Gene Inspector Pro And The Variants That I Found In Connection To My Atypical Neurological Processing
This is a blog post about Gene Inspector Pro and the variants that I found in connection to my atypical neurological processing.
Sergey Andryukhin's Gene Inspector Pro's information
"This tool allows you to explore various aspects of your genetic profile by clicking on panels representing different metabolic pathways and genetic disorders.
Each panel provides a list of genes and their mutations, offering technical information that may be most useful to doctors and geneticists.
Please note that this tool does not offer personalized health advice. If you have concerns about your genetic profile or health, consult with a qualified healthcare provider."
"It finds compromised genes. Its automatic scan leads to discovery of variants with highest probability of impact. It checks metabolic pathways. They include Vitamins, minerals, methylation, autophagy, Energy, Krebs cycle and many more. Genetic variants are sorted, grouped and annotated so that you can see which area in the gene they impact."
https://app.gene-inspector.pro/
https://gene-inspector.pro/dna-analysis
I like that I type in the gene, and Gene Inspector Pro lists all the variants that I have in gene and the consequences and rsID. The rare variants are easily identified, and that includes the novel variants. I like that Gene Inspector shows the allelic depth, genotype quality, and mapping quality of each variant. Sequencing's Genome Explorer doesn't do that.
I find Gene Inspector Pro an excellent, helpful tool to use to deeply explore my genome. I've been using it out of my strong interest in genomics (especially Developmental Neurogenomics) from a medical perspective. I have also been using it out of my strong interest in genomics from an evolutionary perspective.
Thanks to Gene Inspector Pro, I found some very interesting variants that could factor in my atypical neurological processing.
I found two ultra rare variants in coding regions that Varsome site show as having overall In-Silico predictor scores that show potential to be disease causing. They have Combined Annotation Dependent Depletion scores (CADD) scores of more than 20 (top 1% of the most deleterious).
One is a Stop Gained (aka Nonsense) variant in NUAK1, and there are no databases that have any people reported to have the variant. Therefore, it's a novel variant. My mother doesn't have the variant. My father died back in 1993, and so I don't know if I inherited the variant from him. I don't know if it's a de novo mutation. Rare de novo variants of NUAK1 have been associated with Autism, Attention Deficit Hyperactivity Disorder (ADHD), and cognitive impairment. Simons Foundation Autism Research Initiative (SFARI) Gene Database has NUAK1 as being a strong candidate gene for Autism.
The other is a Missense/3 Prime Untranslated (3'UTR) variant in TMEM30A. My mother has the variant too, and so I inherited it from her. Trans-Omics for Precision Medicine (TOPMed) database database is the only database that has reported a perso having the variant. Only one person is found to have the variant. That is out of 150,899 people studied. TOPMed integrates genomic and other data with clinical and environmental data from large cohorts of patients with heart, lung, blood, and sleep (HLBS) disorders. It is a program of National Heart, Lung, and Blood Institute (NHLBI) Center. I emailed them and told them that my mother and I have the variant and about my history and family history of neurological issues and psychiatric issues. I wanted to contribute in any way that I can to help them understand the particular variant. Disruption of TMEM30A has been found to result in cerebellar ataxia and degeneration of Purkinje cells
The Human Phenotypes of both NUAK1 and TMEM30A include:
Focal motor seizures, Focal seixures, Atonic seizures, Supranuclear gaze palsy, Action tremor, Action tremor, Febrile seizures, Visual hallucinations, Dialeptic seizures, Progressive cerebellar ataxia, Truncal ataxia, Dysdiadochokinesis, Poor eye contact, Abnormal eating behavior, Broad-based gait,, EEG with generalized epileptiform discharges, Depression, Anxiety, Impaired social interactions, Insomnia
I gave the following specific information about myself at the Varsome site for each variant profile. It is exactly what I told NHLBI
"I have the variant. I am a neurodivergent male with Dyslexia, Dyspraxia, ADHD. I also have Ataxia. I had auditory therapy, speech therapy, phonics training, and motor skills therapy in early childhood. I was in special education for 3 years in my early childhood. I was mistaken for being intellectually disabled in early childhood but later identified as having above average intelligence. As an adult, I was misdiagnosed as having Schizoaffective Disorder and Bipolar Disorder. I have been diagnosed as having Generalized Anxiety Disorder, Dysthymic Disorder, Social Phobia, Dependent Personality Disorder, and Avoidant Personality Disorder in the past. I am a highly sensitive person that is mainly a picture thinker. I am a visual spatial learner. I have index fingers longer than ring fingers (highly feminine finger ratio) and I have been found to have high estrogen levels."
