Single large-scale mitochondrial DNA deletion syndromes (SLSMDSs) comprise overlapping clinical phenotypes including Kearns-Sayre syndrome (KSS), KSS spectrum, Pearson syndrome (PS), chronic progressive external ophthalmoplegia (CPEO), and CPEO-plus. KSS is a progressive multisystem disorder with onset before age 20 years characterized by pigmentary retinopathy, CPEO, and cardiac conduction abnormality. Additional features can include cerebellar ataxia, tremor, intellectual disability or cognitive decline, dementia, sensorineural hearing loss, oropharyngeal and esophageal dysfunction, exercise intolerance, muscle weakness, and endocrinopathies. Brain imaging typically shows bilateral lesions in the globus pallidus and white matter. KSS spectrum includes individuals with KSS in addition to individuals with ptosis and/or ophthalmoparesis and at least one of the following: retinopathy, ataxia, cardiac conduction defects, hearing loss, growth deficiency, cognitive impairment, tremor, or cardiomyopathy. Compared to CPEO-plus, individuals with KSS spectrum have more severe muscle involvement (e.g., weakness, atrophy) and overall have a worse prognosis. PS is characterized by pancytopenia (typically transfusion-dependent sideroblastic anemia with variable cell line involvement), exocrine pancreatic dysfunction, poor weight gain, and lactic acidosis. PS manifestations also include renal tubular acidosis, short stature, and elevated liver enzymes. PS may be fatal in infancy due to neutropenia-related infection or refractory metabolic acidosis. CPEO is characterized by ptosis, ophthalmoplegia, oropharyngeal weakness, variable proximal limb weakness, and/or exercise intolerance. CPEO-plus includes CPEO with additional multisystemic involvement including neuropathy, diabetes mellitus, migraines, hypothyroidism, neuropsychiatric manifestations, and optic neuropathy. Rarely, an SLSMDS can manifest as Leigh syndrome, which is characterized as developmental delays, neurodevelopmental regression, lactic acidosis, and bilateral symmetric basal ganglia, brain stem, and/or midbrain lesions on MRI.

SAMD9L ataxia-pancytopenia (ATXPC) syndrome is characterized by cerebellar ataxia, variable hematologic cytopenias, and predisposition to marrow failure, myelodysplasia, and myeloid leukemia, sometimes associated with monosomy 7. The onset of hematologic abnormalities has been reported as early as age three months. The cytopenias in all cell lineages range from mild to very severe. Onset of neurologic impairment is variable. Nystagmus, dysmetria, increased deep tendon reflexes, and clonus are common. Gait impairment and other neurologic abnormalities are slowly progressive.