My Novel and Rare Mutations In Connection To My Neurodivergence
Because I am focusing on neurodivergence, I mentioned only things that pertain to nervous system.
This is the snapshot of my account with my genome number
These are my novel variants in regards to my functioning of brain, nervous system.
ERCC6-PGBD3 NC_000010.10:g.50723469G>T
Novel G/T
Nonsense
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Entrez Gene Summary for ERCC6 Gene
This gene encodes a DNA-binding protein that is important in transcription-coupled excision repair. The encoded protein has ATP-stimulated ATPase activity, interacts with several transcription and excision repair proteins, and may promote complex formation at DNA repair sites. Mutations in this gene are associated with Cockayne syndrome type B and cerebrooculofacioskeletal syndrome 1. Alternative splicing occurs between a splice site from exon 5 of this gene to the 3' splice site upstream of the open reading frame (ORF) of the adjacent gene, piggyback-derived-3 (GeneID:267004), which activates the alternative polyadenylation site downstream of the piggyback-derived-3 ORF. The resulting transcripts encode a fusion protein that shares sequence with the product of each individual gene. [provided by RefSeq, Mar 2016]
GeneCards Summary for ERCC6 Gene
ERCC6 (ERCC Excision Repair 6, Chromatin Remodeling Factor) is a Protein Coding gene. Diseases associated with ERCC6 include Cockayne Syndrome B and Cerebrooculofacioskeletal Syndrome 1. Among its related pathways are DNA repair pathways, full network and RNA Polymerase I Promoter Opening. Gene Ontology (GO) annotations related to this gene include chromatin binding and protein C-terminus binding. An important paralog of this gene is CHD2.
UniProtKB/Swiss-Prot Summary for ERCC6 Gene
Essential factor involved in transcription-coupled nucleotide excision repair which allows RNA polymerase II-blocking lesions to be rapidly removed from the transcribed strand of active genes (PubMed:20541997, PubMed:26620705, PubMed:16246722). Upon DNA-binding, it locally modifies DNA conformation by wrapping the DNA around itself, thereby modifying the interface between stalled RNA polymerase II and DNA (PubMed:15548521). It is required for transcription-coupled repair complex formation (PubMed:16916636). It recruits the CSA complex (DCX(ERCC8) complex), nucleotide excision repair proteins and EP300 to the sites of RNA polymerase II-blocking lesions (PubMed:16916636). Plays an important role in regulating the choice of the DNA double-strand breaks (DSBs) repair pathway and G2/M checkpoint activation; DNA-dependent ATPase activity is essential for this function (PubMed:25820262). Regulates the DNA repair pathway choice by inhibiting non-homologous end joining (NHEJ), thereby promoting the homologous recombination (HR)-mediated repair of DSBs during the S/G2 phases of the cell cycle (PubMed:25820262). Mediates the activation of the ATM- and CHEK2-dependent DNA damage responses thus preventing premature entry of cells into mitosis following the induction of DNA DSBs (PubMed:25820262). Acts as a chromatin remodeler at DSBs; DNA-dependent ATPase-dependent activity is essential for this function. Remodels chromatin by evicting histones from chromatin flanking DSBs, limiting RIF1 accumulation at DSBs thereby promoting BRCA1-mediated HR (PubMed:29203878). Required for stable recruitment of ELOA and CUL5 to DNA damage sites (PubMed:28292928). Involved in UV-induced translocation of ERCC8 to the nuclear matrix (PubMed:26620705). Essential for neuronal differentiation and neuritogenesis; regulates transcription and chromatin remodeling activities required during neurogenesis (PubMed:24874740). ERCC6_HUMAN,Q03468
Involved in repair of DNA damage following UV irradiation, acting either in the absence of ERCC6 or synergistically with ERCC6. Involved in the regulation of gene expression. In the absence of ERCC6, induces the expression of genes characteristic of interferon-like antiviral responses. This response is almost completely suppressed in the presence of ERCC6. In the presence of ERCC6, regulates the expression of genes involved in metabolism regulation, including IGFBP5 and IGFBP7. In vitro binds to PGBD3-related transposable elements, called MER85s; these non-autonomous 140 bp elements are characterized by the presence of PGBD3 terminal inverted repeats and the absence of internal transposase ORF.