The other variant is a variant with a 12.3 CADD score in KIAA0319L which is a gene that is in Dyslexia Susceptibility 8 (DYX8) Genetic Locus. It is involved in neuronal migration during development of the cerebral neocortex. Variants in KIAA0319L have been associated with Dyslexia, Reading Disorder, Learning Disability, and Autism.
I found two uncommon variants in regulatory regions with CADD scores of more than 10 (top 10% of the most deleterious)
One is a regulatory region variant with a 16.7 CADD score in HTR1B which is a gene connected to Serotonin. Variants in HTR1B have been associated with Obsessive Compulsive Disorder, Personality Disorders, Mood Disorders, Depression, Anxiety, Autism, ADHD, and Substance Dependence.
The other is a 3'UTR variant with a 13.3 CADD score in NOVA1 which is a gene connected to regulating alternative splicing in neurons. I learned about the gene from watching a youtube presentation video 'Neuro-archealization: Resurrecting Genetic Variations in Human Brain Organoids'. Variants in NOVA1 have been associated with Dementia, Neuromuscular Disease, Epilepsy, and Autism.
All six of the genes have significant expression in the nervous system and overall areas of the brain. They also have significant expresion in vestibular system which creates the sense of balance and spatial orientation for the purpose of coordinating movement with balance.
My variants from Sequencing data in Integrative Genomics Viewer
12-106067419-T-A NC_000012.12:g.106067419T>A
Novel
NUAK1
Stop Gained
40.0
NUAK1 (NUAK Family Kinase 1) is a Protein Coding gene. Diseases associated with NUAK1 include Omphalocele and Supratentorial Primitive Neuroectodermal Tumor. Among its related pathways are Gene expression (Transcription) and Regulation of TP53 Activity. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein tyrosine kinase activity. An important paralog of this gene is NUAK2.
Enables p53 binding activity and protein serine/threonine kinase activity. Involved in several processes, including protein phosphorylation; regulation of cellular senescence; and regulation of myosin-light-chain-phosphatase activity. Located in cytoplasm; microtubule cytoskeleton; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]
https://www.genecards.org/cgi-bin/carddisp.pl?gene=NUAK1
Strong candidate gene for Autism
https://gene.sfari.org/database/human-gene/NUAK1
NUAK1 linked to Attention Deficit Hyperactivity Disorder
https://onlinelibrary.wiley.com/doi/10.1002/ajmg.b.32341
Mayaan Labs Human Phenotypes: Cereberal aneurysm, Focal motor seizures, Focal seizures, Difficulty running, Action tremor, Visual hallucinations, Atonic seizures, Supranuclear gaze palsy, Difficulty climbing stairs, Epileptic encephalopathy, Mutism, Drooling, Progressive cerebellar ataxia, Epileptiform EEG discharges, Absence seizures, Dysdiadochokinesis, Generalized tonic-clonic seizures, Spastic gait, Abnormal eating behavior, Poor eye contact, Febrile seizures, Broad-based gait, Dialeptic seizures, EEG with generalized epileptiform discharges, Depression, Truncal ataxia, Dysmetria, , Impaired social interactions, , Abnormal social behavior, Insomnia, Anxiety, Delayed gross motor development
https://maayanlab.cloud/archs4/gene/NUAK1
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery: Brain (Nervous System) Cerebral Cortex, Oligodendrocyte-like cells
mRNA differential expression in normal tissues according to GTEx: overexpressed in Brain - Frontal Cortex (BA9) (x4.2)
