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Autism - Gene Symbols

List of autism candidate genes identified so far as extarcted from SFARI gene database. Only genes with ≥ 5 independent studies are included.

Gene Symbol Gene Name Chromosome Number Chromosomal Location Molecular Function Support for Autism No. of gene association studies
CA6 carbonic anhydrase VI 1 1p36.2 The protein encoded by this gene is one of several isozymes of carbonic anhydrase. Rare Single Gene variant 6
DAB1 Disabled homolog 1 (Drosophila) 1 1p32-p31 DAB1 serves as an intracellular adaptor for reelin signaling pathway Functional 6
DISC1 Disrupted in schizophrenia 1 1 1q42.1 This gene encodes a protein with multiple coiled coil motifs and is involved in neurite outgrowth and cortical development through its interaction with other proteins. Syndromic 24
DLGAP3 Discs, large (Drosophila) homolog-associated protein 3 1 1p35.3-p34.1 May play a role in the molecular organization of synapses and neuronal cell signaling. Could be an adapter protein linking ion channel to the subsynaptic cytoskeleton. May induce enrichment of PSD-95/SAP90 at the plasma membrane. Functional 7
DPYD Dihydropyrimidine dehydrogenase 1 1p22 The encoded protein is a pyrimidine catabolic enzyme and participates in the initial and rate-limiting factor in the pathway of uracil and thymidine catabolism. Rare Single Gene variant 6
HSD11B1 Hydroxysteroid (11-beta) dehydrogenase 1 1 1q32-q41 The encoded protein is a microsomal enzyme that catalyzes the conversion of the stress hormone cortisol to the inactive metabolite cortisone. It can also catalyze the reverse reaction, the conversion of cortisone to cortisol. Syndromic 8
KCNJ10 Potassium inwardly-rectifying channel, subfamily J, member 10 1 1q23.2 Responsible for potassium buffering action of glial cells in the brain. Characterized by a greater tendency to allow potassium to flow into the cell rather than out. Voltage dependence on extracellular potassium. Blocked by extracellular barium and cesium. Defects in this gene are a cause of SESAME (seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance) syndrome (OMIM:612780], also known as EAST syndrome. Genetic Association 7
MARK1 MAP/microtubule affinity-regulating kinase 1 1 1q41 Serine/threonine-protein kinase involved in cell polarity and microtubule dynamics regulation. Involved in the regulation of neuronal migration through its dual activities in regulating cellular polarity and microtubule dynamics, possibly by phosphorylating and regulating DCX. Also acts as a positive regulator of the Wnt signaling pathway. Genetic association/Functional 7
MTHFR methylenetetrahydrofolate reductase (NAD(P)H) 1 1p36.3 The encoded protein catalyzes the conversion of 5,10 methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co-substrate for homocysteine remethylation to methionine. Genetic Association 11
NOS1AP nitric oxide synthase 1 (neuronal) adaptor protein 1 1q23.3 An adaptor protein serving as regulator of neuronal nitric oxide synthase Rare single Gene variant 6
NTNG1 netrin G1 1 1p13.3 Netrin G1 (NTNG1) belongs to a conserved family of proteins that act as axon gui dance cues during vertebrate nervous system development Syndromic 8
NTRK1 neurotrophic tyrosine kinase, receptor, type 1 1 1q21-q22 A membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Rare Single Gene variant 7
PTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxyge nase) 1 1q25.2-q25.3 The encoded protein is a key enzyme for prostaglandin synthesis. It has prostagl andin-endoperoxide synthase activity. Genetic Association 5
PTPRC protein tyrosine phosphatase, receptor type, C 1 1q31-q32 The encoded protein is a member of the protein tyrosine phosphatase (PTP) family that is an essential regulator of T- and B-cell antigen receptor signaling Genetic Association 8
RFWD2 ring finger and WD repeat domain 2 1 1q25.1-q25.2 Ubiquitin-protein ligase Genetic Association 8
RGS7 regulator of G-protein signaling 7 1 1q23.1 Inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits thereby driving them into their inactive GDP-bound form. Activity on G(o)-alpha is specifically enhanced by the RGS6/GNG5 dimer. May play a role in synaptic vesicle exocytosis as well as an important role in the rapid regulation of neuronal excitability and the cellular responses to short-lived stimulations. Rare Single Gene variant 6
AGAP1 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 2 2q37 This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Rare Single Gene variant, Genetic Association 5
ARHGAP15 Rho GTPase activating protein 15 2 2q22.2-q22.3 GTPase activator for the Rho-type GTPases by converting them to inactive GDP-bound state. Rare Single Gene variant 5
CNTNAP5 contactin associated protein-like 5 2 2q14.3 A multidomain transmembrane protein involved in cell adhesion and intercellular communication Genetic Association 7
DLX1 distal-less homeobox 1 2 2q32 The encoded protein is a homeobox transcription factor. Genetic Association 8
DLX2 distal-less homeobox 2 2 2q32 The encoded protein is a homeobox transcription factor. Genetic Association 11
DPP10 Dipeptidyl-peptidase 10 2 2q14.1 Binds specific voltage-gated potassium channels and alters their expression and biophysical properties Rare Single Gene variant 9
ERBB4 v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) 2 2q33.3-q34 A transmembrane receptor tyrosine kinase that regulates cell proliferation and differentiation Rare Single Gene variant 11
HDAC4 histone deacetylase 4 2 2q37.3 Regulation of transcription Genetic Association 10
IL1R2 interleukin 1 receptor, type II 2 2q12 Receptor for interleukin-1 alpha, beta, and interleukin-1 receptor antagonist protein. Rare Single Gene variant 5
ITGA4 integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) 2 2q31.3 Cell adhesion molecules Genetic Association 5
MAP2 microtubule-associated protein 2 2 2q34-q35 The encoded protein is a member of microtubule-associated protein family. Rare Single Gene variant 5
MBD5 Methyl-CpG binding domain protein 5 2 2q23.1 This gene encodes a member of the methyl-CpG-binding domain (MBD) family. Mutations in this gene cause mental retardation autosomal dominant type 1. Haploinsufficiency of this gene is associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures. Rare Single Gene Mutation 19
MYT1L Myelin transcription factor 1-like 2 2p25.3 May function as a panneural transcription factor associated with neuronal differentiation and may play a role in the development of neurons and oligodendroglia in the CNS. Multigenic CNV 6
NRP2 neuropilin 2 2 2q33.3 High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF Genetic Association 6
NRXN1 neurexin 1 2 2p16.3 Neurexins function in the vertebrate nervous system as cell adhesion molecules and receptors. Two neurexin genes are among the largest known in human (NRXN1 and NRXN3). By using alternate promoters, splice sites and exons, predictions of hundreds or even thousands of distinct mRNAs have been made. Rare Single Gene variant 51