Gene Ontology (GO) - Biological Process for ERCC6 Gene
nervous system development
neurogenesis
neuron differentiation
neuron projection development
Disorders for ERCC6 Gene
Cerebral Degeneration
Specific Developmental Disorder
Cerebellar Disease
Basal Ganglia Disease
Cranial Nerve Disease
Basal Ganglia Calcification
Central Nervous System Disease
Central Nervous System Abnormality
Progressive Myclonus Epilepsy
Neuromuscular Disease
https://www.genecards.org/cgi-bin/carddisp.pl?gene=ERCC6
GNAS NC_000020.10:g.57428526G>T
Novel G/T
Missense
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Entrez Gene Summary for GNAS Gene
This locus has a highly complex imprinted expression pattern. It gives rise to maternally, paternally, and biallelically expressed transcripts that are derived from four alternative promoters and 5' exons. Some transcripts contain a differentially methylated region (DMR) at their 5' exons, and this DMR is commonly found in imprinted genes and correlates with transcript expression. An antisense transcript is produced from an overlapping locus on the opposite strand. One of the transcripts produced from this locus, and the antisense transcript, are paternally expressed noncoding RNAs, and may regulate imprinting in this region. In addition, one of the transcripts contains a second overlapping ORF, which encodes a structurally unrelated protein - Alex. Alternative splicing of downstream exons is also observed, which results in different forms of the stimulatory G-protein alpha subunit, a key element of the classical signal transduction pathway linking receptor-ligand interactions with the activation of adenylyl cyclase and a variety of cellular reponses. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene result in pseudohypoparathyroidism type 1a, pseudohypoparathyroidism type 1b, Albright hereditary osteodystrophy, pseudopseudohypoparathyroidism, McCune-Albright syndrome, progressive osseus heteroplasia, polyostotic fibrous dysplasia of bone, and some pituitary tumors. [provided by RefSeq, Aug 2012]
GeneCards Summary for GNAS Gene
GNAS (GNAS Complex Locus) is a Protein Coding gene. Diseases associated with GNAS include Mccune-Albright Syndrome and Osseous Heteroplasia, Progressive. Among its related pathways are Development Ligand-independent activation of ESR1 and ESR2 and Signaling by Slit. Gene Ontology (GO) annotations related to this gene include GTP binding and obsolete signal transducer activity. An important paralog of this gene is GNAL.
UniProtKB/Swiss-Prot Summary for GNAS Gene
May inhibit the adenylyl cyclase-stimulating activity of guanine nucleotide-binding protein G(s) subunit alpha which is produced from the same locus in a different open reading frame. ALEX_HUMAN,P84996
Guanine nucleotide-binding proteins (G proteins) function as transducers in numerous signaling pathways controlled by G protein-coupled receptors (GPCRs). Signaling involves the activation of adenylyl cyclases, resulting in increased levels of the signaling molecule cAMP. GNAS functions downstream of several GPCRs, including beta-adrenergic receptors. XLas isoforms interact with the same set of receptors as GNAS isoforms (By similarity). GNAS1_HUMAN,Q5JWF2
Guanine nucleotide-binding proteins (G proteins) function as transducers in numerous signaling pathways controlled by G protein-coupled receptors (GPCRs) (PubMed:17110384). Signaling involves the activation of adenylyl cyclases, resulting in increased levels of the signaling molecule cAMP (PubMed:26206488, PubMed:8702665). GNAS functions downstream of several GPCRs, including beta-adrenergic receptors (PubMed:21488135). Stimulates the Ras signaling pathway via RAPGEF2 (PubMed:12391161). GNAS2_HUMAN,P63092
Tocris Summary for GNAS Gene
Heterotrimeric G proteins are membrane bound GTPases that are linked to 7-TM receptors. Each G protein contains an alpha-, beta- and gamma-subunit and is bound to GDP in the 'off' state. Ligand binding causes a receptor conformational change, detaching the G protein and switching it 'on'.
Super Pathways for GNAS Gene
Neurophysiological process Glutamate regulation of Dopamine D1A receptor signaling
Neuropathic Pain-Signaling in Dorsal Horn Neurons
Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics
Dopamine-DARPP32 Feedback onto cAMP Pathway
Serotonin HTR1 group and FOS pathway
Biological Process for GNAS Gene
adenylate cyclase-activating dopamine receptor signaling pathway
cognition
mRNA expression in embryonic tissues and stem cells
Brain (Nervous System) - Pituitary Gland, Cerebral Cortex
Evidence on tissue expression from TISSUES for GNAS Gene
Nervous System (5)
Disorders for GNAS Gene
Developmental And Epileptic Encephalopathy
https://www.genecards.org/cgi-bin/carddisp.pl?gene=GNAS
FASTKD2 NC_000002.11:g.207634917A>G
Novel A/G
Missense
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Entrez Gene Summary for FASTKD2 Gene
This gene encodes a protein that is localized in the mitochondrial inner compartment and that may play a role in mitochondrial apoptosis. Nonsense mutations have been reported to result in cytochrome c oxidase deficiency. [provided by RefSeq, Oct 2008]
GeneCards Summary for FASTKD2 Gene
FASTKD2 (FAST Kinase Domains 2) is a Protein Coding gene. Diseases associated with FASTKD2 include Combined Oxidative Phosphorylation Deficiency 44 and Mitochondrial Complex Iv Deficiency, Nuclear Type 1. Gene Ontology (GO) annotations related to this gene include RNA binding and protein kinase activity. An important paralog of this gene is TBRG4.
