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| Gene symbol | Gene name and description | Syndrome |
|
| ARFGEF2 | ADP-ribosylation factor GEF2 | Periventricular heterotopia |
| ARHGEF9 | Cdc42 GEF 9 | Hyperekplexia with epilepsy |
| A2BP1 | Ataxin 2-binding protein 1 (RNA binding protein fox-1 homolog 1) | Mental retardation and epilepsy |
| ASPA | Aspartoacylase | Canavan syndrome |
| ATP1A2 | ATPase, Na/K transporting, alpha 2 polypeptide | Familial hemiplegic migraine |
| ATP2A2 | ATPase, Ca transporting, cardiac muscle, slow twitch 2 | Darier-White syndrome |
| ATP6V0A2 | ATPase, H+ transporting, lysosomal V0 subunit a2 | Cutis laxa with epilepsy and mental retardation |
| CACNA1A | Calcium channel, voltage-dependent, P/Q type, alpha 1A subunit | Familial hemiplegic migraine |
| CCDC88C | Coiled-coil domain containing 88C | Hydrocephalus with medial diverticulum |
| CLCNKA | Chloride channel Ka | Bartter syndrome |
| CLCNKB | Chloride channel Kb | Bartter syndrome |
| COH1 | Cohen syndrome protein 1—vacuolar protein sorting 13 homolog B | Cohen syndrome |
| DLGAP2 | Discs, large (Drosophila) homolog-associated protein 2 | Progressive epilepsy with mental retardation |
| GFAP | Glial fibrillary acidic protein | Alexander disease |
| GLI3 | GLI family zinc finger 3 | Pallister-hall syndrome |
| GLRA1 | Glycine receptor, alpha 1 | Hyperekplexia |
| GLRB | Glycine receptor, beta | Hyperekplexia |
| GPHN | Gephyrin | Hyperekplexia |
| KCNA1 | Potassium voltage-gated channel, shaker-related | Episodic ataxia |
| KCNJ1 | Potassium inwardly rectifying channel, subfamily J, member 1 | Bartter syndrome |
| KCNJ10 | Potassium inwardly rectifying channel, subfamily J, member 10 | Seizures, deafness, ataxia, mental retardation |
| KIAA1279 | Kinesin family member 1 binding protein | Goldberg-Shprintzen |
| LAMA2 | Laminin, alpha 2 | Merosin deficiency |
| LBR | Lamin B receptor | Pelger-Huet syndrome |
| LGI1 | Leucine-rich, glioma inactivated 1 | Autosomal dominant lateral temporal lobe epilepsy |
| MLC1 | Megalencephalic leukoencephalopathy with subcortical cysts 1 | Megalencephalic leukoencephalopathy with cysts |
| MLL2 | Myeloid/lymphoid or mixed-lineage leukemia 2 | Kabuki syndrome |
| NF1 | Neurofibromin 1 | Neurofibromatosis |
| NIPBL | Nipped-B homolog (Drosophila) | Cornelia de Lange syndrome |
| PANK2 | Pantothenate kinase 2 | Neurodegeneration with brain iron accumulation |
| PI12 | Serpin peptidase inhibitor, clade I (neuroserpin), member 1 | Encephalopathy with neuroserpin inclusion bodies |
| PIGV | Phosphatidylinositol glycan anchor biosynthesis, class V | Hyperphosphatasia with mental retardation |
| PLA2G6 | Phospholipase A2, group VI (cytosolic, calcium independent) | Infantile neuroaxonal dystrophy |
| RAI1 | Retinoic acid induced 1 | Smith Magenis syndrome |
| SCN8A | Sodium channel, voltage gated, type VIII, alpha subunit | Cerebellar atrophy, ataxia, and mental retardation |
| SETBP1 | SET binding protein 1 | Schinzel-Giedion midface retraction syndrome |
| SHH | Sonic hedgehog | Holoprosencephaly |
| SLC4A10 | Solute carrier family 4, sodium bicarbonate transporter, member 10 | Epilepsy with mental retardation |
| SLC6A5 | Solute carrier family 6 (neurotransmitter transporter, glycine), member 5 | Hyperekplexia |
| SMC1A | Structural maintenance of chromosomes 1A | Cornelia de lange syndrome |
| SMC3 | Structural maintenance of chromosomes 3 | Cornelia de lange syndrome |
| SYNGAP1 | Synaptic Ras GTPase activating protein 1 | Epilepsy and mental retardation |
| TBX1 | T-box 1 | Di George syndrome |
| TSC1 | Tuberous sclerosis 1 | Tuberous sclerosis |
| TSC2 | Tuberous sclerosis 2 | Tuberous sclerosis |
| VPS13A | Vacuolar protein sorting 13 homolog A | Neuroacanthocytosis |
| ZEB2 | Zinc finger E-box binding homeobox 2 | Mowat-Wilson syndrome |
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