RAPGEF4 Rap guanine nucleotide exchange factor (GEF) 4 2 2q31-q32 The encoded protein acts as a cAMP sensor and mediates cAMP-dependent, protein k inase A-independent exocytosis. Rare Single Gene variant, Genetic Association 11
SATB2 SATB homeobox 2 2 2q33 This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and mental retardation. Syndromic 5
SCN1A sodium channel, voltage-gated, type I, alpha subunit 2 2q24.3 This gene encodes the large alpha subunit of the vertebrate voltage-gated sodium channel essential for the generation and propagation of action potentials, mainly in nerve and muscle. Rare Single Gene variant 19
SCN2A sodium channel, voltage-gated, type II, alpha subunit 2 2q23-q24 voltage-gated ion channel essential for the generation and propagation of action potentials, chiefly in nerve and muscle. Rare Single Gene variant 17
SLC25A12 solute carrier family 25 (mitochondrial carrier, Aralar), member 12 2 2q24 The encoded protein has solute:cation symporter activity. Genetic Association 14
SLC4A10 solute carrier family 4, sodium bicarbonate transporter-like, member 10 2 2q23-q24 inorganic anion exchanger activity Genetic Association 5
SNTG2 Syntrophin, gamma 2 2 2p25.3 Adapter protein that binds to and probably organizes the subcellular localization of a variety of proteins. May link various receptors to the actin cytoskeleton and the dystrophin glycoprotein complex. SNTG2 has been shown to interact with neuroligins 3 and 4X, and these interactions were influenced by autism-related mutations, implying that the impaired interaction between NLs and SNTG2 contributes to the etiology of autism (Yamakawa et al., 2007). Rare single gene variant 5
STK39 serine threonine kinase 39 (STE20/SPS1 homolog, yeast) 2 2q24.3 This gene encodes a serine/threonine kinase implicated in the cellular stress re sponse pathway Genetic Association 5
TBR1 T-box, brain, 1 2 2q24 Probable transcriptional regulator involved in developmental processes that is required for normal brain development. Rare Single Gene variant 5
TTN titin 2 2q31 Key component in the assembly and functioning of vertebrate striated muscles. Contributes to fine balance of forces between two halves of the sarcomere. Rare Single Gene variant 9
CACNA1D calcium channel, voltage-dependent, L type, alpha 1D 3 3p14.3 The encoded protein has low voltage-gated calcium channel activity. Functional 6
CNTN4 contactin 4 3 3p26-p25 This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Syndromic 14
CTNNB1 Catenin (cadherin-associated protein), beta 1, 88kDa 3 3p21 Key downstream component of the canonical Wnt signaling pathway. The protein encoded by this gene is part of a complex of proteins that constitute adherens junctions (AJs). AJs are necessary for the creation and maintenance of epithelial cell layers by regulating cell growth and adhesion between cells. The encoded protein also anchors the actin cytoskeleton and may be responsible for transmitting the contact inhibition signal that causes cells to stop dividing once the epithelial sheet is complete. Finally, this protein binds to the product of the APC gene, which is mutated in adenomatous polyposis of the colon. Rare Single Gene variant 5
DRD3 dopamine receptor D3 3 3q13.3 This gene encodes the D3 subtype of dopamine receptor Genetic Association 7
EPHA6 EPH receptor A6 3 3q11.2 The encoded protein is a member of Eph family of receptor tyrosine kinases that are involved in establishing neuronal projections. Rare Single Gene variant 6
FEZF2 FEZ family zinc finger 2 3 3p14.2 Regulation of transcription Genetic Association 7
FHIT fragile histidine triad gene 3 3p14.2 Encodes a diadenosine 5',5'''-P1,P3-triphosphate hydrolase involved in purine metabolism. Genetic Association 8
FOXP1 forkhead box P1 3 3p14.1 Transcriptional repressor. Plays an important role in the specification and differentiation of lung epithelium. Rare Single Gene variant 11
GPX1 glutathione peroxidase 1 3 3p21.3 It functions in the detoxification of hydrogen peroxide Genetic Association 5
HTR3C 5-hydroxytryptamine (serotonin) receptor 3, family member C 3 3q27.1 Ligand-gated ion channel receptor Genetic Association 5
MBD4 methyl-CpG binding domain protein 4 3 3q21-q22 The encoded protein forms a complex with MLH1, binds to methyl-CpG-containing DNA, has homology to bacterial DNA repair glycosylases/lyases, and displays endonuclease activity. Rare Single Gene variant, Genetic Association 5
NLGN1 neuroligin 1 3 3q26.31 This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Genetic Association 13
OXTR oxytocin receptor 3 3p25 The protein encoded by this gene belongs to the G-protein coupled receptor family and acts as a receptor for oxytocin. Its activity is mediated by G proteins which activate a phosphatidylinositol-calcium second messenger system. Genetic Association 26
PLCD1 phospholipase C, delta 1 3 3p22-p21.3 Mediates production of second messenger molecules DAG and IP3. Essential for trophoblast and placental development Rare Single Gene variant 8
ROBO1 roundabout, axon guidance receptor, homolog 1 (Drosophila) 3 3p12 The encoded protein is an axon guidance receptor and a cell adhesion receptor. Functional 7
SETD5 SET domain containing 5 3 3p25.3 This gene is predicted to encode a methyltransferase and resides within the critical interval for the 3p25 microdeletion syndrome. Rare Single Gene variant 6
SLC9A9 solute carrier family 9 (sodium/hydrogen exchanger), member 9 3 3q24 enzyme involved in pH regulation Rare Single Gene variant 8
TBC1D5 TBC1 domain family, member 5 3 3p24.3 The encoded protein may act as a GTPase-activating protein for Rab family protein(s). Rare Single Gene variant 6
XPC xeroderma pigmentosum, complementation group C 3 3p25 This gene encodes a component of the nucleotide excision repair (NER) pathway. It acts as a damage-sensing and DNA-binding factor component of the XPC complex. Rare Single Gene variant 8
CD38 CD38 molecule 4 4p15 CD38 is a novel multifunctional ectoenzyme widely expressed in cells and tissues especially in leukocytes. CD38 also functions in cell adhesion, signal transduction and calcium signaling. CD38 synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. CD38 also has cADPr hydrolase activity and moonlights as a receptor in cells of the immune system. Genetic Association 5
EIF4E eukaryotic translation initiation factor 4E 4 4q21-q25 Translation initiation factor involved in directing ribosomes to the cap structure of mRNAs Rare single gene variant 11
GABRA4 gamma-aminobutyric acid (GABA) A receptor, alpha 4 4 4p12 The encoded protein is a subunit of GABA-A receptor. Neurotransmission is predominantly mediated by a gated chloride channel activity intrinsic to the receptor. Genetic Association 6
GRID2 glutamate receptor, ionotropic, delta 2 4 4q22 Human glutamate receptor delta-2 (GRID2) is a relatively new member of the family of ionotropic glutamate receptors which are the predominant excitatory neurotransmitter receptors in the mammalian brain. GRID2 is a predicted 1,007 amino acid protein that shares 97% identity with the mouse homolog which is expressed selectively in cerebellar Purkinje cells. GRID2 is strongly suggested to have a role in neuronal apoptotic death. Rare Single Gene variant 6