mRNA Expression by UniProt/SwissProt: Tissue specificity: Expressed at high levels in brain
bgee Expression Scores: Brodmann (1909) area 23 (99.13), middle temporal gyrus (98.91), parietal lobe (98.49), postcentral gyrus (98.41), frontal pole (98.40), Brodmann (1909) area 46 (98.34), orbitofrontal cortex (98.00), superior frontal gyrus (97.84), cerebellar vermis (97.44), entorhinal cortex (97.14), cranial nerve II (96.43), medial globus pallidus (96.35), occipital lobe (96.25), pons (96.14), primary visual cortex (95.43), inferior vagus X ganglion (95.29), CA1 field of hippocampus (94.88), corpus callosum (94.47), cortical plate (94.18), dorsal root ganglion (94.09), ventral tegmental area (94.07), superior vestibular nucleus (93.98), lateral globus pallidus (93.50), middle frontal gyrus (93.40), substantia nigra pars reticulata (93.14), subthalamic nucleus (92.99), dorsal motor nucleus of vagus nerve (92.04), dorsolateral prefrontal cortex (91.76), Brodmann (1909) area 9 (90.95), trigeminal ganglion (89.99), lateral nuclear group of thalamus (89.50), right frontal lobe (88.12), cingulate cortex (87.34), anterior cingulate cortex (87.28), ganglionic eminence (85.66), superficial temporal artery (84.60), ventricular zone (83.74), right hemisphere of cerebellum (81.98), spinal cord (80.81), amygdala (79.77), hypothalamus (79.61), C1 segment of cervical spinal cord (79.49), putamen (77.29), caudate nucleus (75.42), nucleus accumbens (73.63), pituitary gland (66.36)
https://www.bgee.org/gene/ENSG00000074590
6-75256290-G-A NC_000006.12:g.75256290G>A my mother has it too
rs1046553575
TMEM30A
Missense, 3'UTR
27.8
1 out of 150,899 (0.00033135%) TOPMed
no frequency any where else including even gnomAD
https://bravo.sph.umich.edu/variant.html?chrom=6&pos=75256290&ref=G&alt=A
TMEM30A (Transmembrane Protein 30A) is a Protein Coding gene. Diseases associated with TMEM30A include Hematologic Cancer and Cerebellar Ataxia, Mental Retardation And Dysequlibrium Syndrome. Among its related pathways is Innate Immune System. An important paralog of this gene is TMEM30B.
Enables aminophospholipid flippase activity. Involved in several processes, including phospholipid transport; positive regulation of transport; and xenobiotic transmembrane transport. Located in endoplasmic reticulum and plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]
https://www.genecards.org/cgi-bin/carddisp.pl?gene=TMEM30A
Mayaan Labs Human Phenotypes: Focal motor seizures, Focal seizures, Visual hallucinations, Atonic seizures, Supranuclear gaze palsy, Action tremor, Absense seizures, Epileptic encephalopathy, Generalized tonic-clonic seizures, Dialeptic seizures, Dysmetria, Intention tremor, Progressive cerebellar ataxia, Cerebral aneurysm, Scanning speech, Spastic gait, Truncal ataxia, Febrile seizures, Anxiety, Dysdiadochokinesis, Depression, Postural instability, Poor eye contact, Agitation, Abnormal eating behavior, Impaired social interactions, Broad-based gait, Drooling, Mutism, Progressive inability to walk, Gaze-evoked nystagmus, Epileptiform EEG discharges, EEG with generalized epileptiform discharges, Generalized myoclonic seizures, Postural tremor, Psychosis, Resting tremor, Gait ataxia, Insomnia, Apathy, Stereotypic behavior, Abnormality of saccadic eye movements, Clumsiness, Hyperacusis, Diminished motivation, Absent speech, Loss of speech
https://maayanlab.cloud/archs4/gene/TMEM30A
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery: Brain (Nervous System) Cerebral Cortex
Evidence on tissue expression from TISSUES: Nervous system(5)
