type 2
System/Concern | Evaluation | Comment |
|---|---|---|
Constitutional | Measure length, weight. | See Gastrointestinal/Feeding recommendations if there is evidence of failure to thrive. Gastrointestinal/ |
Feeding | Gastroenterology / nutrition / feeding team eval | Assess swallowing feeding to determine safety of oral vs gastrostomy feeding. |
Respiratory | Assess airway pulmonary function secretion management. | Consult pulmonologist. |
Neurologic | Eval by pediatric neurologist | Assess for evidence of severe generalized clonus; chorea, spasticity; seizures; impaired central vision. |
Musculoskeletal | Multidisciplinary neuromuscular clinic assessment by orthopedist, physical medicine, OT/PT |
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
Although hyperthermic episodes have been documented in individuals with PCH2, no special risk appears to be associated with generalized anesthesia.
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
View trials for pontocerebellar hypoplasia type 2A
Table 6.
Recommended Surveillance for Individuals with TSEN54 Pontocerebellar Hypoplasia Type 2
System/Concern | Evaluation | Frequency
| Assess airway pulmonary function secretion management. | Monitoring of respiratory function may be needed to detect sleep apnea.
Gastrointestinal/
|
Aspiration risk nutritional status
Monitor for constipation.
| Annually; more frequently if needed
|
PT/OT eval
Assessment for contractures, scoliosis, foot deformities.
Hip/spine x-rays
|
Monitor those w/seizures as clinically indicated.
Monitor for dystonia choreic movements.
| Monitor developmental milestones.
Family support
resources | Family needs
OT = occupational therapy; PT = physical therapy
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
Phenotype severity distribution: 1 always present feature, 4 very common features.
No clinical trials have been registered for pontocerebellar hypoplasia type 2A.
9 publications have been identified in PubMed for pontocerebellar hypoplasia type 2A. Research spans Epidemiology / Natural History (44%), Diagnostic / Biomarker (22%), and Case Report / Case Series (11%).
Kuhn A (2026). [PMID: 40665551](https://pubmed.ncbi.nlm.nih.gov/40665551/). *Developmental medicine and child neurology*. [Epidemiology / Natural History]
Herrmann A (2026). [PMID: 41875837](https://pubmed.ncbi.nlm.nih.gov/41875837/). *Pediatric neurology*. [Diagnostic / Biomarker]
Unknown (2025). [PMID: 40714950](https://pubmed.ncbi.nlm.nih.gov/40714950/). *Developmental medicine and child neurology*. [Clinical Trial Publication]
Pretzel P (2025). [PMID: 40311513](https://pubmed.ncbi.nlm.nih.gov/40311513/). *European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society*. [Diagnostic / Biomarker]
Khan A (2025). [PMID: 39400946](https://pubmed.ncbi.nlm.nih.gov/39400946/). *Clinical genetics*. [Epidemiology / Natural History]
Hayashi Y (2025). [PMID: 40858833](https://pubmed.ncbi.nlm.nih.gov/40858833/). *Journal of human genetics*. [Case Report / Case Series]
Osman N (2025). [PMID: 40524706](https://pubmed.ncbi.nlm.nih.gov/40524706/). *AJOG global reports*. [Epidemiology / Natural History]
Kagermeier T (2024). [PMID: 39034883](https://pubmed.ncbi.nlm.nih.gov/39034883/). *Disease models & mechanisms*. [Basic Science / Preclinical]
Cavusoglu D (2024). [PMID: 38622473](https://pubmed.ncbi.nlm.nih.gov/38622473/). *Cerebellum (London, England)*. [Epidemiology / Natural History]
Data assembled from 6 of 12 sources · Last updated Sep 19, 2026, 1:11 PM UTC
Online Mendelian Inheritance in Man
Genetic and Rare Diseases Info Center
88% |
Pure spasticity | 12% | — |
Epileptic seizures | 82% | — |
Dystonic attacks | 33% | — |
Gastrointestinal | Feeding difficulties | 100% |
GERD | 73% | — |
Sleep disorder | 96% | — |
Apnea | 67% | — |