PCDH10 protocadherin 10 4 4q28.3 encodes a cadherin-related neuronal receptor thought to play a role in the estab lishment and function of specific cell-cell connections in the brain. Rare Single Gene variant 5
ADRB2 adrenergic, beta-2-, receptor, surface 5 5q31-q32 This gene encodes beta-2-adrenergic receptor which is a member of the G protein- coupled receptor superfamily. Genetic Association 10
AFF4 AF4/FMR2 family, member 4 5 5q31 May play a role in transcriptional regulation Rare Single Gene variant 6
APC adenomatosis polyposis coli 5 5q21-q22 The encoded protein is a tumor suppressor. Genetic Association 7
CDH10 cadherin 10, type 2 (T2-cadherin) 5 5p14-p13 cell adhesion Genetic Association 7
CDH9 cadherin 9, type 2 (T1-cadherin) 5 5p14 cell adhesion Genetic Association 6
MEF2C myocyte enhancer factor 2C 5 5q14 The encoded protein is a transcription factor involved in diverse developmental processes including hematopoiesis, cardiogenesis and neurogenesis. Rare Single Gene variant 13
MSNP1AS Moesin??pseudogene 1, antisense 5 5p14.1 A noncoding RNA encoded by the opposite (antisense) strand of??moesin??pseudogene 1 (MSNP1). Chromosome 5p14.1 MSNP1AS is 94% identical and antisense to the X chromosome transcript of MSN, which encodes a protein (moesin) that regulates neuronal architecture. Genetic Association 7
PITX1 paired-like homeodomain 1 5 5q31 Transcription factor Genetic Association 5
SEMA5A sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A 5 5p15.2 The encoded protein is a member of the semaphorin family of membrane proteins that play roles in axonal guidance during neural development. Functional 10
AHI1 Abelson helper integration site 1 6 6q23.3 This gene is apparently required for both cerebellar and cortical development in humans. Mutations in this gene cause specific forms of Joubert syndrome-related disorders. It encodes a modular protein that contains one SH3 motif and seven WD40 repeats Rare Single Gene variant 15
ALDH5A1 aldehyde dehydrogenase 5 family, member A1 (succinate-semialdehyde dehydrogenase) 6 6p22.2-p22.3 The encoded protein is a mitochondrial NAD(+)-dependent succinic semialdehyde dehydrogenase. Syndromic 5
ARID1B AT rich interactive domain 1B (SWI1-like) 6 6q25.1 A component of the SWI/SNF chromatin remodeling complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. Mutations in the ARID1B gene are responsible for mental retardation, autosomal dominant 12 (MRD12; OMIM #614562) and some forms of Coffin-Siris syndrome (CSS; OMIM #135900). Rare single gene variant 10
C4B complement component 4B 6 6p21.3 The encoded protein is part of the classical pathway of the complement system. Genetic Association 5
CNR1 cannabinoid receptor 1 (brain) 6 6q14-q15 The encoded protein has cannabinoid receptor activity. Genetic Association 6
ESR1 estrogen receptor 1 6 6q25.1 Estrogen and its receptors are essential for sexual development and reproductive function, but also play a role in other tissues. Syndromic 8
F13A1 coagulation factor XIII, A1 polypeptide 6 6p25.3-p24.3 The encoded protein has protein-glutamine gamma-glutamyltransferase activity. I t participates in blood coagulation cascade. Functional 5
FABP7 fatty acid binding protein 7, brain 6 6q22-q23 The encoded protein binds long-chain fatty acids and other hydrophobic ligands Genetic Association 6
GLO1 glyoxalase I 6 6p21.3-p21.1 The encoded protein mediates catalysis and formation of S-lactoyl-glutathione from methylglyoxal and reduced glutathione. Genetic Association 8
GRIK2 glutamate receptor, ionotropic, kainate 2 6 6q16.3-q21 This gene product belongs to the kainate family of glutamate receptors, which are composed of four subunits and function as ligand-activated ion channels. Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. Genetic Association 10
HLA-A major histocompatibility complex, class I, A 6 6p21.3 The encoded protein belongs to the MHC class I receptor and plays a central role in the immune response. Genetic Association 6
HLA-DRB1 major histocompatibility complex, class II, DR beta 1 6 6p21.3 The encoded protein belongs to the MHC class II receptor and plays a central role in the immune response. Genetic Association 5
HS3ST5 heparan sulfate (glucosamine) 3-O-sulfotransferase 5 6 6q21 sulfotransferases Genetic Association 5
HTR1B 5-hydroxytryptamine (serotonin) receptor 1B 6 6q13 The encoded protein belongs to G-protein coupled receptor 1 family. Genetic Association 6
JARID2 Jumonji, AT rich interactive domain 2 6 6p24-p23 This gene encodes a Jumonji- and AT-rich interaction domain (ARID)-domain-containing protein that functions as a transcriptional repressor. This protein interacts with the Polycomb repressive complex 2 (PRC2) which plays an essential role in regulating gene expression during embryonic development. During embryogenesis, JARID2 is predominantly expressed in neurons and particularly in dorsal root ganglion cells. Association studies have identified JARID2 as a possible susceptibility gene in schizophrenia (Pedrosa et al., 2007; Liu et al., 2009). Genetic Association 5
PARK2 Parkinson disease (autosomal recessive, juvenile) 2, parkin 6 6q25.2-q27 Ubiquitin-protein ligase Genetic Association 12
SYNE1 spectrin repeat containing, nuclear envelope 1 6 6q25 Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. Rare Single Gene variant 10
SYNGAP1 synaptic Ras GTPase activating protein 1 6 6p21.3 A major component of the postsynaptic density (PSD)associated with NMDA receptors Rare Single Gene variant 21
VIP Vasoactive intestinal peptide 6 6q25 The protein encoded by this gene belongs to the glucagon family. It stimulates myocardial contractility, causes vasodilation, increases glycogenolysis, lowers arterial blood pressure and relaxes the smooth muscle of trachea, stomach and gall bladder. Functional 5
AUTS2 autism susceptibility candidate 2 7 7q11.22 unknown Rare Single Gene variant 22
BRAF v-raf murine sarcoma viral oncogene homolog B 7 7q34 This gene encodes a protein belonging to the raf/mil family of serine/threonine protein kinases. This protein plays a role in regulating the MAP kinase/ERKs signaling pathway, which affects cell division, differentiation, and secretion. Mutations in this gene are associated with cardiofaciocutaneous syndrome (CFC) [MIM:115150], a disease characterized by heart defects, mental retardation and a distinctive facial appearance. Mutations in this gene have also been associated with various cancers, including non-Hodgkin lymphoma, colorectal cancer, malignant melanoma, thyroid carcinoma, non-small cell lung carcinoma, and adenocarcinoma of lung. Syndromic 5
CADPS2 Ca2+-dependent activator protein for secretion 2 7 7q31.3 The encoded protein has calcium-binding activity and mediates vesicle exocytosis. Rare Single Gene variant 9