bgee Expression Scores: trigeminal ganglion (98.47), superior vestibular nucleus (98.38), medial globus pallidus (98.33), dorsal root ganglion (98.31), inferior vagus X ganglion (98.03), subthalamic nucleus (98.02), substantia nigra pars compacta (97.91), ventral tegmental area (97.84), lateral nuclear group of thalamus (97.71), substantia nigra pars reticulata (97.61), lateral globus pallidus (97.50), pons (97.50), cerebellar vermis (97.22), prefrontal cortex (97.20), cortical plate (97.18), superficial temporary artery (97.08), occipital (97.05), corpus callosum (96.95), caudate nucleus (96.94), nucleus accumbens (96.90), entorhinal cortex (96.78), dorsolateral prefrontal cortex (96.88), parietal lobe (96.75), putamen (96.71), superior frontal gyrus (96.69), primary visual cortex (96.63), Brodmann (1909) area 9 (96.61), hypothalamus (96.52), postcentral gyrus (96.50), spinal cord (96.48), C1 segment of cervical spinal cord (96.47), ventricular zone (96.39), Ammon's horn (96.37), amygdala (96.31), cingulate cortex (96.25), anteior cingulate cortex (96.24), ganglionic eminence (96.09), Brodmann (1909) area 23 (96.00), right frontal lobe (94.21), cerebellar hemisphere (94.21), right hemisphere of cerebellum (93.00), orbitofrontal cortex (91.60), CA1 field of hippocampus (89.66), Brodmann (1909) area 46 (88.26), middle temporal gyrus (87.63), dorsal motor nucleus of vagus nerve (77.40), cranial nerve II (71.35)
https://www.bgee.org/gene/ENSG00000112697
7-114415771-C-T NC_000007.14:g.114415771C>T
rs752462042
FOXP2
Intron, Promoter (Enhancer-Encode), (Transcription Factor Binding Site - Ensembl)
19.2
13 out of 151,866 (0.008560%) Filter allele frequency is 0.008904%
https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA165205824
FOXP2 (Forkhead Box P2) is a Protein Coding gene. Diseases associated with FOXP2 include Isolated Childhood Apraxia Of Speech and Speech And Communication Disorders. Among its related pathways are Pathways affected in adenoid cystic carcinoma and Wnt / Hedgehog / Notch. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is FOXP4.
This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. It is expressed in fetal and adult brain as well as in several other organs such as the lung and gut. 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. This gene is required for proper development of speech and language regions of the brain during embryogenesis, and may be involved in a variety of biological pathways and cascades that may ultimately influence language development. Mutations in this gene cause speech-language disorder 1 (SPCH1), also known as autosomal dominant speech and language disorder with orofacial dyspraxia. Multiple alternative transcripts encoding different isoforms have been identified in this gene.[provided by RefSeq, Feb 2010]
https://www.genecards.org/cgi-bin/carddisp.pl?gene=FOXP2
GeneCards Human Phenotypes: Delayed speech and language development, Deficit in grammar, Neurodevelopmental delay, Hyperactivity, Short attention span, Autistic behavior, Delayed early-childhood social milestone development, Receptive language delay, Hypernasal speech, Abnormal prosody, Specific learning disability, Oromotor apraxia, Dysarthria, Expressive language delay, Abnormal temper tantrums, Poor gross motor coordination, Poor fine motor coordination, Incomprehensible speech, Poor speech, Drooling, Abnormality of speech or vocalization, Speech apraxia, Cognitive impairment, Abnormality of eye movement, Neurodevelopmental abnormality, Disinhibition, Atypical behavior, Abnormal nervous system physiology, Hearing abnormality, Recurrent maladaptive behavior, Reduced attention regulation, Abnormal communication, Abnormality of movement, Abnormality of coordination, Abnormality of mental function, Abnormal central motor function, Language impairment, Functional abnormality of the inner ear, Poor motor coordination, Apraxia