UniProtKB/Swiss-Prot Summary for FASTKD2 Gene
Plays an important role in assembly of the mitochondrial large ribosomal subunit (PubMed:25683715). As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mitochondrial ribosomal RNA (16S mt-rRNA), controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation (PubMed:27667664, PubMed:25683715, PubMed:26370583). May play a role in mitochondrial apoptosis. FAKD2_HUMAN,Q9NYY8
mRNA Expression by UniProt/SwissProt for FASTKD2 Gene
Tissue specificity: Expression detected brain
https://www.genecards.org/cgi-bin/carddisp.pl?gene=FASTKD2
These are the genes where I have the rare variants in regards to my functioning of brain, nervous system.
OTUD7A NC_000015.9:g.31775732T>A
rs992534164 T/A
2/147876 (0.00001352)
https://gnomad.broadinstitute.org/variant/15-31483529-T-A?dataset=gnomad_r3
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Entrez Gene Summary for OTUD7A Gene
The protein encoded by this gene is a deubiquitinizing enzyme and possible tumor suppressor. The encoded protein acts on TNF receptor associated factor 6 (TRAF6) to control nuclear factor kappa B expression. However, this gene is downregulated by SNAIL1 in hepatocellular carcinoma cells, contributing to their progression and malignancy. [provided by RefSeq, Aug 2016]
GeneCards Summary for OTUD7A Gene
OTUD7A (OTU Deubiquitinase 7A) is a Protein Coding gene. Diseases associated with OTUD7A include Speech And Communication Disorders and Specific Learning Disability. Among its related pathways are Metabolism of proteins and Ovarian tumor domain proteases. Gene Ontology (GO) annotations related to this gene include cysteine-type deubiquitinase activity. An important paralog of this gene is OTUD7B.
UniProtKB/Swiss-Prot Summary for OTUD7A Gene
Has deubiquitinating activity towards 'Lys-11'-linked polyubiquitin chains. OTU7A_HUMAN,Q8TE49
Evidence on tissue expression from TISSUES for OTUD7A Gene
Nervous system(4.4)
gene expression patterns for OTUD7A gene:
Brodmann Area 23, middle temporal gyrus
Disorders for OTUD7A Gene
Speech And Communication Disorders
Specific Learning Disability
Schizophrenia
https://www.genecards.org/cgi-bin/carddisp.pl?gene=OTUD7A
TMEM87A NC_000015.9:g.42531918C>T
rs1349632476 C/T
Missense
1/152214 (0.000006570)
https://gnomad.broadinstitute.org/variant/15-42239720-C-A?dataset=gnomad_r3
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Entrez Gene Summary for TMEM87A Gene
Involved in retrograde transport, endosome to Golgi. Located in Golgi cisterna membrane. [provided by Alliance of Genome Resources, Apr 2022]
GeneCards Summary for TMEM87A Gene
TMEM87A (Transmembrane Protein 87A) is a Protein Coding gene. Diseases associated with TMEM87A include Hermansky-Pudlak Syndrome 1. Among its related pathways are RHOC GTPase cycle and Signal Transduction. An important paralog of this gene is TMEM87B.
UniProtKB/Swiss-Prot Summary for TMEM87A Gene
May be involved in retrograde transport from endosomes to the trans-Golgi network (TGN). TM87A_HUMAN,Q8NBN3
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
Brain (Nervous System) - Hippocampus, Cerebellum, Cerebral Cortex, Lateral Ventricle
Evidence on tissue expression from TISSUES for TMEM87A Gene
Nervous system(4.9)
gene expression patterns for TMEM87A gene:
corpus callosum
https://www.genecards.org/cgi-bin/carddisp.pl?gene=TMEM87A
SLIT1 NC_000010.10:g.98917636G>C
rs1308576583 G/C
https://gnomad.broadinstitute.org/variant/10-98917636-G-C?dataset=gnomad_r2_1
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Entrez Gene Summary for SLIT1 Gene
Enables Roundabout binding activity. Involved in axon extension involved in axon guidance; motor neuron axon guidance; and negative chemotaxis. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
GeneCards Summary for SLIT1 Gene
SLIT1 (Slit Guidance Ligand 1) is a Protein Coding gene. Diseases associated with SLIT1 include Hepatic Adenomas, Familial and Diaphragm Disease. Among its related pathways are Signaling by Slit and Regulation of commissural axon pathfinding by SLIT and ROBO. Gene Ontology (GO) annotations related to this gene include calcium ion binding and Roundabout binding. An important paralog of this gene is SLIT2.