CNTNAP2 contactin associated protein-like 2 7 7q35-q36 This gene encodes a member of the neurexin family which functions in the vertebrate nervous system as cell adhesion molecules and receptors. This protein is localized at the juxtaparanodes of myelinated axons and associated with potassium channels. Syndromic 39
DLX6 distal-less homeobox 6 7 7q22 Transcription factor Rare Single Gene variant 8
DOCK4 Dedicator of cytokinesis 4 7 7q31.1 Involved in regulation of adherens junction between cells. Plays a role in cell migration. Functions as a guanine nucleotide exchange factor (GEF), which activates Rap1 small GTPase by exchanging bound GDP for free GTP. Genetic association/multigenic CNV 5
DPP6 dipeptidyl-peptidase 6 7 7q36.2 This protein modulates the kinetics of transient A-type currents. Genetic Association 19
EN2 engrailed homolog 2 7 7q36 The encoded protein is a transcription factor. Genetic Association 16
FOXP2 forkhead box P2 7 7q31 This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. The protein product contains a FOX DNA-binding domain and a large polyglutamine tract and is an evolutionarily conserved transcription factor, which may bind directly to approximately 300 to 400 gene promoters in the human genome to regulate the expression of a variety of genes. Rare single gene variant 26
GRM8 glutamate receptor, metabotropic 8 7 7q31.3-q32. The encoded protein has glutamate, GABA-B-like receptor activity. Genetic Association 6
GTF2I general transcription factor IIi 7 7q11.23 A multifunctional phosphoprotein with roles in transcription and signal transduction. Rare Single Gene variant 5
HOXA1 homeobox A1 7 7p15.3 The encoded protein is a transcription factor that plays a major role in brainstem and cranial morphogenesis. Genetic Association 15
IMMP2L IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae) 7 7q31 The encoded protein has serine-like peptidase activity. Syndromic 9
MET met proto-oncogene (hepatocyte growth factor receptor) 7 7q31 The encoded protein is the hepatocyte growth factor receptor with tyrosine-kinase activity. The primary single chain precursor protein is post-translationally cleaved to produce the alpha and beta subunits, which are disulfide linked to form the mature receptor. Genetic Association 29
NRCAM neuronal cell adhesion molecule 7 7q31.1-q31.2 The encoded protein is a cell-cell adhesion molecule that participates in neuro nal outgrowth and guidance processes. Genetic Association 5
PON1 paraoxonase 1 7 7q21.3 The encoded protein hydrolyzes a broad spectrum of organophosphate substrates and a number of aromatic carboxylic acid esters. Genetic Association 5
RELN Reelin 7 7q22 This gene encodes a large secreted extracellular matrix protein thought to control cell-cell interactions critical for cell positioning and neuronal migration during brain development. Genetic Association 27
SND1 staphylococcal nuclease and tudor domain containing 1 7 7q31.3 A component of the RNA-induced silencing complex (RISC) Genetic Association 8
WNT2 wingless-type MMTV integration site family member 2 7 7q31 The encoded protein is a constituent of the extracellular matrix and plays a rol e in signal transduction. Genetic Association 9
CHD7 chromodomain helicase DNA binding protein 7 8 8q12.2 This gene encodes a protein that contains several helicase family domains. Mutations in this gene have been found in some patients with the CHARGE syndrome. Syndromic 7
DLGAP2 discs, large (Drosophila) homolog-associated protein 2 8 8p23 The encoded protein is a membrane-associated guanylate kinase localized at the post-synaptic density in neuronal cells. Rare Single Gene variant 7
FABP5 fatty acid binding protein 5 (psoriasis-associated) 8 8q21.13 The encoded protein binds long-chain fatty acids and other hydrophobic ligands Rare Single Gene variant, Genetic Association 5
KCNQ3 Potassium voltage-gated channel, KQT-like subfamily, member 3 8 8q24 Probably important in the regulation of neuronal excitability. Associates with KCNQ2 or KCNQ5 to form a potassium channel with essentially identical properties to the channel underlying the native M-current, a slowly activating and deactivating potassium conductance which plays a critical role in determining the subthreshold electrical excitability of neurons as well as the responsiveness to synaptic inputs. Defects in KCNQ3 are the cause of benign familial neonatal seizures type 2 (BFNS2) [MIM:121201]. Genetic Association 5
MCPH1 microcephalin 1 8 8p23.1 This protein is implicated in chromosome condensation and DNA damage induced cellular responses. May play a role in neurogenesis and regulation of the size of the cerebral cortex. Rare Single Gene variant 11
PINX1 PIN2/TERF1 interacting, telomerase inhibitor 1 8 8p23 The encoded protein is inhibitor of telomerase activity Rare Single Gene variant 5
VPS13B vacuolar protein sorting 13 homolog B (yeast) 8 8q22.2 This gene encodes a potential transmembrane protein that may function in vesicle-mediated transport and sorting of proteins within the cell. This protein may play a role in the development and the function of the eye, hematological system, and central nervous system. Mutations in this gene have been associated with Cohen syndrome. Multiple splice variants encoding distinct isoforms have been identified for this gene. Syndromic 7
ASTN2 astrotactin 2 9 9q33.1 This gene encodes a protein that is expressed in the brain and may function in neuronal migration, based on functional studies of the related astrotactin 1 gene in human and mouse. A deletion at this locus has been associated with schizophrenia. Rare Single Gene variant 9
CACNA1B Calcium channel, voltage-dependent, N type, alpha 1B subunit 9 9q34 The protein encoded by this gene is the pore-forming subunit of an N-type voltage-dependent calcium channel, which controls neurotransmitter release from neurons. The encoded protein forms a complex with alpha-2, beta, and delta subunits to form the high-voltage activated channel. Variants in CACNA1B have been previously associated with schizophrenia and bipolar disorder (Moskvina et al., 2009; Glessner et al., 2010). Genetic Association 5
KCNT1 Potassium channel, subfamily T, member 1 9 9q34.3 Outwardly rectifying potassium channel subunit that may co-assemble with other Slo-type channel subunits. Activated by high intracellular sodium or chloride levels. Activated upon stimulation of G-protein coupled receptors, such as CHRM1 and GRIA1. May be regulated by calcium in the absence of sodium ions (in vitro). Phosphorylated by protein kinase C. Phosphorylation of the C-terminal domain increases channel activity. Rare single gene variant 5
LAMC3 laminin, gamma 3 9 9q31-q34 Mediates the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Rare Single Gene variant 5
SLC1A1 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 9 9p24 This gene encodes a member of the high-affinity glutamate transporters that play an essential role in transporting glutamate across plasma membranes. This transporter also transports aspartate. Genetic Association 11
