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    SLITRK1 SLIT and NTRK like family member 1 [ Homo sapiens (human) ]

    Gene ID: 114798, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLITRK1provided by HGNC
    Official Full Name
    SLIT and NTRK like family member 1provided by HGNC
    Primary source
    HGNC:HGNC:20297
    See related
    Ensembl:ENSG00000178235 MIM:609678; AllianceGenome:HGNC:20297
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TTM; LRRC12
    Summary
    This gene encodes a member of the SLITRK protein family. Members of this family are integral membrane proteins that are characterized by two N-terminal leucine-rich repeat (LRR) domains and a C-terminal region that shares homology with trk neurotrophin receptors. However, the protein encoded by this gene lacks the region of homology to neurotrophin receptors. This protein is thought to be involved in neurite outgrowth. Mutations in this gene may be associated with Tourette syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Restricted expression toward brain (RPKM 10.6) See more
    Orthologs
    mouse all
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    Genomic context

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    See SLITRK1 in Genome Data Viewer
    Location:
    13q31.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (83877205..83882474, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (83110000..83115269, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (84451340..84456609, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 67, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:84091305-84092504 Neighboring gene uncharacterized LOC105370286 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:84407388-84407977 Neighboring gene VENT homeobox pseudogene 2 Neighboring gene ubiquitin conjugating enzyme E2 D3 pseudogene 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. In Silico Analysis Identified Putative Pathogenic Missense nsSNPs in Human SLITRK1 Gene. Ali MZ, et al. Genes (Basel), 2022 Apr 11. PMID 35456478, Free PMC Article
    2. SLITRK1 trouble in Tourette's syndrome. Burton A. Lancet Neurol, 2005 Dec. PMID 16323357
    3. SLITRK1 mutations in trichotillomania. Zuchner S, et al. Mol Psychiatry, 2006 Oct. PMID 17003809
    4. Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analyses. Keen-Kim D, et al. Hum Mol Genet, 2006 Nov 15. PMID 17035247
    5. Examination of the SLITRK1 gene in Caucasian patients with Tourette syndrome. Deng H, et al. Acta Neurol Scand, 2006 Dec. PMID 17083340

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In Silico Analysis Identified Putative Pathogenic Missense nsSNPs in Human SLITRK1 Gene.
      Title: In Silico Analysis Identified Putative Pathogenic Missense nsSNPs in Human SLITRK1 Gene.
    2. Genomic Alterations of NTRK, POLE, ERBB2, and Microsatellite Instability Status in Chinese Patients with Colorectal Cancer.
      Title: Genomic Alterations of NTRK, POLE, ERBB2, and Microsatellite Instability Status in Chinese Patients with Colorectal Cancer.
    3. Our results indicate an important influence of the neurodevelopment genes, PBX1, LMX1A, and SLITRK1 in obsessive-compulsive disorder susceptibility
      Title: Gene variations in PBX1, LMX1A and SLITRK1 are associated with obsessive-compulsive disorder and its clinical features.
    4. Altogether, these results demonstrate that Slitrk family proteins regulate synapse formation.
      Title: Slitrk1 is localized to excitatory synapses and promotes their development.
    5. Data provide partial support for the implication of SLITRK1 in the pathogenesis of Tourette syndrome.
      Title: Analysis of SLITRK1 in Japanese patients with Tourette syndrome using a next-generation sequencer.
    6. the N400I variant of SLITRK1 may have a role in obsessive-compulsive disorder
      Title: Characterization of SLITRK1 variation in obsessive-compulsive disorder.
    7. The study of chromosomal aberrations in Tourette syndrome etiology has implicated multiple genes, with SLITRK1 being the most prominent example.
      Title: The genetic basis of Gilles de la Tourette Syndrome.
    8. One of the few genes that has been linked to TS is the SLITRK1 (Slit and Trk-like 1) gene, where four variations have been suggested as possible disease-associated changes
      Title: Sequence analysis of SLITRK1 for var321 in Danish patients with Tourette syndrome and review of the literature.
    9. DM1 motoneuron/muscle cell cocultures showed alterations that are consistent with the known role of SLITRK genes in neurite outgrowth, neuritogenesis, and synaptogenesis; functional defects can be directly attributed to SLITRK misexpression.
      Title: Mutant human embryonic stem cells reveal neurite and synapse formation defects in type 1 myotonic dystrophy.
    10. The study of this study support that SLITRK1 var321 is association to Tourette syndrome.
      Title: Additional support for the association of SLITRK1 var321 and Tourette syndrome.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Trichotillomania
    MedGen: C0040953 OMIM: 613229 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
    EBI GWAS Catalog
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study of irritable vs. elated mania suggests genetic differences between clinical subtypes of bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association study of temperament in bipolar disorder reveals significant associations with three novel Loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ54428, KIAA0918, KIAA1910, RP11-395N17.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in adult behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in homeostatic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron projection extension IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in norepinephrine metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of presynapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of presynapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synaptic membrane adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic membrane adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vocalization behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in GABA-ergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in GABA-ergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in GABA-ergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    SLIT and NTRK-like protein 1
    Names
    leucine-rich repeat-containing protein 12
    slit and trk like gene 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016748.1 RefSeqGene

      Range
      4920..10189
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001281503.2 → NP_001268432.1  SLIT and NTRK-like protein 1 precursor

      See identical proteins and their annotated locations for NP_001268432.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal segment compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AB067497, AI500170, AL355481, DC334447, HY157227
      Consensus CDS
      CCDS9464.1
      UniProtKB/Swiss-Prot
      Q5U5I6, Q96PX8, Q96SF9
      UniProtKB/TrEMBL
      B4DRY1
      Related
      ENSP00000501349.1, ENST00000674365.1
      Conserved Domains (3) summary
      sd00033
      Location:377 → 400
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:375 → 435
      LRR_8; Leucine rich repeat
      cl15307
      Location:212 → 250
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. NM_052910.2 → NP_443142.1  SLIT and NTRK-like protein 1 precursor

      See identical proteins and their annotated locations for NP_443142.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AA677641, AB067497, AI500170, DA240278
      Consensus CDS
      CCDS9464.1
      UniProtKB/Swiss-Prot
      Q5U5I6, Q96PX8, Q96SF9
      UniProtKB/TrEMBL
      B4DRY1
      Related
      ENSP00000366288.2, ENST00000377084.3
      Conserved Domains (3) summary
      sd00033
      Location:377 → 400
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:375 → 435
      LRR_8; Leucine rich repeat
      cl15307
      Location:212 → 250
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      83877205..83882474 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      83110000..83115269 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96PX8.2 GenPept UniProtKB/Swiss-Prot:Q96PX8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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