UniProtKB/Swiss-Prot Summary for SLIT1 Gene
Thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions (By similarity). SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb. SLIT1_HUMAN,O75093
Molecular function for SLIT1 Gene
Function:
Thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions (By similarity). SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb. SLIT1_HUMAN,O75093
Biochemistry:
SLIT Drosophila homolog 1,expressed in the brain,ligand of GPC1,involved in histogenesis of central nervous system and in brain diseases
It affects the following cells:
Brain Fetal Dopaminergic Neurons (Substantia Nigra pars Compacta) Fetal Dopaminergic Neurons (Ventral Tegmental Area)
Super Pathways
Nervous System Development
Regulation of commissural axon pathfinding by SLIT and ROBO
Regulation of cortical dendrite branching
Spinal cord injury
Gene Ontology (GO) - Biological Process for SLIT1 Gene
nervous system development
axonogenesis
axon guidance
brain development
motor neuron axon guidance
spinal cord development
retinal ganglion cell axon guidance
dorsal/ventral axon guidance
generation of neurons
neuron projection morphogenesis
negative regulation of axon extension involved in axon guidance
axon extension involved in axon guidance
forebrain morphogenesis
negative regulation of synapse assembly
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
Brain - Hypothalamus, Hippocampus, Thalamus, Cerebellum, Amygdala
Neural Tube (Nervous System) - Astrocyte Precursor Cells pV2 Neural Domain, Astrocyte Precursor Cells pV3 Neural Domain, V2 Neural Progenitor Cells pV2 Neural Domain, Mesencephalic Floor Plate
Glial Cells - VA2 Fibrous Astrocyte Cells Spinal Cord White Matter, VA3 Fibrous Astrocyte Cells Spinal Cord White Matter, Dorsal telencephalic astroglia-like cells, Caudal astroglia-like cells(Krencik R et. al. 2011)
Spinal Cord (Nervous System) - VA2 Fibrous Astrocyte Cells Spinal Cord White Matter, VA3 Fibrous Astrocyte Cells Spinal Cord White Matter
Astrocytes (Nervous System) - Dorsal telencephalic astroglia-like cells, Caudal astroglia-like cells
mRNA differential expression in normal tissues according to GTEx for SLIT1 Gene
This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x7.3), Brain - Nucleus accumbens (basal ganglia) (x5.7), Brain - Frontal Cortex (BA9) (x5.2), Brain - Caudate (basal ganglia) (x5.0), Pituitary (x4.7), Brain - Hippocampus (x4.5), Brain - Cortex (x4.2), and Brain - Amygdala (x4.0).
Protein differential expression in normal tissues from HIPED for SLIT1 Gene
This gene is overexpressed in Cerebrospinal fluid (7.0).
https://www.genecards.org/cgi-bin/carddisp.pl?gene=SLIT1
NCAN NC_000019.9:g.19337864G>T
349/201472 (0.001732)
https://gnomad.broadinstitute.org/variant/19-19337864-G-T?dataset=gnomad_r2_1
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Entrez Gene Summary for NCAN Gene
Neurocan is a chondroitin sulfate proteoglycan thought to be involved in the modulation of cell adhesion and migration.[supplied by OMIM, Jul 2002]
GeneCards Summary for NCAN Gene
NCAN (Neurocan) is a Protein Coding gene. Diseases associated with NCAN include Bipolar Disorder and Schizophrenia. Among its related pathways are ECM proteoglycans and ERK Signaling. Gene Ontology (GO) annotations related to this gene include calcium ion binding and extracellular matrix structural constituent. An important paralog of this gene is VCAN.
UniProtKB/Swiss-Prot Summary for NCAN Gene
May modulate neuronal adhesion and neurite growth during development by binding to neural cell adhesion molecules (NG-CAM and N-CAM). Chondroitin sulfate proteoglycan; binds to hyaluronic acid. NCAN_HUMAN,O14594
Molecular function for NCAN Gene
May modulate neuronal adhesion and neurite growth during development by binding to neural cell adhesion molecules (NG-CAM and N-CAM).
SuperPathways for NCAN Gene
Nervous system development
NCAM signaling for neurite out-growth
Spinal cord injury
Gene Ontology (GO) - Biological Process for NCAN Gene
involved_in central nervous system development
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
Brain (Nervous System) - Mature Endothelial Cells Blood Brain Barrier, Endothelial Cells, Adult Endothelial Cells, Amygdala, Cerebral Cortex
Neural Tube (Nervous System) - Spinal Ventral Columns
Oligodendrocytes (Nervous System) - ligodendrocyte progenitor cells
Spinal Cord (Nervous System) - Oligodendrocyte progenitor cells
mRNA differential expression in normal tissues according to GTEx for NCAN Gene
This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x6.5), Brain - Amygdala (x6.4), Brain - Caudate (basal ganglia) (x6.1), Brain - Cortex (x5.7), Brain - Frontal Cortex (BA9) (x5.5), Brain - Putamen (basal ganglia) (x5.5), Brain - Anterior cingulate cortex (BA24) (x5.2), and Brain - Hippocampus (x4.6)
Protein differential expression in normal tissues from HIPED for NCAN Gene
This gene is overexpressed in Fetal Brain (23.5), Frontal cortex (14.2), Brain (11.3)
mRNA Expression by UniProt/SwissProt for NCAN Gene
Tissue specificity: Brain.