STXBP1 Syntaxin binding protein 1 9 9q34.1 This gene encodes a syntaxin-binding protein that appears to play a role in release of neurotransmitters via regulation of syntaxin, a transmembrane attachment protein receptor. Defects in STXBP1 are the cause of epileptic encephalopathy early infantile type 4 (EIEE4) [MIM:612164]. Affected individuals have neonatal or infantile onset of seizures, suppression-burst pattern on EEG, profound mental retardation, and MRI evidence of hypomyelination. Syndromic 11
TSC1 tuberous sclerosis 1 9 9q34 This gene encodes a growth inhibitory protein thought to play a role in the stabilization of tuberin and has been implicated as a tumor supressor. Rare Single Gene variant 15
ANK3 Ankyrin 3, node of Ranvier (ankyrin G) 10 10q21 Membrane-cytoskeleton linker that may participate in the maintenance/targeting of ion channels and cell adhesion molecules at the nodes of Ranvier and axonal initial segments. Genetic variants in ANK3 have been shown to strongly associate with schizophrenia and bipolar disorder. Genetic Association 11
CTNNA3 catenin (cadherin-associated protein), alpha 3 10 10q22.2 cell adhesion Genetic Association 10
HTR7 5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled) 10 10q21-q24 The encoded protein is a serotonin receptor. Genetic Association 5
KCNMA1 potassium large conductance calcium-activated channel, subfamily M, alpha member 1 10 10q22.3 The encoded protein is the pore forming alpha subunit of large conductance, voltage and calcium-sensitive potassium channels. These channels are fundamental to the control of smooth muscle tone and neuronal excitability. Rare single gene variant 14
PTEN phosphatase and tensin homolog (mutated in multiple advanced cancers 1) 10 10q23.3 The protein encoded this gene is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It contains a tensin like domain as well as a catalytic domain similar to that of the dual specificity protein tyrosine phosphatases. Syndromic 21
CADM1 cell adhesion molecule 1 11 11q23.2 The gene encodes a brain-specific, immunoglobulin domain-containing protein. It binds to intracellular PDZ-domain proteins and functions as a homophilic cell adhesion molecule at the synapse. Rare Single Gene variant 7
CNTN5 Contactin 5 11 11q21-q22.2 Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity in the cerebral cortical neurons but not in hippocampal neurons. Probably involved in neuronal activity in the auditory system Rare single gene variant 5
DHCR7 7-dehydrocholesterol reductase 11 11q13.2-q13.5 This gene encodes an enzyme that removes the C(7-8) double bond in the B ring of sterols and catalyzes the conversion of 7-dehydrocholesterol to cholesterol. Syndromic 7
HEPACAM hepatic and glial cell adhesion molecule 11 11q24.2 Involved in regulating cell motility and cell-matrix interactions. May inhibit cell growth through suppression of cell proliferation Rare Single Gene variant 5
HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog 11 11p15.5 The encoded protein binds GTP and has GTPase activity. Rare Single Gene variant 9
HTR3A 5-hydroxytryptamine (serotonin) receptor 3A 11 11q23.1 ligand-gated ion channel receptor Functional 7
SHANK2 SH3 and multiple ankyrin repeat domains 2 11 11q13.3-q13.4 Shank proteins contain multiple domains for protein-protein interactions and function as molecular scaffolds in the postsynaptic density (PSD). Rare Single Gene variant 15
TH tyrosine hydroxylase 11 11p15.5 The encoded protein has tyrosine 3-monooxygenase activity. Genetic Association 6
AVPR1A arginine vasopressin receptor 1A 12 12q14-q15 The encoded protein is a receptor for arginine vasopressin. It belongs to the G -protein coupled receptor family. Rare Single Gene variant, Genetic Association 12
CACNA1C calcium channel, voltage-dependent, L type, alpha 1C subunit 12 12p13.3 This gene encodes an alpha-1 subunit of a voltage-dependent calcium channel. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. Syndromic 28
GRIN2B glutamate receptor, inotropic, N-methyl D-apartate 2B 12 12p12 NMDA receptor subtype of glutamate-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Genetic Association 18
GRIP1 glutamate receptor interacting protein 1 12 12q14.3 The encoded scaffold protein mediates trafficking and membrane organization of various transmembrane proteins. Rare Single Gene variant, Genetic Association 9
MYO1A myosin IA 12 12q13-q14 Involved in directing the movement of organelles along actin filaments (muscle cells) Rare Single Gene variant 6
SCN8A sodium channel, voltage gated, type VIII, alpha subunit 12 12q13 This gene encodes a member of the sodium channel alpha subunit gene family. The encoded protein forms the ion pore region of the voltage-gated sodium channel. This protein is essential for the rapid membrane depolarization that occurs during the formation of the action potential in excitable neurons. Mutations in this gene are associated with mental retardation, pancerebellar atrophy and ataxia. Alternate splicing results in multiple transcript variants. Rare single gene variant 5
TPH2 tryptophan hydroxylase 2 12 12q21.1 The encoded protein has tryptophan 5-monooxygenase activity. Genetic Association 11
DIAPH3 Diaphanous-related formin 3 13 13q21.2 Actin-nucleating protein involved in the process of neurite outgrowth. Rare Single Gene variant 9
GPC6 glypican 6 13 13q32 A member of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycan family with a putative function of cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases. Rare Single Gene variant 7
HTR2A 5-hydroxytryptamine (serotonin) receptor 2A 13 13q14-q21 The encoded protein is a serotonin receptor. Genetic Association 7
MYO16 myosin XVI 13 13q33.3 motor protein, actin binding Genetic Association 5
PCDH9 protocadherin 9 13 13q21.32 encodes a cadherin-related neuronal receptor that localizes to synaptic junction s Rare Single Gene variant 6
CHD8 chromodomain helicase DNA binding protein 8 14 14q11.2 This gene encodes a DNA helicase that functions as a transcription repressor by remodeling chromatin structure. It binds beta-catenin and negatively regulates Wnt signaling pathway, which plays a pivotal role in vertebrate early development and morphogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. Rare Single Gene variant 5
ESR2 estrogen receptor 2 (ER beta) 14 14q23.2 This gene encodes a member of the family of estrogen receptors Syndromic 7
ESRRB estrogen-related receptor beta 14 12 41.0 cM steroid hormone receptor, transcription factor Genetic Association 7
FOXG1 Forkhead box G1 14 14q13 Transcription factor which plays an important role in the establishment of the regional subdivision of the developing brain and in the development of the telencephalon. Syndromic 8
