Skip to main content

Table 2 NS-ID genes and their protein products and functions Information about subcellular localization and protein domains were found using HPRD (; SMART ( and the NCBI gene database (

From: The genetic basis of non-syndromic intellectual disability: a review

Gene Name NS or Sa Linked to Autism Protein Product Function Subcellular localization (HPRD) Protein Domains (SMART; HPRD; Bold-NCBI gene)
ACSL4 NS N Acyl-CoA synthetase long-chain family member 4 Fatty acid metabolism Microsome; Mitochondia 1 TM
AFF2/FMR2 NS Y Fragile X mental retardation 2 DNA binding protein: Potential activator of transcription Nucleus AF4 homology
AGTR2 NS/S N Angiotensin II receptor, type 2 G-protein-coupled receptor for Angiotensin II; mediator of programmed cell death Plasma membrane 7 TM
AP1S2 NS/S N Adaptor-related protein complex 1 sigma 2 subunit Complex involved in clathrin recruitment and sorting signal recognition. Synaptic vesicles/neurotransmitter release Golgi apparatus Clat Adaptor S
ARHGEF6 NS N Rac/Cdc42 guanine nucleotide exchange factor 6 GEF for Rac and Cdc42 Cytoplasm CH; SH3; RhoGEF; PH; CC
ARX NS/S Y Aristaless related homeobox Transcriptional regulation during development Nucleus HOX; CC
ATRX NS/S N Transcriptional regulator ATRX Chromatin remodeling Nucleus RING; CC; HELICc; DEXDc; SNF2_N
BRWD3 NS/S N Bromo domain and WD repeat domain-containing protein 3 JAK/STAT signaling in drosophila; Putative Chromatin Modifier Nucleus 8x WD40; 2x BROMO
CASK NS/S N Calcium/calmodulin-dependent serine protein kinase Kinase and scaffolding at synapses; MAGUK family protein Synaptic junction, plasma membrane; Nucleus; Cytoplasm S_TKc; 2x L27; PDZ; SH3; GuKc;
CC2D1A NS N Coiled-coil and C2 domain containing 1A Transcriptional regulator of neurotransmitter receptors; NF-kB pathway activator Nucleus; Cytoplasm 2x CC; C2; 4x DM14;
CDH15 NS/S N Cadherin 15 Ca2+ dependant intercellular adhesion protein Plasma membrane SP; 5x CA; 1x TM; Cadherin_C
CRBN NS N Cereblon Expression of potassium channels Plasma membrane; cytoplasm LON
DLG3 NS N Synapse-associated protein 102 Organization and scaffolding at post-synaptic density; MAGUK family protein Synaptic junction, plasma membrane; endoplasmic reticulum; cytoplasm 3x PDZ; SH3; GuKc
DOCK8   N Dedicator of cytokinesis 8 Potential guanine nucleotide exchange factor (GEF); putative organizer of filamentous actin Plasma membrane; cytoplasm; nucleus Ded_cyto; 2x CC; C2; DUF3398
FGD1 NS/S N Faciogenital dysplasia protein GEF for Cdc42 Cytoplasm; cytoskeleton RhoGEF; 2x PH; FYVE; DH
FTSJ1 NS N FtsJ homolog 1 Processing and modification of rRNA Nucleolus AdoMet_MTases
GDI1 NS N GDP dissociation inhibitor 1 Inhibitor of Rab GTPases Cytoplasm NABD_Rossmann
GRIK2 NS Y Glutamate receptor, ionotropic,, kainate 2 Subunit of synaptic glutamate receptor (KARs) Plasma membrane-synapse SP; 4x TM; Lig_chan; PBPe; ANF_receptor; Periplasmic_Binding_Protein_Type_1
HUWE1 NS/S N HECT, UBA and WWE domain containing 1 Ubiquitin E3 ligase; protein ubiquitination pathway Nucleus; cytoplasm DUF908; DUF913; UBA; WWE; UIM; HECTc; 2x CC
IL1RAPL1 NS Y Interleukin 1 receptor accessory protein-like 1 Part of the interleukin 1 receptor family; neuronal calcium-regulated vesicle release and dendrite differentiation Plasma membrane SP; 2x IG; IGc2; 1x TM; TIR
JARID1C/KDM5C NS Y Jumonji, AT rich interactive domain 1C Transcriptional regulation and chromatin remodeling Nucleus JmjN; BRIGHT; 2x PHD; JmjC; CC; Zf-C5HC2; PLU-1
KIRREL3 NS/S N kin of IRRE like 3 Unknown: Potentially involved in synaptogenesis Plasma membrane; cytoplasm; extracellular SP; 3x IG; IGc2; 1x TM
MAGT1 NS N Magnesium transporter 1 Cellular Mg2+ uptake; oligosaccharide transferase; N-glycosylation ER membrane 5x TM; OST3_OST6; TRX_family
MBD5 NS/S N methyl-CpG binding domain protein 5 Putative role in transcriptional regulation Nucleus PWWP; MBD