Evidence on tissue expression from TISSUES for NCAN Gene
Nervous system(4.7) Heart(3) Intestine(2.2) Adrenal gland(2.1)
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NCAN Gene
rs146011974 - Uncertain Significance: Developmental dyslexia
Disorders for NCAN Gene
Bipolar Disorder
Schizophrenia
https://www.genecards.org/cgi-bin/carddisp.pl?gene=NCAN
PLXNA2 NC_000001.10:g.208257797G>T
Missense
2/282874 (0.000007070)
https://gnomad.broadinstitute.org/variant/1-208257797-G-T?dataset=gnomad_r2_1
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Entrez Gene Summary for PLXNA2 Gene
This gene encodes a member of the plexin-A family of semaphorin co-receptors. Semaphorins are a large family of secreted or membrane-bound proteins that mediate repulsive effects on axon pathfinding during nervous system development. A subset of semaphorins are recognized by plexin-A/neuropilin transmembrane receptor complexes, triggering a cellular signal transduction cascade that leads to axon repulsion. This plexin-A family member is thought to transduce signals from semaphorin-3A and -3C. [provided by RefSeq, Jul 2008]
GeneCards Summary for PLXNA2 Gene
PLXNA2 (Plexin A2) is a Protein Coding gene. Diseases associated with PLXNA2 include Generalized Anxiety Disorder and Tetralogy Of Fallot. Among its related pathways are Ectoderm differentiation and Semaphorin interactions. Gene Ontology (GO) annotations related to this gene include signaling receptor activity and semaphorin receptor activity. An important paralog of this gene is PLXNA4.
UniProtKB/Swiss-Prot Summary for PLXNA2 Gene
Coreceptor for SEMA3A and SEMA6A. Necessary for signaling by SEMA6A and class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (By similarity). PLXA2_HUMAN,O75051
Gene Ontology (GO) - Cellular Components for PLXNA2 Gene
part_of semaphorin receptor complex
SuperPathway
Semaphorin interactions
Nervous system development
Neuroscience
Development Slit-Robo signaling
Neurophysiological process Receptor-mediated axon growth repulsion0.44
NRP1-triggered signaling pathways in pancreatic cancer
Spinal cord injury
Gene Ontology (GO) - Biological Process for PLXNA2 Gene
neural tube development
cerebellar granule cell precursor tangential migration
positive regulation of axonogenesis
semaphorin-plexin signaling pathway
semaphorin-plexin signaling pathway involved in axon guidance
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
Neural Crest (Gastrulation Derivatives) - Cardiac Neural Crest Cells "Branchial Arch 3,4,6", Neural Crest Outflow Tract Cells Outflow Tract
Head Mesenchyme (Muscoskeletal System) - Cardiac Neural Crest Cells "Branchial Arch 3,4,6"
Heart (Cardiovascular System) - Neural Crest Outflow Tract Cells Outflow Tract
Brain (Nervous System)
Spinal Cord (Nervous System)
Protein differential expression in normal tissues from HIPED for PLXNA2 Gene
This gene is overexpressed in Fetal Brain (41.8), rontal cortex (6.9)
mRNA Expression by UniProt/SwissProt for PLXNA2 Gene: O75051-PLXA2_HUMAN
Tissue specificity: Detected in fetal brain.
Evidence on tissue expression from TISSUES for PLXNA2 Gene
Nervous system(4.9)
gene expression patterns for PLXNA2 gene:
Expressed in ganglionic eminence, cortical plate
Disorders for PLXNA2 Gene
Generalized Anxiety Disorder
Schizophrenia
Autistic Spectrum Disorder
https://www.genecards.org/cgi-bin/carddisp.pl?gene=PLXNA2
IFT172 NC_000002.11:g.27703011C>A
Missense
2/250402 (0.000007987)
https://gnomad.broadinstitute.org/variant/2-27703011-C-A?dataset=gnomad_r2_1
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Entrez Gene Summary for IFT172 Gene
This gene encodes a subunit of the intraflagellar transport subcomplex IFT-B. Subcomplexes IFT-A and IFT-B are necessary for ciliary assembly and maintenance. Mutations in this gene have been associated with skeletal ciliopathies, with or without polydactyly, such as such short-rib thoracic dysplasias 1, 9 or 10. [provided by RefSeq, Mar 2014]
GeneCards Summary for IFT172 Gene
IFT172 (Intraflagellar Transport 172) is a Protein Coding gene. Diseases associated with IFT172 include Short-Rib Thoracic Dysplasia 10 With Or Without Polydactyly and Retinitis Pigmentosa 71. Among its related pathways are Signaling by Hedgehog and Organelle biogenesis and maintenance. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is IFT140.
