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

Summary

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

Location:: 13q31.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (83877205..83882474, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (83110000..83115269, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (84451340..84456609, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Altogether, these results demonstrate that Slitrk family proteins regulate synapse formation.
Title: Slitrk1 is localized to excitatory synapses and promotes their development.
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.
the N400I variant of SLITRK1 may have a role in obsessive-compulsive disorder
Title: Characterization of SLITRK1 variation in obsessive-compulsive disorder.
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.
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.
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.
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
Tourette syndrome MedGen: C0040517 OMIM: 137580 GeneReviews: Not available	Compare labs
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 EBI GWAS CatalogPubMed
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of irritable vs. elated mania suggests genetic differences between clinical subtypes of bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of temperament in bipolar disorder reveals significant associations with three novel Loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH66461 (e-PCR)
- UniSTS:22855

WI-21805 (e-PCR)
- UniSTS:22856

btcn17872 (e-PCR)
- UniSTS:519248

G31128 (e-PCR)
- UniSTS:48537

WI-20640 (e-PCR)
- UniSTS:40145

D13S865E (e-PCR)
- UniSTS:151527

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 homeostatic process	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	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

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 postsynaptic density membrane	IEA Inferred from Electronic Annotation 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

NG_016748.1 RefSeqGene

Range

4920..10189

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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