GPHN Gephyrin 14 14q23.3 This gene encodes a neuronal assembly protein that anchors inhibitory neurotransmitter receptors to the postsynaptic cytoskeleton via high affinity binding to a receptor subunit domain and tubulin dimers. Defects in GPHN are the cause of molybdenum cofactor deficiency type C (MOCOD type C) [MIM:252150], an autosomal recessive disease which leads to the pleiotropic loss of all molybdoenzyme activities and is characterized by severe neurological damage, neonatal seizures and early childhood death. Mutations in this gene may also be associated with the neurological condition hyperplexia. Rare single gene variant 5
MDGA2 MAM domain containing glycosylphosphatidylinositol anchor 2 14 14q21.3 The encoded protein is a member of the immunoglobulin domain cell adhesion molecule subfamily and and is proposed to be involved in regulating neuronal migration and axonal guidance Genetic Association 5
NRXN3 neurexin 3 14 14q31 Neurexins are a family of proteins that function in the vertebrate nervous system as cell adhesion molecules and receptors. NRXN3 is one of the largest known human genes. It utilizes two alternate promoters and includes numerous alternatively spliced exons to generate thousands of distinct mRNA transcripts and protein isoforms. The majority of transcripts are produced from the upstream promoter and encode alpha-neurexin isoforms; a much smaller number of transcripts are produced from the downstream promoter and encode beta-neurexin isoforms. Rare Single Gene variant 8
APBA2 amyloid beta (A4) precursor protein-binding, family A, member 2 15 15q11-q12 A neuronal adapter protein essential for synaptic transmission. Rare Single Gene variant 5
ARNT2 aryl-hydrocarbon receptor nuclear translocator 2 15 15q24 A member of the basic-helix-loop-helix-Per-Arnt-Sim (bHLH-PAS) superfamily of transcription factors Syndromic 9
CHD2 Chromodomain helicase DNA binding protein 2 15 15q26 This gene enocdes a member of the CHD family of proteins, which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Multigenic CNV 8
CHRNA7 cholinergic receptor, nicotinic, alpha 7 15 15q14 The nicotinic acetylcholine receptors (nAChRs) are members of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. The nAChRs are thought to be hetero-pentamers composed of homologous subunits. The protein encoded by this gene forms a homo-oligomeric channel, displays marked permeability to calcium ions and is a major component of brain nicotinic receptors that are blocked by, and highly sensitive to, alpha-bungarotoxin. Once this receptor binds acetylcholine, it undergoes an extensive change in conformation that affects all subunits and leads to opening of an ion-conducting channel across the plasma membrane. Rare single gene variant 9
CYFIP1 cytoplasmic FMR1 interacting protein 1 15 15q11 Component of the CYFIP1-EIF4E-FMR1 complex which binds to the mRNA cap and mediates translational repression. In the CYFIP1-EIF4E-FMR1 complex this subunit is an adapter between EIF4E and FMR1. Promotes the translation repression activity of FMR1 in brain probably by mediating its association with EIF4E and mRNA. Regulates formation of membrane ruffles and lamellipodia. Plays a role in axon outgrowth. Binds to F-actin but not to RNA. Part of the WAVE complex that regulates actin filament reorganization via its interaction with the Arp2/3 complex. Actin remodeling activity is regulated by RAC1. Regulator of epithelial morphogenesis. May act as an invasion suppressor in cancers. Multigenic CNV 6
GABRB3 gamma-aminobutyric acid (GABA) A receptor, beta 3 15 15q11.2-q12 The encoded protein is a subunit of GABA-A receptor. Neurotransmission is predominantly mediated by a gated chloride channel activity intrinsic to the receptor. Genetic Association 20
NTRK3 neurotrophic tyrosine kinase, receptor, type 3 15 15q25 A membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway Rare Single Gene variant, Genetic Association 12
RORA RAR-related orphan receptor A 15 15q22.2 A member of the nuclear hormone-receptor superfamily Functional 14
ST8SIA2 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 15 15q26 The protein encoded by this gene is a type II membrane protein that is thought to catalyze the transfer of sialic acid from CMP-sialic acid to N-linked oligosaccharides and glycoproteins. The encoded protein may be found in the Golgi apparatus and may be involved in the production of polysialic acid, a modulator of the adhesive properties of neural cell adhesion molecule (NCAM1). Variants in the ST8SIA2 gene have been found to associate with schizophrenia and bipolar disorder (Arai et al., 2006; Tao et al., 2007; McAuley et al., 2012). Genetic association 5
UBE3A ubiquitin protein ligase E3A 15 15q11.2 This gene encodes an E3 ubiquitin-protein ligase, part of the ubiquitin protein degradation system. This imprinted gene is maternally expressed in brain and biallelically expressed in other tissues. Genetic Association 13
ANKRD11 ankyrin repeat domain 11 16 16q24.3 Transcription factor that may recruit HDACs to the p160 coactivators/nuclear receptor complex to inhibit ligand-dependent transactivation. Defects in ANKRD11 are the cause of KBG syndrome (KBGS) [MIM:148050], a syndrome characterized by macrodontia of the upper central incisors, distinctive craniofacial findings, short stature, skeletal anomalies, and neurologic involvement that includes global developmental delay, seizures, and intellectual disability. Rare Single Gene variant 9
CACNA1H calcium channel, voltage-dependent, alpha 1H subunit 16 16p13.3 This gene encodes a T-type member of the alpha-1 subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. Rare Single Gene variant 14
CDH8 cadherin 8, type 2 16 16q22.1 An integral membrane proteins that mediates calcium-dependent cell-cell adhesion Rare Single Gene variant 6
CNTNAP4 Contactin associated protein-like 4 16 16q23.1 This gene product belongs to the neurexin family, members of which function in the vertebrate nervous system as cell adhesion molecules and receptors. Rare Single Gene variant 5
CREBBP CREB binding protein 16 16p13.3 This gene is ubiquitously expressed and is involved in the transcriptional coactivation of many different transcription factors. First isolated as a nuclear protein that binds to cAMP-response element binding protein (CREB), this gene is now known to play critical roles in embryonic development, growth control, and homeostasis by coupling chromatin remodeling to transcription factor recognition. Mutations in this gene cause Rubinstein-Taybi syndrome (RTS). Chromosomal translocations involving this gene have been associated with acute myeloid leukemia. Alternative splicing results in multiple transcript variants encoding different isoforms. Syndromic 5
CTCF CCCTC-binding factor (zinc finger protein) 16 16q21-q22.3 This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. Depending upon the context of the site, the protein can bind a histone acetyltransferase (HAT)-containing complex and function as a transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as a transcriptional repressor.?? Functional 5
GPR139 G protein-coupled receptor 139 16 16p12.3 G-protein coupled receptor; transducer Rare Single Gene variant 5
GRIN2A glutamate receptor, ionotropic, N-methyl D-aspartate 2A 16 16p13.2 The encoded protein is a subunit of N-methyl-D-aspartate (NMDA) selective glutamate receptors. Genetic Association 17
