Table 2 The verification of 47 genes in the Han population.
Gene | Consequence | rs | VID | hgvs | Function |
|---|---|---|---|---|---|
APBA3 | missense_variant | rs146584090 | 19:3751091:T/C | NM_004886.3:c.1661 A > G(p.His554Arg) | It is an adapter protein that interacts with the Alzheimer’s disease amyloid precursor protein. This gene product is believed to be involved in signal transduction processes. This gene is a candidate gene for Alzheimer’s disease. |
ARHGAP39 | missense_variant | . | 8:145755853:C/T | NM_025251.1:c.3298 G > A(p.Val1100Met) | Predicted to enable GTPase activator activity. Involved in postsynapse organization. Is active in glutamatergic synapse. |
ARHGEF11 | missense_variant | . | 1:156906736:G/C | NM_014784.3:c.4382 C > G(p.Thr1461Ser) | The encoded protein may form a complex with G proteins and stimulate Rho-dependent signals. A similar protein in rat interacts with glutamate transporter EAAT4 and modulates its glutamate transport activity. |
BAI2 | missense_variant | rs200836738 | 1:32222059:G/A | NM_001703.2:c.379 C > T(p.Arg127Trp) | The encoded protein is a brain-specific inhibitor of angiogenesis. The mature peptide may be further cleaved into additional products (PMID:20367554). Alternative splicing results in multiple transcript variants. |
C14orf177 | missense_variant | . | 14:99183438:T/C | NM_182560.2:c.205 T > C(p.Cys69Arg) | NA |
CDH10 | missense_variant | . | 5:24487935:G/C | NM_006727.3:c.2204 C > G(p.Thr735Ser) | This gene encodes a type II classical cadherin of the cadherin superfamily. This particular cadherin is predominantly expressed in brain and is putatively involved in synaptic adhesions, axon outgrowth and guidance. |
CLTCL1 | inframe_deletion | rs782037820 | 22:19175545:TTG/- | NM_007098.3:c.4380_4382delCAA(p.Asn1460del) | This gene is a member of the clathrin heavy chain family and encodes a major protein of the polyhedral coat of coated pits and vesicles. |
CPLX4 | missense_variant | . | 18:56985594:G/A | NM_181654.3:c.101 C > T(p.Pro34Leu) | This gene likely encodes a member of the complexin family. The encoded protein may be involved in synaptic vesicle exocytosis. |
DNAH5 | missense_variant | rs200983202 | 5:13759047:C/G | NM_001369.2:c.10327 G > C(p.Asp3443His) | This gene encodes a dynein protein.This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. |
DPPA4 | missense_variant | . | 3:109047930:T/C | NM_018189.3:c.685 A > G(p.Arg229Gly) | This gene encodes a nuclear factor that is involved in the maintenance of pluripotency in stem cells and essential for embryogenesis. |
ERC1 | missense_variant | . | 12:1291147:A/T | NM_178039.2:c.1848A>T(p.Gln616His) | The protein encoded by this gene is a member of a family of RIM-binding proteins. RIMs are active zone proteins that regulate neurotransmitter release. |
FUBP1 | missense_variant | . | 1:78430904:C/A | NM_003902.3:c.485 G > T(p.Arg162Leu) | The protein encoded by this gene is a single stranded DNA-binding protein that binds to multiple DNA elements. Aberrant expression of this gene has been found in malignant tissues, and this gene is important to neural system and lung development. |
GEMIN7,ZNF296 | missense_variant | . | 19:45579582:G/A | NM_145288.1:c.50 C > T(p.Pro17Leu) | The protein encoded by this gene is a component of the core SMN complex, which is required for pre-mRNA splicing in the nucleus. |
IL21R-AS1,IL21R | missense_variant | . | 16:27460434:G/A | NM_181079.4:c.1513 G > A(p.Ala505Thr) | The protein encoded by this gene is a cytokine receptor for interleukin 21. This receptor transduces the growth promoting signal of IL21, and is important for the proliferation and differentiation of T cells, B cells, and natural killer (NK) cells. |
IL6R | missense_variant | rs780683821 | 1:154437680:G/A | NM_000565.3:c.1231 G > A(p.Gly411Arg) | This gene encodes a subunit of the interleukin 6 (IL6) receptor complex. Interleukin 6 is a potent pleiotropic cytokine that regulates cell growth and differentiation and plays an important role in the immune response. |