UniProtKB/Swiss-Prot Summary for IFT172 Gene
Required for the maintenance and formation of cilia. Plays an indirect role in hedgehog (Hh) signaling, cilia being required for all activity of the hedgehog pathway (By similarity). IF172_HUMAN,Q9UG01
Gene Ontology (GO) - Biological Process for IFT172 Gene
neural tube formation
neural tube closure
spinal cord motor neuron differentiation
neural tube development
Evidence on tissue expression from TISSUES for IFT172 Gene
Nervous system(4.6)
Disorders for IFT172 Gene
Congenital Nervous System Abnormality
https://www.genecards.org/cgi-bin/carddisp.pl?gene=IFT172
MAGI2 NC_000007.13:g.77649200G>A
Missense
3/280520 (0.00001069)
https://gnomad.broadinstitute.org/variant/7-77649200-G-A?dataset=gnomad_r2_1
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Entrez Gene Summary for MAGI2 Gene
The protein encoded by this gene interacts with atrophin-1. Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral and pallidoluysian atrophy. This encoded protein is characterized by two WW domains, a guanylate kinase-like domain, and multiple PDZ domains. It has structural similarity to the membrane-associated guanylate kinase homologue (MAGUK) family. [provided by RefSeq, Jul 2008]
GeneCards Summary for MAGI2 Gene
MAGI2 (Membrane Associated Guanylate Kinase, WW And PDZ Domain Containing 2) is a Protein Coding gene. Diseases associated with MAGI2 include Nephrotic Syndrome, Type 15 and Genetic Steroid-Resistant Nephrotic Syndrome. Among its related pathways are Nephrin family interactions and Pathways affected in adenoid cystic carcinoma. Gene Ontology (GO) annotations related to this gene include obsolete signal transducer activity and SMAD binding. An important paralog of this gene is MAGI3.
UniProtKB/Swiss-Prot Summary for MAGI2 Gene
Seems to act as scaffold molecule at synaptic junctions by assembling neurotransmitter receptors and cell adhesion proteins. May play a role in regulating activin-mediated signaling in neuronal cells. Enhances the ability of PTEN to suppress AKT1 activation. Plays a role in nerve growth factor (NGF)-induced recruitment of RAPGEF2 to late endosomes and neurite outgrowth. MAGI2_HUMAN,Q86UL8
Gene Ontology (GO) - Cellular Components for MAGI2 Gene
located_in postsynaptic density
located_in dendrite
neuron projection
located_in synapse
Gene Ontology (GO) - Biological Process for MAGI2 Gene
nervous system development
positive regulation of neuron projection development
nerve growth factor signaling pathway
cellular response to nerve growth factor stimulus
Protein differential expression in normal tissues from HIPED for MAGI2 Gene
This gene is overexpressed in Frontal cortex (12.3)
mRNA Expression by UniProt/SwissProt for MAGI2 Gene: Q86UL8-MAGI2_HUMAN
Tissue specificity: Specifically expressed in brain.
Evidence on tissue expression from TISSUES for MAGI2 Gene
Nervous system(4.9)
Bgee gene expression patterns for MAGI2 gene:
corpus callosum
https://www.genecards.org/cgi-bin/carddisp.pl?gene=MAGI2
TULP3 NC_000012.11:g.3030007C>T
Missense
Uncertain significance
16/282874 (0.00005656)
https://gnomad.broadinstitute.org/variant/12-3030007-C-T?dataset=gnomad_r2_1
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Entrez Gene Summary for TULP3 Gene
This gene encodes a member of the tubby gene family of bipartite transcription factors. Members of this family have been identified in plants, vertebrates, and invertebrates, and they share a conserved N-terminal transcription activation region and a conserved C-terminal DNA and phosphatidylinositol-phosphate binding region. The encoded protein binds to phosphoinositides in the plasma membrane via its C-terminal region and probably functions as a membrane-bound transcription regulator that translocates to the nucleus in response to phosphoinositide hydrolysis, for instance, induced by G-protein-coupled-receptor signaling. It plays an important role in neuronal development and function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, May 2009]
GeneCards Summary for TULP3 Gene
TULP3 (TUB Like Protein 3) is a Protein Coding gene. Diseases associated with TULP3 include Hepatorenocardiac Degenerative Fibrosis and Spina Bifida Occulta. Among its related pathways are Signaling by Hedgehog and Signal Transduction. Gene Ontology (GO) annotations related to this gene include enzyme binding and phosphatidylinositol binding. An important paralog of this gene is TUB.
UniProtKB/Swiss-Prot Summary for TULP3 Gene
Negative regulator of the Shh signaling transduction pathway: recruited to primary cilia via association with the IFT complex A (IFT-A) and is required for recruitment of G protein-coupled receptor GPR161 to cilia, a promoter of PKA-dependent basal repression machinery in Shh signaling. Binds to phosphorylated inositide (phosphoinositide) lipids. Both IFT-A- and phosphoinositide-binding properties are required to regulate ciliary G protein-coupled receptor trafficking. Not involved in ciliogenesis. During adipogenesis, regulates ciliary trafficking of FFAR4 in preadipocytes. TULP3_HUMAN,O75386
Molecular function for TULP3 Gene
Biochemistry:
tubby-like protein 3,expressed in spinal cord,brain
Gene Ontology (GO) - Biological Process for TULP3 Gene
neural tube formation
neural tube closure
brain development
dorsal/ventral neural tube patterning
negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning
neural tube development
central nervous system neuron differentiation
embryonic neurocranium morphogenesis
smoothened signaling pathway involved in dorsal/ventral neural tube patterning
negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning
mRNA Expression by UniProt/SwissProt for TULP3 Gene: O75386-TULP3_HUMAN
Tissue specificity: Expressed at high levels in spinal chord.
