Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	114798
Gene name	SLIT and NTRK like family member 1
Gene symbol	SLITRK1
Synonyms (NCBI Gene)	LRRC12TTM
Chromosome	13
Chromosome location	13q31.1
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 re

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs191284403	C>A,T	Pathogenic	3 prime UTR variant
rs193302861	G>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (67)

miRTarBase ID	miRNA	Experiments	Reference
MIRT005653	hsa-miR-24-1-5p	GFP reporter assayIn situ hybridizationLuciferase reporter assay	16224024
MIRT018680	hsa-miR-335-5p	Microarray	18185580
MIRT1369719	hsa-miR-15a	CLIP-seq
MIRT1369720	hsa-miR-15b	CLIP-seq
MIRT1369721	hsa-miR-16	CLIP-seq
MIRT1369722	hsa-miR-181a	CLIP-seq
MIRT1369723	hsa-miR-181b	CLIP-seq
MIRT1369724	hsa-miR-181c	CLIP-seq
MIRT1369725	hsa-miR-181d	CLIP-seq
MIRT1369726	hsa-miR-195	CLIP-seq
MIRT1369727	hsa-miR-28-5p	CLIP-seq
MIRT1369728	hsa-miR-29a	CLIP-seq
MIRT1369729	hsa-miR-29b	CLIP-seq
MIRT1369730	hsa-miR-29c	CLIP-seq
MIRT1369731	hsa-miR-3065-5p	CLIP-seq
MIRT1369732	hsa-miR-3139	CLIP-seq
MIRT1369733	hsa-miR-338-5p	CLIP-seq
MIRT1369734	hsa-miR-3973	CLIP-seq
MIRT1369735	hsa-miR-424	CLIP-seq
MIRT1369736	hsa-miR-4262	CLIP-seq
MIRT1369737	hsa-miR-4633-3p	CLIP-seq
MIRT1369738	hsa-miR-4649-5p	CLIP-seq
MIRT1369739	hsa-miR-4699-3p	CLIP-seq
MIRT1369740	hsa-miR-497	CLIP-seq
MIRT1369741	hsa-miR-520g	CLIP-seq
MIRT1369742	hsa-miR-520h	CLIP-seq
MIRT1369743	hsa-miR-708	CLIP-seq
MIRT1369744	hsa-miR-922	CLIP-seq
MIRT2109757	hsa-miR-103a	CLIP-seq
MIRT2109758	hsa-miR-107	CLIP-seq
MIRT2109759	hsa-miR-128	CLIP-seq
MIRT1369719	hsa-miR-15a	CLIP-seq
MIRT1369720	hsa-miR-15b	CLIP-seq
MIRT1369721	hsa-miR-16	CLIP-seq
MIRT1369726	hsa-miR-195	CLIP-seq
MIRT2109760	hsa-miR-27a	CLIP-seq
MIRT2109761	hsa-miR-27b	CLIP-seq
MIRT2109762	hsa-miR-3685	CLIP-seq
MIRT2109763	hsa-miR-384	CLIP-seq
MIRT1369735	hsa-miR-424	CLIP-seq
MIRT1369740	hsa-miR-497	CLIP-seq
MIRT2109764	hsa-miR-5096	CLIP-seq
MIRT2109765	hsa-miR-513a-5p	CLIP-seq
MIRT2109759	hsa-miR-128	CLIP-seq
MIRT2109760	hsa-miR-27a	CLIP-seq
MIRT2109761	hsa-miR-27b	CLIP-seq
MIRT1369733	hsa-miR-338-5p	CLIP-seq
MIRT1369734	hsa-miR-3973	CLIP-seq
MIRT1369739	hsa-miR-4699-3p	CLIP-seq
MIRT2109764	hsa-miR-5096	CLIP-seq
MIRT2109765	hsa-miR-513a-5p	CLIP-seq
MIRT1369741	hsa-miR-520g	CLIP-seq
MIRT1369742	hsa-miR-520h	CLIP-seq
MIRT2627402	hsa-miR-185	CLIP-seq
MIRT2627403	hsa-miR-4306	CLIP-seq
MIRT2627404	hsa-miR-4644	CLIP-seq
MIRT2627405	hsa-miR-498	CLIP-seq
MIRT2627406	hsa-miR-622	CLIP-seq
MIRT2627407	hsa-miR-651	CLIP-seq
MIRT2627408	hsa-miR-767-3p	CLIP-seq
MIRT2627402	hsa-miR-185	CLIP-seq
MIRT2627403	hsa-miR-4306	CLIP-seq
MIRT2627404	hsa-miR-4644	CLIP-seq
MIRT2627405	hsa-miR-498	CLIP-seq
MIRT2627406	hsa-miR-622	CLIP-seq
MIRT2627407	hsa-miR-651	CLIP-seq
MIRT2627408	hsa-miR-767-3p	CLIP-seq

