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

Gene ID: 114798, updated on 2-Nov-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
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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 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)

Genotypes

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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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

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