MKL2 MKL/myocardin-like 2 16 16p13.12 A strong transcriptional co-activator of promoters containing serum response elements (SRE) Genetic Association 8
RBFOX1 RNA binding protein, fox-1 homolog (C. elegans) 1 16 16p13.3 RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis. Genetic Association 23
SEZ6L2 SEZ6L2 seizure related 6 homolog (mouse)-like 2 16 16p11.2 transmembrane receptor, may contribute to specialized endoplasmic reticulum functions in neurons Rare Single Gene variant 5
TSC2 tuberous sclerosis 2 16 16p13.3 The product of this gene is believed to be a tumor suppressor and is able to stimulate specific GTPases. Genetic Association 15
BAIAP2 BAI1-associated protein 2 17 17q25 An adaptor protein of post-synaptic density that links membrane bound G-proteins to cytoplasmic effector proteins Genetic Association 10
CACNA1G calcium channel, voltage-dependent, T type, alpha 1G subunit 17 17q22 Voltage-activated calcium channels Genetic Association 11
HOXB1 homeobox B1 17 17q21.3 The encoded protein is a transcription factor. Genetic Association 8
ITGB3 integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61) 17 17q21.32 The encoded protein is the integrin beta chain beta 3 that participates in cell adhesions and cell-surface mediated signalling. Genetic Association 11
NF1 neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) 17 17q11.2 The encoded protein has Ras GTPase activity and appears to be a negative regulator of cell proliferation. Rare Single Gene variant, Genetic Association 16
NOS2A nitric oxide synthase 2A (inducible, hepatocytes) 17 17q11.2-q12 This gene encodes a nitric oxide synthase which is inducible by a combination o f lipopolysaccharide and certain cytokines. Genetic Association 6
PER1 period homolog 1 (Drosophila) 17 17p13.1-p12 This gene is a member of the Period family of genes and is expressed in a circad ian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in t he mammalian brain. Genetic Association 5
RAI1 retinoic acid induced 1 17 17p11.2 Mutations in RAI1 cause Smith-Magenis Syndrome. Rare Single Gene variant 8
SLC6A4 solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 17 17q11.1-q12 The encoded protein has serotonin transporter activity, serotonin:sodium symport er activity. Genetic Association 19
BCL2 B-cell CLL/lymphoma 2 18 18q21.3 An integral outer mitochondrial membrane protein that blocks the apoptotic cell death Functional 10
CELF4 CUGBP, Elav-like family member 4 18 18q12 RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. When expressed ubiquitously, CELF4 is strongly expressed in the cerebellum, hippocampus, amygdala, temporal and frontal cortex and frontal lobes. Functional 5
MBD1 methyl-CpG binding domain protein 1 18 18q21 The encoded protein binds specifically to methylated DNA and can repress transcription Rare Single Gene variant 5
TCF4 Transcription factor 4 18 18q21.1 This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor that binds to the immunoglobulin enchancer Mu-E5/KE5-motif and is involved in the initiation of neuronal differentiation. Defects in this gene are associated with Pitt-Hopkins syndrome (PTHS) [MIM:610954], a syndrome characterized by mental retardation, wide mouth and distinctive facial features, and intermittent hyperventilation followed by apnea. Syndromic 11
DMPK dystrophia myotonica-protein kinase 19 19q13.3 The protein encoded by this gene is a serine-threonine kinase that is closely related to other kinases that interact with members of the Rho family of small GTPases. Genetic Association 5
ADA adenosine deaminase 20 20q12-q13.11 The encoded protein catalyzes the hydrolysis of adenosine to inosine. Genetic Association 5
KCNQ2 Potassium voltage-gated channel, KQT-like subfamily, member 2 20 20q13.3 Probably important in the regulation of neuronal excitability. Associates with KCNQ3 to form a potassium channel with essentially identical properties to the channel underlying the native M-current, a slowly activating and deactivating potassium conductance which plays a critical role in determining the subthreshold electrical excitability of neurons as well as the responsiveness to synaptic inputs. Defects in this gene are involved in benign familial neonatal seizures 1 (BFNS1) [MIM:121200] and early infantile epileptic encephalopathy 7 (EIEE7) [MIM:613720]. Genetic association 6
MACROD2 MACRO domain containing 2 20 20p12.1 Removes ADP-ribose from glutamate residues in proteins bearing a single ADP-ribose moiety. Inactive towards proteins bearing poly-ADP-ribose. Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. Genetic Association 12
PLCB1 phospholipase C, beta 1 (phosphoinositide-specific) 20 20p12 The protein encoded by this gene catalyzes the formation of inositol 1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. This reaction uses calcium as a cofactor and plays an important role in the intracellular transduction of many extracellular signals. This gene is activated by two G-protein alpha subunits, alpha-q and alpha-11. Two transcript variants encoding different isoforms have been found for this gene. Rare Single Gene variant 6
TGM3 transglutaminase 3 20 20q11.2 Catalyzes the calcium-dependent formation of isopeptide cross-links between glutamine and lysine residues, as well as conjugation of polyamines to proteins. Rare Single Gene variant 5
DYRK1A Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A 21 21q22.13 This gene encodes a member of the Dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) family. It may play a significant role in a signaling pathway regulating cell proliferation and may be involved in brain development. It is localized in the Down syndrome critical region of chromosome 21, and is considered to be a strong candidate gene for learning defects associated with Down syndrome. Defects in DYRK1A are the cause of mental retardation autosomal dominant type 7 (MRD7) [MIM:614104]. Syndromic 6
ADORA2A adenosine A2a receptor 22 22q11.23 The encoded protein is a receptor subtypes for adenosine Syndromic 7
SHANK3 SH3 and multiple ankyrin repeat domains 3 22 22q13.3 Shank proteins are multidomain scaffold proteins of the postsynaptic density that connect neurotransmitter receptors, ion channels, and other membrane proteins to the actin cytoskeleton and G-protein-coupled signaling pathways. Shank proteins also play a role in synapse formation and dendritic spine maturation. Rare Single Gene variant 33
AFF2 AF4/FMR2 family, member 2 X Xq28 This gene encodes a putative transcriptional activator that is a member of the AF4FMR2 gene family. This gene is associated with the folate-sensitive fragile X E locus on chromosome X. A repeat polymorphism in the fragile X E locus results in silencing of this gene causing Fragile X E syndrome. Fragile X E syndrome is a form of nonsyndromic X-linked mental retardation. Alternate splicing results in multiple transcript variants. Syndromic 10