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	19640509, 32296183
GO:0005576	Component	Extracellular region	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006897	Process	Endocytosis	IEA
GO:0007399	Process	Nervous system development	IEA
GO:0007409	Process	Axonogenesis	IBA
GO:0007409	Process	Axonogenesis	IEA
GO:0007416	Process	Synapse assembly	IMP	27273464
GO:0010467	Process	Gene expression	IEA
GO:0016020	Component	Membrane	IEA
GO:0030534	Process	Adult behavior	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042415	Process	Norepinephrine metabolic process	IEA
GO:0042592	Process	Homeostatic process	IEA
GO:0045202	Component	Synapse	IEA
GO:0045202	Component	Synapse	ISS
GO:0050772	Process	Positive regulation of axonogenesis	IMP	23990902
GO:0051965	Process	Positive regulation of synapse assembly	IBA
GO:0051965	Process	Positive regulation of synapse assembly	IEA
GO:0071625	Process	Vocalization behavior	IEA
GO:0098839	Component	Postsynaptic density membrane	IBA
GO:0098839	Component	Postsynaptic density membrane	IEA
GO:0098978	Component	Glutamatergic synapse	IBA
GO:0098978	Component	Glutamatergic synapse	IDA	23345436
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0098978	Component	Glutamatergic synapse	IMP	23345436
GO:0098982	Component	GABA-ergic synapse	IBA
GO:0098982	Component	GABA-ergic synapse	IDA	23345436
GO:0098982	Component	GABA-ergic synapse	IMP	23345436
GO:0099560	Process	Synaptic membrane adhesion	IDA	23345436
GO:0099560	Process	Synaptic membrane adhesion	IMP	23345436
GO:1905606	Process	Regulation of presynapse assembly	IDA	23345436
GO:1905606	Process	Regulation of presynapse assembly	IMP	23345436
GO:1990138	Process	Neuron projection extension	IEA

MIM	HGNC	e!Ensembl
609678	20297	ENSG00000178235

Q96PX8

Protein name

SLIT and NTRK-like protein 1 (Leucine-rich repeat-containing protein 12)

Protein function

It is involved in synaptogenesis and promotes excitatory synapse differentiation (PubMed:27273464, PubMed:27812321). Enhances neuronal dendrite outgrowth (PubMed:16224024, PubMed:19640509). {ECO:0000269|PubMed:16224024, ECO:0000269|PubMed:196405

PDB

4RCA , 4RCW

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13855	LRR_8	83 → 142	Leucine rich repeat	Repeat
PF13855	LRR_8	138 → 189	Leucine rich repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Expressed predominantly in the frontal lobe of the cerebral cortex of the brain. Also expressed in some astrocytic brain tumors such as astrocytomas, oligodendrogliomas, glioblastomas, gangliogliomas and primitive neuroectodermal tumor