Evidence on tissue expression from TISSUES for TULP3 Gene
Nervous system(2.5)
https://www.genecards.org/cgi-bin/carddisp.pl?gene=TULP3
TGM6 NC_000020.10:g.2384137G>A
Missense
Uncertain significance
Supporting for pathogenic
Supporting for benign
1/251480 (0.000003976)
https://gnomad.broadinstitute.org/variant/20-2384137-G-A?dataset=gnomad_r2_1
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Entrez Gene Summary for TGM6 Gene
The protein encoded by this gene belongs to the transglutaminase superfamily. It catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins. Mutations in this gene are associated with spinocerebellar ataxia type 35 (SCA35). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
GeneCards Summary for TGM6 Gene
TGM6 (Transglutaminase 6) is a Protein Coding gene. Diseases associated with TGM6 include Spinocerebellar Ataxia 35 and Leukemia, Acute Myeloid. Gene Ontology (GO) annotations related to this gene include protein-glutamine gamma-glutamyltransferase activity. An important paralog of this gene is ENSG00000286022.
UniProtKB/Swiss-Prot Summary for TGM6 Gene
Catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins. TGM3L_HUMAN,O95932
Evidence on tissue expression from TISSUES for TGM6 Gene
Nervous system
Disorders for TGM6 Gene
Spinocerebellar Ataxia
Hereditary Ataxia
Cerebellar Ataxia Type
Spinocerebellar Ataxia, Autosomal Recessive
Cerebellar Disease
Autosomal Dominant Cerebellar Ataxia
https://www.genecards.org/cgi-bin/carddisp.pl?gene=TGM6
ERCC2 NC_000019.9:g.45867321C>A
Missense
1/190010 (0.000005263)
https://gnomad.broadinstitute.org/variant/19-45867321-C-A?dataset=gnomad_r2_1
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Entrez Gene Summary for ERCC2 Gene
The nucleotide excision repair pathway is a mechanism to repair damage to DNA. The protein encoded by this gene is involved in transcription-coupled nucleotide excision repair and is an integral member of the basal transcription factor BTF2/TFIIH complex. The gene product has ATP-dependent DNA helicase activity and belongs to the RAD3/XPD subfamily of helicases. Defects in this gene can result in three different disorders, the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
CIViC Summary for ERCC2 Gene
ERCC2 functions as a DNA repair gene involved in separating the double helix via 5’-3’ helicase activity. It forms a part of the transcription factor II Human (TFIIH) complex and is ATP-dependent. The TFIIH complex is known to be involved in the nucleotide excision repair pathway (NER) which can repair DNA damage caused by chemotherapeutic treatment and basal transcription. ERCC2 variants have been observed in a variety of cancers. A number of studies have suggested ERCC2 variants can act as biomarkers to predict response to neoadjuvant treatment, and cancer prognosis. Additionally the Lys751Gln polymorphism has been observed to increase risk in a number of cancer types; however, results have been conflicting.
GeneCards Summary for ERCC2 Gene
ERCC2 (ERCC Excision Repair 2, TFIIH Core Complex Helicase Subunit) is a Protein Coding gene. Diseases associated with ERCC2 include Cerebrooculofacioskeletal Syndrome 2 and Xeroderma Pigmentosum, Complementation Group D. Among its related pathways are DNA repair pathways, full network and Formation of HIV elongation complex in the absence of HIV Tat. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and protein C-terminus binding. An important paralog of this gene is RTEL1.
Gene Ontology (GO) - Biological Process for ERCC2 Gene
spinal cord development
central nervous system myelin formation
Evidence on tissue expression from TISSUES for ERCC2 Gene
Nervous system
Disorders for ERCC2 Gene
Congenital Nervous Abnormality
https://www.genecards.org/cgi-bin/carddisp.pl?gene=ERCC2
TMEM63A NC_000001.10:g.226054864C>G
Splice Acceptor
1/31396 (0.00003185)
https://gnomad.broadinstitute.org/variant/1-226054864-C-G?dataset=gnomad_r2_1
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Entrez Gene Summary for TMEM63A Gene
Enables mechanosensitive ion channel activity. Predicted to be involved in cation transmembrane transport. Located in centriolar satellite and lysosomal membrane. Implicated in hypomyelinating leukodystrophy. [provided by Alliance of Genome Resources, Apr 2022]
GeneCards Summary for TMEM63A Gene
TMEM63A (Transmembrane Protein 63A) is a Protein Coding gene. Diseases associated with TMEM63A include Leukodystrophy, Hypomyelinating, 19, Transient Infantile and Hypomyelinating Leukodystrophy. Among its related pathways are Innate Immune System. Gene Ontology (GO) annotations related to this gene include nucleotide binding. An important paralog of this gene is TMEM63B.