Mayaan Labs Human Phenotypes: Focal motor seizures, Febrile seizures, Broad-based gait, Gait imbalance, Specific learning disability, Epileptic encephalopathy, Dialeptic seizures, Drooling, Epileptiform EEG discharges, Focal seizures, Progressive inability to walk, EEG with generalized epileptiform discharges, Atonic seizures, Agitation, Inability to walk, Absence seizures, Progressive cerebellar ataxia, Gaze-evoked nystagmus, Absent speech,
https://maayanlab.cloud/archs4/gene/FOXP2
Protein differential expression in normal tissues from HIPED: overexpressed in Fetal Brain (69.0)
mRNA Expression by UniProt/SwissProt: Tissue specificity: Isoform 1 and isoform 6 are expressed in adult and fetal brain, caudate nucleus
Evidence on tissue expression from TISSUES: Nervous system(4.6)
bgee Expression Scores: cortical plate (81.99), ventricular zone (79.88), superficial temporal artery (79.63), Brodmann (1909) area 46 (78.08), ganglionic eminence (77.26), lateral nuclear group of thalamus (72.54), prefrontal cortex (72.13), primary visual cortex (71.92), ventral tegmental area (71.26), ventral tegmental area (71.26), corpus callosum (70.86), Brodmann (1909) area 23 (70.01), subthalamic nucleus (69.39), hypothalamus (69.30), medial globus pallidus (69.07), superior frontal gyrus (69.00), postcentral gyrus (68.71), dorsolateral prefrontal cortex (68.35), caudate nucleus (68.14), nucleus accumbens (68.10), trigeminal ganglion (67.44), Brodmann (1909) area 9 (67.18), substantia nigra (66.63), medulla oblongata (66.53), superior vestibular nucleus (65.50), dorsal root ganglion (65.18), substantia nigra pars compacta (64.81), substantia nigra pars reticulata (64.49), putamen (63.47), entorhinal cortex (62.98), spinal cord (62.66), C1 segment of cervical spinal cord (62.54), cingulate cortex (61.71), anterior cingulate cortex (61.68), right frontal lobe (61.50), Ammon's horn (58.84), amygala (58.81), pituitary gland (56.71), cerebellum cortex (49.78), cerebellar hemisphere (49.47), right hemisphere of cerebellum (49.39)
https://www.bgee.org/gene/ENSG00000128573
1-35452674-A-C NC_000001.11:g.35452674A>C
rs553688873
KIAA0319L
Intron, Promoter flanking region, (Open Chromatin Region - Ensembl)
12.3
132 out of 152,344 (0.08665%) Filter allele frequency is 0.2622%
https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA20633286
KIAA0319L (KIAA0319 Like) is a Protein Coding gene. Diseases associated with KIAA0319L include Limited Scleroderma and Dyslexia. An important paralog of this gene is KIAA0319.
Possible role in axon guidance through interaction with RTN4R. ( K319L_HUMAN,Q8IZA0 ) (Microbial infection) Acts as a receptor for adeno-associated virus and is involved in adeno-associated virus infection through endocytosis system. ( K319L_HUMAN,Q8IZA0 )
https://www.genecards.org/cgi-bin/carddisp.pl?gene=KIAA0319L
Mayaan Labs Human Phenotypes: Aneurysm, Cerebral aneurysm, Difficulty running, Dysmetric saccades, Supranuclear gaze palsy
https://maayanlab.cloud/archs4/gene/KIAA0319L
mRNA Expression by UniProt/SwissProt: Tissue specificity: Expressed in cortical neurons in the brain cortex (at protein level).
