| ACTL6B | actin like 6B | 3 | Yes | – | S | No |
| ADNP | Activity-dependent neuroprotector homeobox | 14 | No | 1 | | Yes |
| ADORA2A | Adenosine A2a receptor | 2 | Unknown | 3 | | No |
| AHI1 | Abelson helper integration site 1 | 5 | Unknown | – | S | Yes |
| ALDH5A1 | Aldehyde Dehydrogenase 5 family, member A1 | 4 | Unknown | 1 | | Yes |
| ANK2 | ankyrin 2, neuronal | 5 | No | 1 | | No |
| ANKRD11 | ankyrin repeat domain 11 | 3 | Unknown | 1 | | No |
| ANKS1B | ankyrin repeat and sterile alpha motif domain containing 1B | 2 | No | 3 | S | No |
| APBA2 | amyloid beta (A4) precursor protein-binding, family A, member 2 | 2 | Unknown | 3 | | No |
| ARHGAP32 | Rho GTPase activating protein 32 | 3 | No | 3 | | Yes |
| ARHGEF10 | Rho guanine nucleotide exchange factor 10 | 1 | No | 3 | | No |
| ARID1B | AT-rich interaction domain 1B | 14 | No | 1 | | Yes |
| ARX | aristaless related homeobox | 5 | Unknown | 1 | | No |
| ASH1L | ASH1 like histone lysine methyltransferase | 6 | No | 1 | | Yes |
| ASPM | assembly factor for spindle microtubules | 1 | Yes | 2 | | No |
| ATP1A3 | Sodium potassium ATPase alpha 3 subunit | 2 | Unknown | 3 | S | Yes |
| ATP2B2 | TPase, Ca++ transporting, plasma membrane 2 | 1 | No | 2 | | No |
| AUTS2 | AUTS2, activator of transcription and developmental regulator | 21 | No | 1 | | Yes |
| AVPR1A | Arginine vasopressin receptor 1A | 2 | Unknown | 2 | | No |
| BCKDK | branched chain ketoacid dehydrogenase kinase | 3 | No | 1 | | Yes |
| BCL11A | B-cell CLL/lymphoma 11A | 2 | Yes | 1 | | No |
| BRINP3 | BMP/retinoic acid inducible neural specific 3 | 1 | Yes | 3 | | No |
| CACNA1C | calcium voltage-gated channel subunit alpha1 C | 13 | Unknown | 1 | | No |
| CACNA1F | Calcium channel, voltage-dependent, L type, alpha 1F subunit | 1 | No | 3 | | No |
| CACNA1G | Cav3.1 T-type Ca2+ Channel | 6 | Unknown | 3 | | No |
| CACNA1H | calcium channel, voltage-dependent, T type, alpha 1H subunit | 1 | Unknown | 2 | | No |
| CACNA2D3 | calcium voltage-gated channel auxiliary subunit alpha2delta 3 | 2 | Yes | 1 | | No |
| CADM1 | cell adhesion molecule 1 | 4 | Unknown | 3 | | No |
| CADPS2 | Ca2+-dependent activator protein for secretion 2 | 5 | Yes | 3 | | No |
| CAMK2A | calcium/calmodulin dependent protein kinase II alpha | 2 | No | 3 | S | No |
| CAPRIN1 | RNA granule protein 105 (Caprin 1) | 2 | Unknown | 1 | | No |
| CC2D1A | Coiled-coil and C2 domain containing 1A | 10 | No | 2 | | No |
| CD38 | CD38 molecule | 2 | Unknown | 3 | | No |
| CDKL5 | cyclin-dependent kinase-like 5 | 10 | No | 1 | | Yes |
| CELF4 | CUGBP, Elav-like family member 4 | 7 | No | 1 | | No |
| CELF6 | CUGBP, Elav-like family member 6 | 1 | No | 3 | | No |
| CHD2 | chromodomain helicase DNA binding protein 2 | 5 | No | 1 | | Yes |
| CHD7 | Chromodomain Helicase DNA Binding Protein 7 | 4 | No | 1 | | Yes |
| CHD8 | chromodomain helicase DNA binding protein 8 | 24 | No | 1 | | Yes |
| CIC | capicua transcriptional repressor | 8 | Yes | 1 | | Yes |