Recurrent infections | 52% | Based on 33 individuals homozygous for the common missense variant, p.Ala307Ser, from nonconsanguineous parents surviving until age 11 years Pregnancy is usually unremarkable. Newborns have no external dysmorphic features and no visceral abnormalities. |
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
CASK |
ID microcephaly w/pontine cerebellar hypoplasia (See CASK Disorders.) |
XL |
Neocortical dysplasia (simplified gyral pattern, thin brain stem w/flattening of the pons) severe cerebellar hypoplasia (pontocerebellar hypoplasia) |
Heterozygous females have severe or profound ID structural brain anomalies incl mild congenital microcephaly severe postnatal microcephaly.; Hemizygous males are more severely affected. |
CHMP1A | PCH82 | AR | MRI findings similar to those of PCH2 | Microcephaly, delayed walking, variable foot deformities, chorea, dystonic posturing, impaired cognition EXOSC3 EXOSC8 SLC25A46 |
VRK1 | PCH12,3 (See EXOSC3-PCH.) | AR | Pontine atrophy may not be present in some individuals. | Lower motor neuron deficits due to loss of anterior horn cells; manifestations of peripheral denervation incl weakness muscle hypotonia from birth; Mixed central (spastic, dystonic) peripheral pareses may be present in those w/prolonged survival; some children w/PCH1 die at an early age.4 |
40 genes (e.g., PMM25) | Congenital disorders of glycosylation (CDG); see also PMM2-CDG (CDG-Ia). | AR(XL) | Pontocerebellar hypoplasia w/superimposed atrophy, delayed myelination | Dysmorphic features, ataxia, organ failure in neonatal period |
PCLO | PCH32 | AR | — | — |
RARS2 | PCH62 | AR | Very rare; CSF lactate concentration | — |
RELN | Lissencephaly 2 (OMIM 257320) | AR | Classic lissencephaly w/coexistent cerebellar pontine hypoplasia | — |
SEPSECS | PCH22 | AR | Progressive cerebello-cerebral atrophy closely resembles mild PCH2. | Clinical findings closely resemble mild PCH2. |
TOE1 | PCH72 | AR | PCH | Disorders of sex development VLDLR |
VLDLR cerebellar hypoplasia | AR | Gross cerebellar hypoplasia, a flat ventral pons, simplified gyri | Ataxia ID AR = autosomal recessive; ID = intellectual disability; MOI = mode of inheritance; PCH = pontocerebellar hypoplasia; XL = X-linked 1. OMIM Phenotypic Series: Muscular dystrophy-dystroglycanopathy, type A 2. 3. | — |
Source: GeneReviews — "TSEN54 Pontocerebellar Hypoplasia"
To incl assessment of:; Contractures, clubfoot, kyphoscoliosis; Need for positioning devices
Palliative care | Refer to palliative care specialist. | When deemed appropriate by family care providers Genetic |
counseling | By genetics professionals1 | To inform affected individuals their families re nature, MOI, implications of TSEN54-PCH2 to facilitate medical personal decision making Family support/ resources |
Treatment of Manifestations in Individuals with TSEN54 Pontocerebellar Hypoplasia Type 2 Manifestation/Concern | Treatment | Considerations/Other |
Seizures | Per standard practice | By neurologist experienced in epilepsy management |
Irritability | None | Often related to chorea (involuntary movements) |
Musculoskeletal | Multidisciplinary neuromuscular clinic physical medicine, OT/PT | Maximize gross motor fine motor skills through PT/OT use of adaptive devices.; Alternative casting/splinting stretching Orthopedics |
Dysphagia | Gastroenterology / nutrition / feeding team | Modify food consistency to aspiration risk /or consider NG feeding gastrostomy. |
Speech | Speech/language eval | Consider involving speech therapist OT to improve communication skills. |
Respiratory | Manage pulmonary complications; treatment of respiratory infections | Per treating pulmonologist |
Neurodevelopmental | Early intervention / individual education program based on needs | See . NG = nasogastric, OT = occupational therapy, PT = physical therapy The following information represents typical management recommendations for individuals with developmental delay / intellectual disability in the United States; standard recommendations may vary from country to country. |