UniProtKB/Swiss-Prot Summary for TMEM63A Gene
Acts as an osmosensitive calcium-permeable cation channel (PubMed:30382938, PubMed:31587869). Mechanosensitive ion channel that converts mechanical stimuli into a flow of ion (PubMed:30382938, PubMed:31587869). CSCL1_HUMAN,O94886
mRNA differential expression in normal tissues according to GTEx for TMEM63A Gene
This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.3).
https://www.genecards.org/cgi-bin/carddisp.pl?gene=TMEM63A
AR NC_000023.10:g.66766231C>T
X Chromosome
rs767010987 T
Missense
23/148742 (0.0001546)
https://gnomad.broadinstitute.org/variant/X-66766231-C-T?dataset=gnomad_r2_1
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Entrez Gene Summary for AR Gene
The androgen receptor gene is more than 90 kb long and codes for a protein that has 3 major functional domains: the N-terminal domain, DNA-binding domain, and androgen-binding domain. The protein functions as a steroid-hormone activated transcription factor. Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. This gene contains 2 polymorphic trinucleotide repeat segments that encode polyglutamine and polyglycine tracts in the N-terminal transactivation domain of its protein. Expansion of the polyglutamine tract from the normal 9-34 repeats to the pathogenic 38-62 repeats causes spinal bulbar muscular atrophy (SBMA, also known as Kennedy's disease). Mutations in this gene are also associated with complete androgen insensitivity (CAIS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]
GeneCards Summary for AR Gene
AR (Androgen Receptor) is a Protein Coding gene. Diseases associated with AR include Androgen Insensitivity, Partial and Spinal And Bulbar Muscular Atrophy, X-Linked 1. Among its related pathways are Metabolism of proteins and COPI-independent Golgi-to-ER retrograde traffic. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and chromatin binding. An important paralog of this gene is PGR.
UniProtKB/Swiss-Prot Summary for AR Gene
Steroid hormone receptors are ligand-activated transcription factors that regulate eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues (PubMed:19022849). Transcription factor activity is modulated by bound coactivator and corepressor proteins like ZBTB7A that recruits NCOR1 and NCOR2 to the androgen response elements/ARE on target genes, negatively regulating androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Transcription activation is also down-regulated by NR0B2. Activated, but not phosphorylated, by HIPK3 and ZIPK/DAPK3. ANDR_HUMAN,P10275
[Isoform 3]: Lacks the C-terminal ligand-binding domain and may therefore constitutively activate the transcription of a specific set of genes independently of steroid hormones. ANDR_HUMAN,P10275
[Isoform 4]: Lacks the C-terminal ligand-binding domain and may therefore constitutively activate the transcription of a specific set of genes independently of steroid hormones. ANDR_HUMAN,P10275
Evidence on tissue expression from TISSUES for AR Gene
Nervous system(4.6)
Disorders for AR Gene
Motor Neuron Disease
Spinal Disease
Non-Syndromic X-Linked Intellectual Disability
Asperger Syndrome
Spinocerebellar Ataxia
Neuromuscular Disease
Autistic Spectrum Disorder
Autosomal Dominant Cerebellar Ataxia
Nervous System Disease
https://www.genecards.org/cgi-bin/carddisp.pl?gene=AR
CHD9 NC_000016.9:g.53262992A>G
rs367960322 A/G
Missense
0/217238
https://gnomad.broadinstitute.org/variant/16-53262992-A-G?dataset=gnomad_r2_1
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Entrez Gene Summary for CHD9 Gene
Predicted to enable ATP binding activity; ATP-dependent activity, acting on DNA; and DNA binding activity. Predicted to be involved in DNA duplex unwinding and chromatin organization. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
GeneCards Summary for CHD9 Gene
CHD9 (Chromodomain Helicase DNA Binding Protein 9) is a Protein Coding gene. Diseases associated with CHD9 include Choanal Atresia, Posterior and Floating-Harbor Syndrome. Among its related pathways are Circadian Clock and PPARA activates gene expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is CHD7.
UniProtKB/Swiss-Prot Summary for CHD9 Gene
Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA. Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis (By similarity). CHD9_HUMAN,Q3L8U1
SuperPathways for CHD9 Gene
Nervous system development
Evidence on tissue expression from TISSUES for CHD9 Gene
Nervous system(4.8)
https://www.genecards.org/cgi-bin/carddisp.pl?gene=CHD9
KDM1B NC_000006.11:g.18191470A>G
rs1386879766
Missense
connections to Autism
1/152096 (0.000006575)
https://gnomad.broadinstitute.org/variant/6-18191239-A-G?dataset=gnomad_r3
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Entrez Gene Summary for KDM1B Gene
Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]
GeneCards Summary for KDM1B Gene
KDM1B (Lysine Demethylase 1B) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Chromatin organization. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and obsolete histone demethylase activity (H3-dimethyl-K4 specific). An important paralog of this gene is KDM1A.
UniProtKB/Swiss-Prot Summary for KDM1B Gene
Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri-methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-, di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys-36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of histone H4. KDM1B_HUMAN,Q8NB78
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
Brain (Nervous System) - Hypothalamus, Medulla Oblongata
Neural Tube (Nervous System) - Diencephalon
Evidence on tissue expression from TISSUES for KDM1B Gene
Nervous system(4.4)
https://www.genecards.org/cgi-bin/carddisp.pl?gene=KDM1B
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