KCNAB1 | missense_variant | . | 3:155861100:C/T | NM_003471.3:c.133 C > T(p.Pro45Ser) | This gene encodes a member of the potassium channel, voltage-gated, shaker-related subfamily. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. |
KIF17 | missense_variant | rs200844482 | 1:21009232:C/T | NM_020816.2:c.2377 G > A(p.Gly793Arg) | Predicted to enable microtubule binding activity and plus-end-directed microtubule motor activity. Predicted to be involved in anterograde dendritic transport of neurotransmitter receptor complex and cell projection organization. Predicted to act upstream of or within microtubule-based process; protein-containing complex localization; and vesicle-mediated transport. |
KNDC1 | missense_variant | rs985546165 | 10:135009249:G/A | NM_152643.6:c.1658 G > A(p.Arg553His) | The protein encoded by this gene is a Ras guanine nucleotide exchange factor that appears to negatively regulate dendritic growth in the brain. |
MAP2 | missense_variant | . | 2:210574665:A/G | NM_002374.3:c.4760 A > G(p.Lys1587Arg) | The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The products of similar genes in rat and mouse are neuron-specific cytoskeletal proteins that are enriched in dentrites, implicating a role in determining and stabilizing dentritic shape during neuron development. |
NPTX2 | missense_variant | rs377548219 | 7:98256538:C/T | NM_002523.2:c.950 C > T(p.Thr317Met) | This gene encodes a member of the family of neuronal petraxins, synaptic proteins that are related to C-reactive protein. This protein is involved in excitatory synapse formation. |
PGAM2 | missense_variant | rs770622502 | 7:44104852:C/T | NM_000290.3:c.277 G > A(p.Gly93Arg) | This gene encodes muscle-specific Phosphoglycerate mutase subunit. |
PLA2G4B,JMJD7-PLA2G4B | missense_variant | . | 15:42138538:C/G | NM_005090.3:c.2431 C > G(p.His811Asp) | This gene encodes a member of the cytosolic phospholipase A2 protein family. |
PTCH1 | missense_variant | . | 9:98209454:G/A | NM_000264.3:c.4084 C > T(p.Pro1362Ser) | This gene encodes a member of the patched family of proteins and a component of the hedgehog signaling pathway. Hedgehog signaling is important in embryonic development and tumorigenesis |
SCN11A | missense_variant | . | 3:38921541:G/A | NM_014139.2:c.3293 C > T(p.Thr1098Ile) | This gene encodes one member of the sodium channel alpha subunit gene family, and is highly expressed in nociceptive neurons of dorsal root ganglia and trigeminal ganglia. |
SH3TC2 | missense_variant | rs760656119 | 5:148392170:C/T | NM_024577.3:c.3181 G > A(p.Glu1061Lys) | The gene product has been proposed to be an adapter or docking molecule. Mutations in this gene result in autosomal recessive Charcot-Marie-Tooth disease type 4 C, a childhood-onset neurodegenerative disease characterized by demyelination of motor and sensory neurons. |
SHANK1 | missense_variant | rs577804387 | 19:51172180:G/A | NM_016148.2:c.3037 C > T(p.Pro1013Ser) | This gene encodes a member of the SHANK (SH3 domain and ankyrin repeat containing) family of proteins. Members of this family act as scaffold proteins that are required for the development and function of neuronal synapses. Deletions in this gene may be associated with autism spectrum disorder in males. |
SLC39A6 | missense_variant | . | 18:33702217:T/C | NM_012319.3:c.1157 A > G(p.His386Arg) | SLC39A6 belongs to a subfamily of proteins that show structural characteristics of zinc transporters |
SORL1 | missense_variant | . | 11:121420769:G/A | NM_003105.5:c.2152 G > A(p.Val718Met) | The encoded preproprotein is proteolytically processed to generate the mature receptor, which likely plays roles in endocytosis and sorting. |
SSH1 | missense_variant | . | 12:109182656:T/A | NM_018984.3:c.2258 A > T(p.Lys753Met) | The protein encoded by this gene belongs to the slingshot homolog (SSH) family of phosphatases, which regulate actin filament dynamics. |
SYNJ1 | missense_variant | . | 21:34053882:C/A | NM_203446.2:c.1394 G > T(p.Arg465Leu) | This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. |