Evidence on tissue expression from TISSUES: Nervous system(4.9)
bgee Expression Scores: pituitary gland (94.58), cerebellar hemisphere (93.66), right hemisphere of cerebellum (93.60), corpus callosum (93.56), right frontal lobe (93.29), nucleus accumbens (93.14), cingulate cortex (92.72), anterior cingulate cortex (92.71), prefontal cortex (92.68), laternal nuclear group of thalamus (92.46), caudate nucleus (92.39), amygala (92.14), putamen (92.06), ventricular zone (91.86), Brodmann (1909) area 9 (91.66), cerebellar vermis (91.51), C1 segment of cervical spinal (91.47), trigeminal ganglion (91.10), middle temporal gyrus (90.96), ventral tegmental area (90.75), primary visual cortex (90.62), substantia nigra pars reticulata (90.54), lateral globus pallidus (90.51), superior vestibular nucleus (90.02), dorsal root ganglion (89.84), Ammon's horn (89.93), inferior vagus x ganglion (89.89), subthalamic nucleus (89.65), ganglionic eminence (89.41), Brodmann (1909) area 23 (89.40), substantia nigra pars compacta (89.10), superior frontal gyrus (89.09), cortical plate (88.88), hypothalamus (88.11), parietal lobe (88.00), postcentral gyrus (87.28), medial globus pallidus (86.21), entorhinal cortex (86.04), pons (85.33), Brodmann (1909) area 46 (84.89), orbitofrontal cortex (84.81), superficial temporal artery (83.34)
https://www.bgee.org/gene/ENSG00000142687
6-77464338-C-G NC_000006.12:g.77464338C>G
rs550500898
HTR1B
2KB Upstream, Promoter (Proximal Enhancer: Encode), (Transcription Factor Binding Site - Ensembl)
16.7
405 out of 152,320 (0.2659%) Filter allele frequency is 0.8773%
HTR1B (5-Hydroxytryptamine Receptor 1B) is a Protein Coding gene. Diseases associated with HTR1B include Pineal Dysgerminoma and Malignant Pineal Area Germ Cell Neoplasm. Among its related pathways are GPCR downstream signalling and Class A/1 (Rhodopsin-like receptors). Gene Ontology (GO) annotations related to this gene include G protein-coupled receptor activity and G protein-coupled serotonin receptor activity. An important paralog of this gene is HTR1E.
The protein encoded by this intronless gene is a G-protein coupled receptor for serotonin (5-hydroxytryptamine). Ligand binding activates second messengers that inhibit the activity of adenylate cyclase and manage the release of serotonin, dopamine, and acetylcholine in the brain. The encoded protein may be involved in several neuropsychiatric disorders and therefore is often a target of antidepressant and other psychotherapeutic drugs. [provided by RefSeq, Nov 2015]
https://www.genecards.org/cgi-bin/carddisp.pl?gene=HTR1B
Mayaan Labs Human Phenotypes: Focal motor seizures, Focal seizures, Febrile seizures, Atonic seizures, Epileptic encephalopathy, Absence seizures, Progressive cerebellar ataxia, Visual hallucinations, Action tremor, Dialeptic seizures, Difficulty climbing stairs, Broad-based gait, Gaze-evoked nystagmus, Absent speech, Dysdiadochokinesis, Drooling, Truncal ataxia, Anxiety, Cerebral aneurysm, Poor eye contact, Dysmetria, Scanning speech, Impaired smooth pursuit, Depression, Stereotypic behavior, Supranuclear gaze palsy, Impaired social interactions, Abnormal social behavior, Postural instability, Inappropriate behavior, Abnormal eating behavior
https://maayanlab.cloud/archs4/gene/HTR1B
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery: Brain (Nervous System) Hypothalamus, Hippocampus, Thalamus, Cerebellum, Amygdala
Neural Tube (Nervous System) Metencephalic Alar Plate
Protein differential expression in normal tissues from HIPED: overexpressed in Frontal cortex (69.0)
mRNA Expression by UniProt/SwissProt: Tissue specificity: Detected in cerebral artery smooth muscle cells (at protein level). Detected in brain cortex, striatum, amygdala, medulla, hippocampus, caudate nucleus and putamen.
Evidence on tissue expression from TISSUES: Nervous system(3.4)
bgee Expression Scores: prefrontal cortex (64.88), nucleus accumbens (64.86), caudate nucleus (60.02), putamen (59.82), Brodmann (1909) area 9 (57.54), right frontal lobe (56.55), cingulate cortex (56.17), anterior cingulate cortex (55.77), hypothalamus (54.79), primary visual cortex (52.61), amygala (50.76), substantia nigra (48.88), Ammon's horn (45.18), superior frontal gyrus (44.69), spinal cord (43.70), C1 segment of cervical spinal cord (43.54), hindbrain (38.10), cerebellum (38.04), right hemisphere of cerebellum (37.89), pituitary gland (37.63)
https://www.bgee.org/gene/ENSG00000135312
14-26444154-A-G NC_000014.9:g.26444154A>G
rs17111228
NOVA1
3'UTR
13.3
3,308 out 152,174 (2.174%) Filter allele frequency is 7.399%
https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA258133168
Neuro-archealization: Resurrecting Genetic Variations in Human Brain Organoids
https://www.youtube.com/watch?v=qy7HuFtfbKw
NOVA1 (NOVA Alternative Splicing Regulator 1) is a Protein Coding gene. Diseases associated with NOVA1 include Anus Rhabdomyosarcoma and Partial Fetal Alcohol Syndrome. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important para
This gene encodes a neuron-specific RNA-binding protein, a member of the Nova family of paraneoplastic disease antigens, that is recognized and inhibited by paraneoplastic antibodies. These antibodies are found in the sera of patients with paraneoplastic opsoclonus-ataxia, breast cancer, and small cell lung cancer. Alternatively spliced transcripts encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]log of this gene is NOVA2.