AR androgen receptor X Xq11.2-q12 The protein functions as a steroid-hormone activated transcription factor. Genetic Association 6
ARX aristaless related homeobox X Xp22.1-22.3 This gene is a homeobox-containing gene expressed during development. The encoded protein is a transcription factor required for normal brain development. Syndromic 9
ATRX alpha thalassemia/mental retardation syndrome X-linked X Xq21.1 The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. Mutations in this gene are associated with an X-linked mental retardation (XLMR) syndrome most often accompanied by alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. Syndromic 7
CACNA1F calcium channel, voltage-dependent, alpha 1F X Xp11.23 The encoded protein has low voltage-gated calcium channel activity. Genetic Association 7
CDKL5 cyclin-dependent kinase-like 5 X Xp22 This gene is a member of Ser/Thr protein kinase family and encodes a phosphorylated protein with protein kinase activity. Syndromic 15
CXCR3 chemokine (C-X-C motif) receptor 3 X Xq13 A G protein-coupled receptor with selectivity for the chemokines IP10, Mig and I-TAC. Rare Single Gene variant 7
DCX doublecortex, lissencephaly, X-linked (doublecortin) X Xq22.3-q23 The encoded protein binds to microtubules and participates in neuronal migration. Rare Single Gene variant 6
DMD dystrophin (muscular dystrophy, Duchenne and Becker types) X Xp21.2 The dystrophin gene is the largest gene found in nature, measuring 2.4 Mb. It is highly complex, containing at least eight independent, tissue-specific promoters and two polyA-addition sites. Dystrophin is a large, rod-like cytoskeletal protein which is found at the inner surface of muscle fibers and is part of a complex which bridges the inner cytoskeleton (F-actin) and the extra-cellular matrix. Genetic Association 23
FMR1 fragile X mental retardation 1 X Xq27.3 The protein encoded by this gene binds RNA and is associated with polysomes. The encoded protein may be involved in mRNA trafficking from the nucleus to the cytoplasm. Functional 30
GLRA2 glycine receptor, alpha 2 X Xp22.1-p21.3 A ligand-gated channel mediating a chloride-dependent inhibitory neurotransmission Rare Single Gene variant 8
GRPR Gastrin-releasing peptide receptor X Xp22.2-p22.13 The encoded protein has G-protein coupled receptor activity. Genetic Association 7
IL1RAPL1 interleukin 1 receptor accessory protein-like 1 X Xp22.1-p21.3 This protein may regulate calcium-dependent exocytosis. Rare single gene variant 14
KDM5C Lysine (K)-specific demethylase 5C X Xp11.22-p11.21 Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Defects in KDM5C are the cause of mental retardation syndromic X-linked JARID1C-related (MRXSJ) [MIM:300534]. Syndromic 12
MAOA monoamine oxidase A X Xp11.3 The encoded protein degrades amine neurotransmitters. Genetic Association 11
MECP2 Methyl CpG binding protein 2 X Xq28 The encoded protein has methylation-dependent transcriptional repressor activity . It is also involved in regulation of RNA splicing. Syndromic 40
MED12 mediator complex subunit 12 X Xq13 Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Defects in MED12 are the cause of Opitz-Kaveggia syndrome (OKS) [MIM:305450] (also known as FG syndrome type 1 (FGS1) or FG syndrome (FGS); an X-linked disorder characterized by mental retardation, relative macrocephaly, hypotonia and constipation) and Lujan-Fryns syndrome (LUJFRYS) [MIM:309520] (also known as X-linked mental retardation with marfanoid habitus). Genetic Association 11
NLGN3 neuroligin 3 X Xq13.1 This gene encodes a member of a family of neuronal cell-adhesion proteins located at the postsynaptic side of the synapse. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Rare Single Gene variant 24
NLGN4X neuroligin 4, X-linked X Xp22.32-p22.31 Neuroligins are cell-adhesion molecules at the postsynaptic side of the synapse . Rare Single Gene variant 20
OPHN1 oligophrenin 1 X Xq12 A Rho-GTPase-activating protein involved in cell migration and outgrowth of axons and dendrites. Rare Single Gene variant 9
PCDH19 protocadherin 19 X Xq13.3 A calcium-dependent cell-adhesion protein that is primarily expressed in the brain Rare Single Gene variant 13
PSMD10 proteasome (prosome, macropain) 26S subunit, non-ATPase, 10 X Xq22.3 This gene encodes a non-ATPase proteasome subunit of the 19S regulator involved in protein degradation Rare Single Gene variant 6
PTCHD1 patched domain containing 1 X Xp22.11 PTCHD1 is suggested to be a transmembrane protein containing a patched-related domain with twelve transmembrane helices, highly related to the Hedgehog (Hh) receptors PATCHED1 (PTCH1) and PTCH2 as well as to Niemann-Pick Type C1 protein (NPC1). Rare Single Gene variant 5
RPL10 ribosomal protein L10 X Xq28 This gene encodes a ribosomal protein that is a component of the 60S subunit. Th e protein belongs to the L10E family of ribosomal proteins. Rare single gene variant 8
RPS6KA3 Ribosomal protein S6 kinase, 90kDa, polypeptide 3 X Xp22.2-p22.1 This gene encodes a member of the RSK (ribosomal S6 kinase) family of serine/threonine kinases. This kinase contains 2 non-identical kinase catalytic domains and phosphorylates various substrates, including members of the mitogen-activated kinase (MAPK) signalling pathway. The activity of this protein has been implicated in controlling cell growth and differentiation. Mutations in this gene are associated with Coffin-Lowry syndrome (CLS) [MIM:303600], a X-linked mental retardation associated with facial and digital dysmorphisms, progressive skeletal malformations, growth retardation, hearing deficit and paroxysmal movement disorders, as well as with mental retardation, X-linked 19 (MRX19) [MIM:300844], a non-syndromic form of mild-to-moderate mental retardation. Syndromic 6
SLC6A8 solute carrier family 6 (neurotransmitter transporter, creatine), member 8 X Xq28 The encoded protein has creatine:sodium symporter activity. Rare Single Gene variant 6
SLC9A6 solute carrier family 9 (sodium/hydrogen exchanger), member 6 X Xq26.3 This gene encodes a sodium-hydrogen exchanger that is a member of the solute carrier family 9. The encoded protein may be involved in regulating endosomal pH and volume. Syndromic 7
SYN1 Synapsin 1 X Xp11.23 Synapsin 1 is a peripheral membrane protein on synaptic vesicles that mediates vesicle binding to the cytoskeleton. Rare Single Gene variant 14
TSPAN7 tetraspanin 7 X Xp11.4 A cell surface glycoprotein with a role in the control of neurite outgrowth Rare Single Gene variant 6
UPF3B UPF3 regulator of nonsense transcripts homolog B (yeast) X Xq25-q26 Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is indepenedent of association with UPF2 and components of the EJC core. Syndromic 6
WNK3 WNK lysine deficient protein kinase 3 X Xp11.23-p11.21 The encoed protein belongs to the family of serine-threonine kinases that functions as modulator of diverse ion transport pathways. Rare Single Gene variant 6
ASMT acetylserotonin O-methyltransferase X,Y Xp22.3 or Yp11.3 melatonin biosynthesis Rare Single Gene variant, Genetic Association 9