SYT8 | splice_acceptor_variant | . | 11:1857115:G/C | NM_138567.3:c.301–1 G > C(.) | This gene encodes a member of the synaptotagmin protein family. Synaptotagmins are membrane proteins that are important in neurotransmission and hormone secretion, both of which involve regulated exocytosis. |
TAOK2 | missense_variant | rs768000716 | 16:29998819:C/T | NM_001252043.1:c.2887 C > T(p.Arg963Trp) | This gene encodes a serine/threonine protein kinase that is involved in many different processes, including, cell signaling, microtubule organization and stability, and apoptosis. |
TENM1 | missense_variant | . | X:123695656:C/T | NM_014253.3:c.2299 G > A(p.Gly767Arg) | It is expressed in the neurons and may function as a cellular signal transducer. |
TMEM132A | missense_variant | rs777345475 | 11:60696363:G/A | NM_017870.3:c.797 G > A(p.Arg266Gln) | This gene encodes a protein that is highly similar to the rat Grp78-binding protein (GBP). |
TSEN34 | missense_variant | . | 19:54696153:G/A | NM_024075.3:c.674 G > A(p.Arg225Lys) | A mutation in this gene results in the neurological disorder pontocerebellar hypoplasia type 2. |
TUFM | missense_variant | . | 16:28856781:C/T | NM_003321.4:c.268 G > A(p.Ala90Thr) | This gene encodes a protein which participates in protein translation in mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency resulting in lactic acidosis and fatal encephalopathy. |
YLPM1 | missense_variant | . | 14:75276681:C/T | NM_019589.2:c.5008 C > T(p.Pro1670Ser) | Enables RNA binding activity. Predicted to be involved in regulation of telomere maintenance. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. |
TRIO | missense_variant | . | 5:14488193:T/C | NM_007118.2:c.7456 T > C(p.Trp2486Arg) | This gene encodes a large protein that functions as a GDP to GTP exchange factor. This protein promotes the reorganization of the actin cytoskeleton, thereby playing a role in cell migration and growth. |
RAB41 | missense_variant | . | X:69502652:G/C | NM_001032726.2:c.181 G > C(p.Ala61Pro) | This gene encodes a small GTP-binding protein that belongs to the largest family within the Ras superfamily. These proteins function as regulators of membrane trafficking. |
GPRASP2 | missense_variant | rs770886846 | X:101970390:C/T | NM_138437.5:c.593 C > T(p.Pro198Leu) | The encoded protein has been shown to be capable of interacting with several GPCRs, including the M1 muscarinic acetylcholine receptor and the calcitonin receptor. |
INADL | inframe_deletion | . | 1:62240913:TAA/- | NM_176877.2:c.757_759delAAT(p.Asn253del) | This gene encodes a protein with multiple PDZ domains. PDZ domains mediate protein-protein interactions, and proteins with multiple PDZ domains often organize multimeric complexes at the plasma membrane. |
FOXP1 | missense_variant | . | 3:71102805:C/A | NM_032682.5:c.402 G > T(p.Gln134His) | This gene belongs to subfamily P of the forkhead box (FOX) transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. |
NLRC5 | missense_variant | rs1053181583 | 16:57060387:C/T | NM_032206.4:c.1532 C > T(p.Ala511Val) | This gene plays a role in cytokine response and antiviral immunity through its inhibition of NF-kappa-B activation and negative regulation of type I interferon signaling pathways. |
LPCAT2 | stop_gained | rs144432562 | 16:55575825:C/T | XM_005256006.1:c.928 C > T(p.Arg310Ter) | The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. |
ABCA10 | missense_variant | . | 17:67211999:A/G | NM_080282.3:c.815 T > C(p.Leu272Ser) | NA |
SUCLG2 | missense_variant | . | 3:67459404:G/C | XM_005264773.1:c.1117 C > G(p.His373Asp) | This gene encodes a GTP-specific beta subunit of succinyl-CoA synthetase. Succinyl-CoA synthetase catalyzes the reversible reaction involving the formation of succinyl-CoA and succinate. |
PIK3C2A | missense_variant | . | 11:17113578:C/T | NM_002645.2:c.4607 G > A(p.Arg1536His) | The protein encoded by this gene belongs to the phosphoinositide 3-kinase (PI3K) family. PI3-kinases play roles in signaling pathways involved in cell proliferation, oncogenic transformation, cell survival, cell migration, and intracellular protein trafficking. |