| CNTN4 | contactin 4 | 3 | Unknown | 2 | | No |
| CNTNAP2 | contactin associated protein-like 2 | 37 | Unknown | 2 | S | Yes |
| CNTNAP4 | contactin associated protein-like 4 | 7 | No | 2 | | Yes |
| CSNK1E | casein kinase 1, epsilon | 1 | No | 3 | | No |
| CTNNB1 | catenin (cadherin associated protein), beta 1 | 1 | Yes | 1 | | No |
| CTNND2 | Catenin(cadherin associated protein), delta 2 | 1 | No | 2 | | No |
| CTTNBP2 | cortactin binding protein 2ÃÂ | 19 | No | 2 | | Yes |
| CUL3 | cullin 3 | 15 | No | 1 | | Yes |
| CYFIP1 | Cytoplasmic FMR1 interacting protein 1 | 3 | No | 2 | | Yes |
| DAGLA | diacylglycerol lipasealpha | 4 | No | 3 | | No |
| DEAF1 | DEAF1, transcription factor | 9 | Yes | 1 | | No |
| DHCR7 | 7-dehydrocholesterol reductase | 5 | No | 1 | | No |
| DIP2A | disco interacting protein 2 homolog A | 2 | No | 1 | | Yes |
| DISC1 | Disrupted in schizophrenia 1 | 13 | Unknown | 2 | | Yes |
| DLG4 | discs, large homolog 4 (Drosophila) | 4 | Unknown | 1 | | No |
| DLGAP1 | DLG associated protein 1 | 4 | No | 2 | | No |
| DLGAP2 | DLG associated protein 2 | 2 | Yes | 3 | | No |
| DMD | Dystrophin | 6 | Unknown | – | S | No |
| DMPK | dystrophia myotonica-protein kinase | 2 | Unknown | 1 | | No |
| DNMT3A | DNA methyltransferase 3 alpha | 2 | Yes | 1 | | No |
| DPP6 | dipeptidyl- petidase 6 | 1 | No | 3 | | No |
| DPYSL3 | dihydropyrimidinase like 3 | 1 | Yes | 3 | | No |
| DRD1 | Dopamine receptor D1 | 2 | No | 3 | | No |
| DRD3 | Dopamine receptor D3 | 3 | Unknown | 3 | | No |
| DSCAM | DS cell adhesion molecule | 11 | No | 1 | | No |
| DVL3 | Dishevelled segment polarity protein 3 | 5 | No | 3 | | Yes |
| DYRK1A | dual specificity tyrosine-Y- phosphorylation regulated kinase 1A | 3 | No | 1 | | No |
| EEF1A2 | eukaryotic translation elongation factor 1 alpha 2 | 7 | No | – | S | No |
| EIF4E | Eukaryotic translation initiation factor 4E | 5 | Yes | 3 | | Yes |
| EIF4G1 | eukaryotic translation initiation factor 4 gamma 1 | 2 | No | 3 | | No |
| EN2 | Engrailed homeobox 2 | 5 | Unknown | 3 | | No |
| ERBIN | erbb2 interacting protein | 2 | No | 2 | | No |
| ESRRB | Estrogen-related receptor beta | 2 | Unknown | 3 | | No |
| EXT1 | exostosin 1 | 1 | No | 3 | | No |
| FEZF2 | FEZ family zinc finger 2 | 1 | Unknown | 3 | | No |
| FMR1 | fragile X mental retardation 1 | 64 | Unknown | 1 | | Yes |
| FOXG1 | Forkhead Box G1 | 1 | Unknown | 1 | | No |
| FOXP1 | Forkhead box P1 | 8 | Unknown | 1 | | No |
| FOXP2 | forkhead box P2 | 8 | Unknown | 1 | | No |
| GABRB2 | gamma-aminobutyric acid type A receptor subunit beta2 | 8 | No | 1 | | Yes |
| GABRB3 | gamma-aminobutyric acid type A receptor beta3 subunit | 22 | Unknown | 1 | | Yes |
| GLRA2 | glycine receptor, alpha 2 | 1 | Unknown | 3 | | No |
| GRIA2 | Glutamate receptor, ionotropic, AMPA 2 | 1 | Unknown | 1 | | No |
| GRID2 | glutamate receptor, ionotropic, delta 2 | 2 | No | 3 | | No |
| GRIK2 | glutamate receptor, ionotropic, kainate 2 | 4 | No | 2 | | Yes |
