Table 2 Detailed information of 7 genes identified from our human amygdala snRNA-seq screen and found in the 80 (GFAP, KCNQ3) and 271 (all 7) amygdala gene lists

C13

Fibrous astrocytes

Glial Fibrillary Acidic Protein encodes one of the major intermediate filament proteins of mature astrocytes. It is used as a marker to distinguish astrocytes from other glial cells during development. Mutations in this gene cause Alexander disease, a rare disorder of astrocytes in the central nervous system. Involved in responses to brain injury and disease states.

Edmonson et al., 2014. Altered glial marker expression in in autistic post-mortem prefrontal cortex and cerebellum. Molecular Autism.

C10

Excitatory neurons

Potassium Voltage-Gated Channel Subfamily Q Member 3 gene encodes a protein involved in the regulation of neuronal excitability and responsiveness to synaptic inputs by contributing to the slow component of synaptic AHP (afterhyperpolarization) that determines the firing pattern of a neuron. Diseases associated with KCNQ3 include seizures, Benign Familial Neonatal convulsions type 2, and Benign Familial Neonatal Epilepsy.

Sands et al., 2019. Autism and developmental disability caused by KCNQ3 gain-of-function variants. Ann Neurol.

PHF21A

C10

Excitatory neurons

PHD Finger Protein 21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that represses transcription of neuron-specific genes in non-neuronal cells through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS). Disorders associated with PHF21A include Potocki-Shaffer Syndrome and Parietal Foramina.

Kim et al., 2019. Disruption of PHF21A causes syndromic intellectual disability with craniofacial anomalies, epilepsy, hypotonia, and neurobehavioral problems including autism. Molecular Autism.

RANBP17

C10

Excitatory neurons

RAN Binding Protein 17 is a nuclear pore-associated transport receptor, member of the importin-beta superfamily. The small GTPase RAN plays a key role in the import of proteins with a nuclear localization signal (NLS). RANBP17 expression decreases with aging and in human fetal brain exhibited higher expression in females. Lower expression may be linked to altered nuclear pore function.

Mertens et al., 2015. Directly reprogrammed human neurons retain aging-associated transcriptomic signatures and reveal age-related nucleocytoplasmic defects. Cell Stem Cell.

ELP4

C10

Excitatory neurons

Elongator Acetyltransferase Complex Subunit 4 encodes a component of the elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. Elongators may play a role in chromatin remodeling and regulate the maturation of cortical projection neurons. This gene has also been associated with Rolandic epilepsy.

Reinthaler et al., 2014. Analysis of ELP4, SRPX2, and interacting genes in typical and atypical rolandic epilepsy. Epilepsia.

CNKSR2

C10

Excitatory neurons

Connector Enhancer of Kinase Suppressor of Ras 2 encodes a synaptic protein that functions as a scaffold in the postsynaptic density (PSD). CNKSR2 regulates Ras signaling, which controls neuronal proliferation, migration, differentiation, apoptosis and synaptogenesis. Diseases associated with CNKSR2 include: mental retardation, language deficits, attentional problems/hyperactivity, and brief childhood epilepsy.

AK Vaags, S Bowdin, ML Smith et al., 2014. Absent CNKSR2 causes seizures and intellectual, attention, and language deficits. Ann Neurol.

NAV2

C13

Fibrous astrocytes

Neuron Navigator 2 encodes a member of the neuron navigator family. Highly expressed in fetal and adult brain, Nav2 is a retinoic acid-responsive gene involved in nervous system development. Nav2 may play a role in cellular growth, migration and neuronal development of different sensory organs. It possesses helicase activity and exonuclease activity. Diseases associated with NAV2 include neuroblastoma.

Marzinke MA, Mavencamp T, Duratinsky J, Clagett-Dame M. 2013. 14-3-3ε and NAV2 interact to regulate neurite outgrowth and axon elongation. Arch Biochem Biophys.