Table 3. Phenotypes of individuals in the schizophrenia exome meta-analysis who carry LoF variants in SETD1A.

Variant	Data set	Mode	Clinical features	Intellectual functioning
16:30970178_T/T GATG frameshift	UK10K-Finns	Case	Psychotic episodes with hallucinations and prominent disorganization, requiring psychiatric hospitalization. Chronic illness with deterioration.	Probable mild intellectual disability. Completed compulsory education, but repeated several grades.
16:30974752_A/G splice acceptor	UK10K-Finns	De novo	Disorganized schizophrenia with severe positive and negative symptoms with hallucinations delusions and aggression. Chronic, severe symptoms requiring long psychiatric hospitalization. Early onset at age 10. Has mild facial dysmorphology.	Severe learning difficulties, diagnosed with minimal brain damage, abnormal EEG; mild mental retardation. Unable to complete compulsory education. Development delay.
16:30976334_AC/A frameshift	Takata et al.13	De novo	Psychotic with persecutory delusions and thought disorder in addition to obsessional thoughts, compulsive behaviors and rituals. Persistent negative symptoms, disorgnized bahavior and delusional thinking. First psychotic break at age 21. As a child (age <10 years), displayed social isolation, excessive fears, inattentiveness, learning difficulties and obsessive-compulsive disorder–like rituals. Moderately deteriorating course.	Learning difficulties noted as a child. Delayed milestones. School performance declined from age 16. Worked as security officer.
16:30977140_C/G stop gained	UK10K	Case	Chronic hallucinations and delusions, partially controlled by depot medication.	Minor problems with memory or understanding. No secondary school diploma.
16:30977405_CAG/C frameshift	Swedish	Case	Two brief admissions, no record of antipsychotic treatment. No immediate family history of psychiatric disorders.	No information on intellectual functioning or educational attainment.
16:30980962_C/T stop gained	Swedish	Case	Multiple hospitalizations, with 8 years of antipsychotic medication. No immediate family history of psychiatric disorders.	No information on intellectual functioning or educational attainment.
16:30992057_CAG/C splice acceptor	UK10K	Case	Breech delivery. Epilepsy with seizures from ages 2 to 18. Socially isolated and dependent on parents till age 40, when presented with bizarre somatic delusions, paranoid delusions and auditory hallucinations including running commentary. Developed negative symptoms alongside ongoing psychotic symptoms and required long-term institutional care. Symptoms were persistent and unresponsive to antipsychotic medication.	Borderline intelligence. Attended mainstream school and left age 17 without a secondary school diploma. Worked as warehouseman.
16:30992057_CAG/C splice acceptor	Swedish	Case	Multiple hospitalizations, with 8 years of antipsychotic medication. No immediate family history of psychiatric disorders.	No information on intellectual functioning or educational attainment.
16:30992057_CAG/C splice acceptor	Takata et al.13	De novo	Developed schizophrenia aged 18 with delusions, disorganized behavior, poor motivation, flattened affect and social isolation. Compulsive behaviors since 4th grade. Since first episode of psychosis, did not return to previous level of functioning.	Finished high school, but slow learner and inattentive. Delayed developmental milestones.
16:30992057_CAG/C splice acceptor	Guiponni et al.20	De novo	Undifferentiated schizophrenia.	Developmental delay.

For each individual, we provide the genomic coordinates of the variant, its mode of inheritance and the study from which each patient was first recruited. ‘Clinical features’ describes notable neuropsychiatric or neurodevelopmental symptoms in each individual and ‘Intellectual functioning’ provides information on reported cognitive phenotypes.