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spinocerebellar ataxia 49 (SCA49) - Clinical Profile, Genes & Research | Kisho | Kisho

Rare Disease

spinocerebellar ataxia 49

MONDO:0030805

Also known as:SCA49

Overview

GeneticsAutosomal dominant · SAMD9L (chr 7)

OnsetLATE, MIDDLE_AGE

Clinical Presentation

Built from Human Phenotype Ontology (HPO) phenotype annotations and GeneReviews clinical descriptions. Features represent findings documented across known cases — not an exhaustive list of possible symptoms.

Features include always present findings: Gaze-evoked nystagmus, Shrinkage of the cerebellum (cerebellar atrophy), and Overactive reflexes (hyperreflexia); and common findings: Diplopia, Dysmetria, Dysarthria, and Ataxia and others. 16 total HPO annotations.

Organ System	Phenotype Count	Example Features
Brain and nerves	8	Babinski sign, Dysarthria, Ataxia

Genetic Landscape

Assembled from HGNC gene records, ClinGen gene-disease validity evidence, and ClinVar pathogenic variant data. Validity classifications reflect the strength of published evidence linking each gene to this disease.

SAMD9L function has not been fully characterized.

Spinocerebellar ataxia 49 is associated with mutations in the SAMD9L gene on chromosome 7.

GeneReviews

Clinical Guidance

With respect to validated pathogenic variants in SAMD9L, no genotype-phenotype correlations have been observed.

Diagnosis

Drawn from GeneReviews diagnostic guidelines, newborn screening panel status (RUSP), and ClinGen gene-disease validity classifications. Reflects current clinical evidence and consensus where available.

GeneReviews

Diagnostic Criteria

Formal clinical diagnostic criteria for SAMD9L ataxia-pancytopenia (ATXPC) syndrome have not been established.

Suggestive Findings

SAMD9L-ATXPC syndrome should be suspected in individuals with one or more of the following clinical, imaging, and family history findings.

Clinical features

Cerebellar ataxia

Treatment

Compiled from FDA-approved drug records, orphan drug designations, and FDA Adverse Event Reporting System (FAERS) safety data. GeneReviews management guidance is included where available.

No approved treatments are currently available for spinocerebellar ataxia 49. The disease remains an area of unmet medical need.

GeneReviews

Management Guidelines

Evaluations Following Initial Diagnosis

To establish the extent of disease and guide clinical care in an individual diagnosed with SAMD9L ataxia-pancytopenia (ATXPC) syndrome, the evaluations summarized (if not performed as part of the evaluation that led to diagnosis) are recommended.

Table 4.

Recommended Evaluations Following Initial Diagnosis in Individuals with SAMD9L Ataxia-Pancytopenia Syndrome

Prognosis

Based on GeneReviews surveillance recommendations, HPO phenotype frequency and severity annotations, and published prevalence estimates from Orphanet and OMIM.

GeneReviews

Surveillance Guidelines

Table 6.

Recommended Surveillance for Individuals with SAMD9L Ataxia-Pancytopenia Syndrome

System/Concern | Evaluation | Frequency

Hematologic/

Oncologic

| Complete blood count | At lease annually1

Neurologic

Research Landscape

Sourced from ClinicalTrials.gov and PubMed. Publication types are classified using NLM-curated article metadata; research type breakdowns reflect the nature of published work for this disease.

No clinical trials have been registered for spinocerebellar ataxia 49.

33 publications have been identified in PubMed for spinocerebellar ataxia 49. Research spans Basic Science / Preclinical (21%), Epidemiology / Natural History (21%), and Diagnostic / Biomarker (15%).

Research Type	Count	% of Total
Laboratory research	7	21%

Data assembled from 7 of 12 sources · Last updated Sep 19, 2026, 6:57 PM UTC

MONDOHPOClinicalTrials.govFDAPubMedHGNCClinVarClinGenGeneReviewsOrphanetOMIMRUSP

Medical References

External Resources

OMIM

Online Mendelian Inheritance in Man

OMIM:619806

Orphanet

European rare disease database

Orphanet:631106

Questions for Your Care Team

→Should I pursue genetic testing for SAMD9L, and what would the results mean for my family?
→Are there specialists or centers of excellence for this condition in my area?
→Is there a patient registry I should consider joining?

← Back to All Diseases

GeneReviews

Clinical Guidance

To date, 85 individuals from 36 families have been identified with a pathogenic variant in SAMD9L [; ; ; ; ; ; ; ; ; ; ; ; Author, unpublished data]. In addition, approximately 15% of children with myelodysplastic syndrome are found to have a germline pathogenic variant in SAMD9L. The following description of the phenotypic features associated with this condition is based on these reports. Table 2. Select Features of SAMD9L Ataxia-Pancytopenia Syndrome

Feature	% of Personsw/Feature	Comment
Neurologic manifestatioms1	75%2	Nystagmus is most frequent; gait ataxia may develop later.
Bone marrow failure (cytopenias)	~80%3	Thrombocytopenia mild red cell macrocytosis are most frequent.
Myelodysplasia /or monosomy 7q	~41%3	—
Myeloid leukemia	4%4	May be an underestimate of risk as MDS or monosomy 7q may trigger HSCT. HSCT = hematopoietic stem cell transplant; MDS = myelodysplasia 1. One or more of nystagmus, ataxia, pyramidal signs, neuropathy, abnormal brain imaging 2. Not all persons had neurologic evaluations or neuroimaging.

Source: GeneReviews — "SAMD9L Ataxia-Pancytopenia Syndrome"

Kisho

spinocerebellar ataxia 49

Overview

Clinical Presentation

Genetic Landscape

Clinical Guidance

Diagnosis

Diagnostic Criteria

Suggestive Findings

Treatment

Management Guidelines

Evaluations Following Initial Diagnosis

Prognosis

Surveillance Guidelines

Oncologic

Neurologic

Research Landscape

Medical References

External Resources

OMIM

Orphanet

Questions for Your Care Team

Questions for Your Care Team

Clinical Guidance

Explore clinical features

Penetrance

Differential Diagnosis

ABCB7

WRAP53

Oncologic

Neurologic

Clinical Guidance

Therapies Under Investigation

Clinical Trials

Dysarthria

Dysphagia

Recent Publications

Latest News & Developments

Frequency of ZFHX3-Mediated Spinocerebellar Ataxia 4 in a US Undiagnosed Ataxia Cohort.

spinocerebellar ataxia 49

Overview

Clinical Presentation

Genetic Landscape

Clinical Guidance

Diagnosis

Diagnostic Criteria

Suggestive Findings

Treatment

Management Guidelines

Evaluations Following Initial Diagnosis

Prognosis

Surveillance Guidelines

Oncologic

Neurologic

Research Landscape

Medical References

External Resources

OMIM

Orphanet

Related Diseases

Questions for Your Care Team

Questions for Your Care Team

Clinical Guidance

Explore clinical features

Penetrance

Differential Diagnosis

ABCB7

WRAP53

Oncologic

Neurologic

Clinical Guidance

Therapies Under Investigation

Clinical Trials

Dysarthria

Dysphagia

Recent Publications

Latest News & Developments

Frequency of ZFHX3-Mediated Spinocerebellar Ataxia 4 in a US Undiagnosed Ataxia Cohort.