MECP2 NS/S Y Methyl CpG binding protein 2 Methyl binding to control transcription Nucleus MBD; 2x AT Hook
NLGN4X NS Y X-linked neuroligin 4 Synapse adhesion protein Plasma membrane-synapse SP; 2x TM; PnbA; esterase_lipase
OPHN1 NS/S N Oligophrenin 1 Rho-GTPase activating protein Cytoplasm CC; PH; RhoGAP
PAK3 NS N p21-activated kinase 3 Downstream effector of Rho-GTPases Cytoplasm PBD; S_TKc
PQBP1 NS/S N Polyglutamine binding protein 1 Transcriptional activation Nucleus; cytoplasm; nucleolus WW
PRSS12 NS N Neurotrypsin Synaptic protease, cleaves agrin; synaptic plasticity Extracelluar SP; KR; 4x SR; Tryp_SPc
PTCHD1 NS Y Patched domain 1 Putative Hedgehog receptor Plasma membrane 12x TM; Ptc; MMPL
RPS6KA3 NS/S N Ribosomal protein S6 kinase, 90kDa, polypeptide 3 Ras/Map/ERK signaling pathway Cytoplasm 2x S_TKc; S_TK_X
SHANK2 NS Y SH3 and multiple ankyrin repeat domains 2 Scaffolding and cell adhesion protein; Synaptic plasticity Dendrite; cytoplasm; post-synaptic density 6x ANK; SH3; PDZ; SAM
SHROOM4 NS/S N Shroom family member 4 Cytoskeletal architecture Cytoplasm PDZ; 3x CC; ASD2
SLC6A8 NS N Solute carrier family 6 member 8 Creatine transporter Plasma membrane 12x TM; SNF
STXBP1 NS N Syntaxin-binding protein 1 Synaptic vesicle docking and fusion; neurotransmission Plasma membrane-synapse; cytoplasm SEC1
SYNGAP1 NS N Synaptic Ras GTPase activating protein 1 Part of the NMDA receptor complex; Negative regulation of Ras/Map/ERK pathway Plasma membrane-synapse PH; C2; RasGAP; CC; DUF3498
SYP NS/S N Synaptophysin Synaptic vesicle protein Synapse/vesicle membrane 4x TM; MARVEL
TSPAN7 NS/S N Tetraspanin 7 Unknown: Transmembrane protein potentially involved in synapse maturation Plasma membrane/synapse Tetraspanin/4x TM
TRAPPC9 NS N NIK- and IKKB-binding protein Neuronal NF-kB signalling, vesicular transport Golgi; ER; Cytoplasm Trs120
TUSC3 NS N Tumor suppressor candidate 3 Mg2+ uptake, oligosaccharide transferase; N-glycosylation ER membrane 5x TM; OST3_OST6
UPF3B NS/S Y UPF3 regulator of nonsense transcripts homolog B mRNA nuclear export and surveillance Nucleus; Cytoplasm; Nucleolus SMG4_UPF3; 2x CC; 5x NLS
ZNF41 NS N Zinc finger protein 41 Putative repressor of transcription Nucleus KRAB; 17x ZnF_C2H2
ZNF674 NS N Zinc finger protein 674 Putative repressor of transcription Nucleus KRAB; 11x ZnF_C2H2;
ZNF711 NS N Zinc finger protein 711 Unknown: Putative activator of transcription Nucleus Zfx_Zfy; 12x ZnF_C2H2;
ZNF81 NS N Zinc finger protein 81 Putative repressor of transcription Nucleus KRAB; 12x ZnF_C2H2;
  1. aS represents syndromic, NS represents nonsyndromic
  2. CH calponin homology; PH pleckstrin homology; SH3 Src homology 3; CC coiled-coil; TM transmembrane; RhoGEF Rho guanine exchange factor; MBD Methyl CpG Binding; HOX homeodomain; DEXDc DEAD-like helicase superfamily; HELICc helicase superfamily c-terminal domain; S_TKc serine/threonine kinase catalytic domain; GuKc Guanylate kinase homologues; C2 Protein kinase C conserved region 2; CA Cadherin; SP signal peptide; Cadherin_C cadherin cytoplasmic region; DUF domain of unknown function; Ded_cyto dedicator of cytokinesis; DH DBL-homology; AdoMet_MTases SAM methyltranferase; NADB_Rossmann Rossmann-fold NAD(P)(+)-binding proteins; UBA Ubiquitin associated domain; UIM Ubiquitin interacting motif; Lig_chan-Glu_bd Ligated ion channel L-glutamate- and glycine-binding site; IG Immunoglobulin domain; IGc2 Immunoglobulin C-2 type; TIR Toll-interleukin resistance 1; JmjN jumonji; PHD plant homeodomain; PLU-1 PLU-like protein; KR Kringle; SR scavenger receptor Cys-rich; SNF sodium:neurotransmitter symporter family; ZnF Zinc finger; KRAB Kruppel associated box; SAM Sterile alpha motif; PnbA Carboxylesterase type B; zf- C5HC2 C5HC2 zinc finger; PBD P21-Rho-binding domain; Tryp_SPc Trypsin-like serine protease; S_TK_X Extension to Ser/Thr-type protein kinases; RasGAP Ras-GTPase Activating Domain; ASD2 Apx/Shroom domain ASD2; ANK Ankyrin repeats; NLS nuclear localization signal