Sequence

MLLWILLLETSLCFAAGNVTGDVCKEKICSCNEIEGDLHVDCEKKGFTSLQRFTAPTSQF
YHLFLHGNSLTRLFPNEFANFYNAVSLHMENNGLHEIVPGAFLGLQLVKRLHINNNKIKS
FRKQTFLGLDDLEYLQADFNLLRDIDPGAFQDLNKLEVLILNDNLISTLPANVFQYVPIT
HLDLRGNRLKTLPYEEVLEQIPGIAEILLEDNPWDCTCDLLSLKEWLENIPKNALIGRVV
CEAPTRLQGKDLNETTEQDLCPLKNRVDSSLPAPPAQEETFAPGPLPTPFKTNGQEDHAT
PGSAPNGGTKIPGNWQIKIRPTAAIATGSSRNKPLANSLPCPGGCSCDHIPGSGLKMNCN
NRNVSSLADLKPKLSNVQELFLRDNKIHSIRKSHFVDYKNLILLDLGNNNIATVENNTFK
NLLDLRWLYMDSNYLDTLSREKFAGLQNLEYLNVEYNAIQLILPGTFNAMPKLRILILNN
NLLRSLPVDVFAGVSLSKLSLHNNYFMYLPVAGVLDQLTSIIQIDLHGNPWECSCTIVPF
KQWAERLGSEVLMSDLKCETPVNFFRKDFMLLSNDEICPQLYARISPTLTSHSKNSTGLA
ETGTHSNSYLDTSRVSISVLVPGLLLVFVTSAFTVVGMLVFILRNRKRSKRRDANSSASE
INSLQTVCDSSYWHNGPYNADGAHRVYDCGSHSLSD

Sequence length

696

Interactions

View interactions

	KEGG		Reactome
	Cell adhesion molecules		Receptor-type tyrosine-protein phosphatases

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Tourette syndrome	Pathogenic	rs193302861, rs191284403	RCV000001644 RCV000001646	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichotillomania	Pathogenic	rs193302861	RCV000001645	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
COLOR VISION DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GILLES DE LA TOURETTE SYNDROME	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEROPIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIPHERAL NEUROPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLITRK1-related disorder	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL LUNG CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREATMENT-RESISTANT HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (32)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alopecia	Alopecia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	BEFREE	19640509		★★★★★ ★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar disorder	Pubtator	36085162	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	19153192	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Ductal Breast	Ductal carcinoma of breast	Pubtator	19153192	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Hypertrophic	Hypertrophic cardiomyopathy	Pubtator	27600940	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	18197083, 23333760		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyssomnias	Dyssomnia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Gilles de la Tourette syndrome	Tourette Syndrome	BEFREE	16224024, 16678301, 17035247, 17083340, 17671968, 17702041, 17712845, 18004766, 18698576, 18722020, 19018236, 19105198, 19640509, 19913658, 23333760, 23528612, 23990902, 26317387 View all (3 more)		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gilles de la Tourette syndrome	Tourette Syndrome	LHGDN	16323357, 17712845, 18004766, 18413575, 18722020		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gilles de la Tourette syndrome	Tourette Syndrome	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gilles de la Tourette syndrome	Tourette Syndrome	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Impaired cognition	Impaired Cognition	BEFREE	29326145		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28986383		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	28986383		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental disorders	Mental Disorders	BEFREE	23990902		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myoclonic dystonia	Myoclonic Dystonia	BEFREE	17702041		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	23098292		★★★★★ ★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Tourette syndrome	Tourette Syndrome	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Obsessive compulsive behavior	Obsessive-Compulsive Disorder	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Obsessive-Compulsive Disorder	Obsessive-Compulsive Disorder	BEFREE	18197083, 18722020, 19640509, 23990902, 30377043		★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	30082721		★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	Pubtator	30082721, 36085162	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Disorders	Sleep Disorders	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
ST segment elevation myocardial infarction	ST Segment Elevation Myocardial Infarction	BEFREE	29326145		★★★★★ ★☆☆☆☆ Found in Text Mining only
Tourette Syndrome	Tourette syndrome	Pubtator	35456478	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichotillomania	Trichotillomania	UNIPROT_DG	16224024, 17003809, 27812321		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichotillomania	Trichotillomania	BEFREE	23990902		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichotillomania	Trichotillomania	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichotillomania	Trichotillomania	CTD_human_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichotillomania	Trichotillomania	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

SLITRK1 (SLIT and NTRK like family member 1)