| GRIK4 | Glutamate receptor, ionotropic, kainate 4 | 12 | No | 3 | | Yes |
| GRIN1 | glutamate receptor, ionotropic, N-methyl D-aspartate 1 | 7 | No | 2 | | Yes |
| GRIN2B | Glutamate receptor, ionotropic, N-methyl D-aspartate 2B | 10 | No | 1 | | No |
| GRID1 | glutamate receptor, ionotropic, delta 1 | 1 | No | 2 | | No |
| GRIP1 | Glutamate receptor interacting protein 1 | 3 | Unknown | 2 | | No |
| GRM5 | glutamate receptor, metabotropic 5 | 12 | No | 3 | | No |
| GSTM1 | Glutathione S-transferase mu 1 | 1 | Unknown | 3 | | No |
| GTF2I | general transcription factor Iii | 2 | Unknown | 3 | | No |
| HDAC4 | Histone deacetylase 4 | 2 | Unknown | 3 | S | No |
| HMGN1 | High mobility group nucleosome binding domain 1 | 2 | Unknown | 2 | | No |
| HOMER1 | homer scaffolding protein 1 | 4 | No | 3 | | No |
| HOXA1 | Homeobox A1 | 3 | Unknown | – | S | No |
| HTR1B | 5-hydroxytryptamine (serotonin) receptor 1B | 2 | Unknown | 3 | | No |
| HTR3A | 5-hydroxytryptamine (serotonin) receptor 3A | 3 | Unknown | 3 | | No |
| IL1RAPL1 | interleukin 1 receptor accessory protein-like 1 | 2 | Unknown | 3 | | No |
| IMMP2L | IMP2 inner mitochondrial membrane peptidase-like | 2 | Unknown | 3 | | No |
| IQSEC2 | IQ motif and Sec7 domain 2 | 1 | Yes | 1 | | No |
| ITGB3 | integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) | 2 | Unknown | 2 | | No |
| KCNMA1 | potassium large conductance calcium-activated channel, subfamily M, alpha member 1 | 3 | Yes | 3 | | No |
| KCNQ2 | potassium voltage-gated channel, KQT-like subfamily, member 2 | 1 | Unknown | 2 | | No |
| KCTD13 | potassium channel tetramerization domain containing 13 | 6 | Yes | 3 | | No |
| KIRREL3 | Kin of Irregular Chiasm-like 3 | 1 | No | 2 | | No |
| KMT2A | Lysine methyltransferase 2A | 3 | No | 1 | | No |
| LRFN2 | leucine rich repeat and fibronectin type III domain containing 2 | 2 | No | 3 | | No |
| LRRC4 | leucine rich repeat containing 4 | 4 | No | 3 | | Yes |
| MAGEL2 | MAGE like 2 | 1 | No | 1 | | No |
| MAOA | Monoamine Oxidase A | 3 | Unknown | 3 | | No |
| MBD3 | methyl-CpG binding domain protein 3 | 1 | Unknown | 3 | | No |
| MBOAT7 | membrane bound O-acyltransferase domain containing 7ÃÂ | 1 | Yes | 1 | | No |
| MCPH1 | microcephalin 1 | 2 | Unknown | 3 | | No |
| MDGA2 | MAM domain containing glycosylphosphatidylinositol anchor 2 | 2 | No | 3 | | No |
| MECP2 | methyl-CpG binding protein 2 | 92 | Yes | 1 | | Yes |
| MEF2C | Myocyte Enhancer Factor 2C | 13 | Unknown | 1 | | Yes |
| MET | MET proto-oncogene, receptor tyrosine kinase | 10 | Unknown | 2 | | No |
| MIR137 | microRNA 137 | 6 | No | 2 | | Yes |
| MTHFR | methylenetetrahydrofolate reductase (NAD(P)H) | 4 | No | 3 | | Yes |
| MTOR | mechanistic target of rapamycin kinase | 3 | Yes | 2 | S | Yes |
| NBEA | Neurobeachin | 3 | Unknown | 1 | | No |
| NEGR1 | neuronal growth regulator 1 | 9 | No | 3 | | Yes |
| NEXMIF | neurite extension and migration factor | 1 | No | 2 | | No |