https://www.genecards.org/cgi-bin/carddisp.pl?gene=NOVA1
Mayaan Labs Human Phenotypes: Focal motor seizures, Focal seizures, Atonic seizures, Progressive cerebellar ataxia, Febrile seizures, Absence seizures, Broad-based gait, Visual hallucinations, Drooling, Dialeptic seizures, Generalized tonic-clonic seizures, Progressive inability to walk, Supranuclear gaze palsy, Abnormal eating behavior, Action tremor, Truncal ataxia, Agitation, Poor eye contact, Spastic gait, Dysdiadochokinesis, Depression, Anxiety, Absent speech, Gaze-evoked nystagmus, Impaired social interactions, Abnormal social behavior, Specific learning disability, Gait imbalance, Dysmetria, Poor coordination, Epileptiform EEG discharges, EEG with generalized epileptiform discharges, Inability to walk, Autism, Stereotypic behavior, Scanning speech, Inappropriate behavior, Postural instability, Psychosis, Intention tremor
https://maayanlab.cloud/archs4/gene/NOVA1
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery: Brain (Nervous System) Oligodendrocyte Precursor Cells Forebrain White Matter, Cerebellum
Neural Tube (Nervous System) Primitive Spinal Cord
mRNA differential expression in normal tissues according to GTEx: overexpressed in Brain - Cerebellar Hemisphere (x5.6) and Brain - Cerebellum (x4.1).
Protein differential expression in normal tissues from HIPED: overexpressed in Fetal Brain (43.1) and Frontal cortex (21.8)
mRNA Expression by UniProt/SwissProt: Tissue specificity: Expressed in cerebellum, brain stem, hippocampus, and frontal cortex.
Evidence on tissue expression from TISSUES: Nervous system(4.9)
bgee Expression Scores: cortical plate (95.92), cerebellum (95.46), cerebellar hemisphere (95.43), C1 segment of cervical spinal cord (94.48), hypothalamus (94.48), Brodmann (1909) area 46 (94.28), right hemisphere of cerebellum (94.27), prefrontal cortex (93.99), pons (93.93), ganglionic emininence (93.83), dorsolateral prefrontal cortex (93.64), superior vestibular nucleus (93.57), Brodmann (1909) area 9 (93.43), Brodmann (1909) area 10 (93.09), cingulate cortex (92.73), anterior cingulate cortex (92.67), postcentral gyrus (92.66), right frontal lobe (92.57), substantia nigra (92.50), amygala (92.38), ventricular zone (92.33), corpus callosum (92.20), substantia nigra pars compacta (91.52), putamen (91.46), superior frontal gyrus (91.40), nucleus accumbens (91.20), ventral tegmental area (91.12), Ammon's horn (90.92), frontal pole (90.46), subthalamic nucleus (90.38), orbitofrontal cortex (90.31), lateral nuclear group of thalamus (90.02), dorsal motor nucleus of vagus nerve (89.91), inferior vagus X ganglion (89.35), occipital lobe (88.85), primary visual cortex (88.35), entorhinal cortex (88.09), middle frontal gyrus (86.74), cerebellar vermis (86.42), CA1 field of hippocampus (86.42), lateral globus pallidus (86.17), cranial nerve II (84.56), medial globus pallidus (83.95), middle temporal gyrus (83.15), Brodmann (1909) area 23 (81.69), trigeminal ganglion (75.52), dorsal root ganglion (74.34), superficial temporary artery (68.34)
https://www.bgee.org/gene/ENSG00000139910
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