| NF1 | neurofibromin 1 | 10 | Unknown | 1 | | Yes |
| NLGN1 | neuroligin 1 | 10 | Unknown | 2 | | No |
| NLGN2 | neuroligin 2 | 4 | No | 1 | | No |
| NLGN3 | neuroligin 3 | 47 | Yes | 1 | | Yes |
| NLGN4X | neuroligin 4, X-linked | 3 | Unknown | 1 | | No |
| NPAS2 | neuronal PAS domain protein 2 | 2 | Unknown | 3 | | No |
| NR2F1 | nuclear receptor subfamily 2 group F member 1 | 2 | Yes | 3 | S | Yes |
| NR3C2 | nuclear receptor subfamily 3, group C, member 2 | 2 | Unknown | 1 | | No |
| NRCAM | Neural cell adhesion molecule | 1 | Unknown | 3 | | No |
| NRP2 | neuropilin 2 | 4 | Unknown | 3 | | No |
| NRXN1 | neurexin 1 | 2 | Unknown | 1 | | No |
| NRXN2 | Neurexin2 | 3 | No | 1 | | No |
| NTNG1 | Netrin G1 | 1 | Unknown | 3 | S | No |
| NTNG2 | Netrin G2 | 1 | Unknown | – | S | No |
| NUAK1 | NUAK family, SNF1-like kinase, 1 | 6 | Unknown | 2 | | No |
| OPHN1 | Oligophrenin 1 | 1 | Unknown | 2 | | No |
| OTUD7A | OTU deubiquitinase 7A | 2 | Yes | 2 | | No |
| OXT | oxytocin/neurophysin I prepropeptide [Homo sapiens (human) | 7 | Yes | 3 | | Yes |
| OXTR | Oxytocin receptor | 17 | Unknown | 2 | | Yes |
| PAK2 | p21 (RAC1) activated kinase 2 | 3 | No | 2 | | Yes |
| PCDH10 | protocadherin 10 | 3 | Unknown | 3 | | Yes |
| PCDH19 | protocadherin 19 | 4 | No | 1 | | No |
| PER1 | Period homolog 1 | 1 | Unknown | 3 | | No |
| PITX1 | paired-like homeodomain 1 | 1 | Unknown | 3 | | No |
| PLAUR | plasminogen activator, urokinase receptor | 1 | Unknown | 3 | | No |
| PLN | Phospholamban | 1 | Unknown | 3 | | No |
| POGZ | pogo transposable element derived with ZNF domain | 6 | No | 1 | | Yes |
| PRICKLE1 | prickle homolog 1 (Drosophila) | 5 | No | 2 | | No |
| PRICKLE2 | prickle homolog 2 (Drosophila) | 2 | No | 2 | | No |
| PRKCB | Protein Kinase C, beta | 1 | Unknown | 2 | | No |
| PRKDC | Protein kinase, DNA activated, catalytic peptide | 2 | No | 3 | | Yes |
| PTCHD1 | Patched domain containing 1 | 7 | No | 1 | | Yes |
| PTEN | phosphatase and tensin homolog | 29 | Unknown | 1 | | Yes |
| PTGS2 | prostaglandin-endoperoxide synthase 2 | 1 | No | 3 | | No |
| RAB39B | RAB39B, member RAS oncogene family | 2 | Yes | 3 | | No |
| RAI1 | retinoic acid induced 1 | 12 | Unknown | 1 | | Yes |
| RAPGEF4 | Rap guanine nucleotide exchange factor (GEF) 4 | 2 | Unknown | 3 | | No |
| RBFOX1 | RNA binding protein, fox-1 homolog | 2 | Unknown | 2 | | No |
| RELN | Reelin | 9 | Unknown | 1 | | Yes |
| RHEB | Ras homolog, mTORC1 binding | 3 | No | – | S | No |
| RIMS1 | regulating synaptic membrane exocytosis 1 | 10 | Yes | 1 | | No |
| RPS6KA3 | ribosomal protein S6 kinase, 90kDa, polypeptide 3 | 1 | No | 3 | S | No |
| SCN1A | sodium channel, voltage-gated, type I, alpha subunit | 19 | Unknown | 1 | | Yes |
| SCN2A | sodium voltage-gated channel alpha subunit 2 | 7 | Unknown | 1 | | Yes |
| SCN8A | sodium channel, voltage gated, type VIII, alpha subunit | 1 | Unknown | 1 | | No |
| SEMA5A | Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A | 1 | Unknown | 2 | | No |
| SETD5 | SET domain containing 5 | 2 | No | 1 | | No |
| SHANK1 | SH3 and multiple ankyrin repeat domains 1 | 2 | Unknown | 2 | | No |
| SHANK2 | SH3 and multiple ankyrin repeat domains 2 | 24 | No | 1 | | Yes |
| SHANK3 | SH3 and multiple ankyrin repeat domains 3 | 96 | Unknown | 1 | | Yes |
| SLC1A2 | solute carrier family 1 (glial high affinity glutamate transporter), member 2 | 8 | No | – | S | Yes |
| SLC25A12 | solute carrier family 25 (Mitochondrial carrier, Aralar), member 12 | 4 | Unknown | 3 | | No |
| SLC4A10 | Solute carrier 4, sodium bicarbonate transporter, member 10 | 1 | Unknown | 3 | | No |
| SLC6A1 | Solute carrier family 6 member 1 | 1 | No | 1 | | No |
| SLC6A3 | solute carrier family 6 member 3 | 15 | No | 2 | | Yes |
| SLC6A4 | solute carrier family 6 member 4 | 14 | Unknown | 3 | | Yes |
| SLC6A8 | Solute carrier family 6 member 8 | 2 | Yes | 3 | | No |
| SLC7A5 | solute carrier family 7 member 5 | 2 | No | 2 | | Yes |
| SLC9A6 | solute carrier family 9, subfamily A | 3 | No | 1 | | No |
| SLC9A9 | solute carrier family 9 member A9 | 3 | Yes | 3 | | No |
| SLITRK5 | SLIT and NTRK-like family, member 5 | 2 | No | 2 | | No |
| SPAST | Spastin | 1 | No | 1 | | No |
| ST8SIA2 | ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 | 5 | Unknown | 2 | | Yes |
| STK39 | Serine threonine Kinase 39 (STE20/SPS1 homolog, yeast) | 1 | Unknown | 3 | | No |
| STXBP1 | syntaxin binding protein 1 | 6 | Yes | 1 | | Yes |
| SYBU | syntabulin | 1 | Yes | 3 | | No |
| SYN2 | Synapsin II | 3 | No | 3 | | Yes |
| SYNGAP1 | synaptic Ras GTPase activating protein 1a | 14 | Unknown | 1 | | No |
| TAOK2 | TAO kinase 2 | 5 | No | 2 | | Yes |
| TBR1 | T-box, brain 1 | 30 | No | 1 | | Yes |
| SYN1 | Synapsin I | 1 | No | 1 | | No |
| TBX1 | T-box1 | 1 | Unknown | – | S | No |
| TCF20 | transcription factor 20 | 5 | Yes | 1 | | Yes |
| TCF4 | transcription factor 4 | 4 | No | 1 | | Yes |
| THRA | thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian) | 1 | Unknown | 3 | | No |
| TOP3B | Topoisomerase (DNA) 3 Beta | 3 | No | 3 | | No |
| TRIM32 | Tripartite motif containing 32 | 4 | No | 3 | | Yes |
| TRIO | Trio Rho guanine nucleotide exchange factor | 2 | No | 1 | | No |
| TRPC6 | Transient receptor potential cation channel, subfamily C, member 6 | 4 | No | 2 | | Yes |
| TSC1 | tuberous sclerosis 1 | 32 | Unknown | 1 | | Yes |
| TSC2 | tuberous sclerosis 2 | 16 | Unknown | 1 | | Yes |
| UBE3A | ubiquitin protein ligase E3A | 30 | Unknown | 1 | | Yes |
| TSHZ3 | Teashirt zinc finger homeobox 3 | 2 | No | 1 | | No |
| KDM5A | lysine demethylase 5A | 0 | Yes | 2 | | No |
| UPF2 | UPF2regulator of nonsense mediated mRNA decay | 3 | No | 3 | | Yes |
| UPF3B | UPF3B, regulator of nonsense mediated mRNA decay | 3 | No | 1 | | Yes |
| USP7 | Ubiquitin specific peptidase 7 | 1 | No | 2 | S | No |
| WDFY3 | WD repeat and FYVE domain containing 3 | 4 | Unknown | 1 | | No |