SLITRK1

SLIT and NTRK like family member 1, the group of SLIT and NTRK like family

Basic information

Region (hg38): 13:83877205-83882474

Previous symbols: [ "LRRC12" ]

Links

ENSG00000178235 ∙ NCBI:114798 ∙ OMIM:609678 ∙ HGNC:20297 ∙ Uniprot:Q96PX8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown
• Tourette syndrome (Limited), mode of inheritance: AD
• trichotillomania (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Trichotillomania; Tourette syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	16224024; 17083340; 18021920; 17712845

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLITRK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLITRK1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			8	1	1	10
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			69	8		77
Total	0	0	118	11	1

Variants in SLITRK1

This is a list of pathogenic ClinVar variants found in the SLITRK1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-83877210-G-T		Tourette syndrome	Uncertain significance (Feb 16, 2018)
13-83877214-A-G		Tourette syndrome	Uncertain significance (Jan 12, 2018)
13-83877231-A-T		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877329-C-T		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877330-A-G		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877373-TA-T		Tourette syndrome	Likely benign (Jun 14, 2016)
13-83877375-A-T		Tourette syndrome	Likely benign (Jun 14, 2016)
13-83877454-G-A		Tourette syndrome	Likely benign (Jan 12, 2018)
13-83877473-T-C		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877535-T-A		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877632-T-C		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877675-A-C		Tourette syndrome	Uncertain significance (Apr 20, 2018)
13-83877679-G-T		Tourette syndrome	Uncertain significance (Jan 15, 2018)
13-83877695-T-G		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877699-T-G		Tourette syndrome	Uncertain significance (Jan 12, 2018)
13-83877751-G-A		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83877845-G-C		Tourette syndrome	Uncertain significance (Jan 12, 2018)
13-83878104-G-C		Tourette syndrome	Uncertain significance (Jan 12, 2018)
13-83878125-C-T		Tourette syndrome	Uncertain significance (Apr 27, 2017)
13-83878182-C-T		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83878257-C-T		Tourette syndrome	Likely benign (Jun 14, 2016)
13-83878267-G-GA		Tourette syndrome	Uncertain significance (Jun 14, 2016)
13-83878283-A-G		Tourette syndrome	Likely benign (Jun 14, 2016)
13-83878320-T-C		Tourette syndrome	Uncertain significance (Jan 13, 2018)
13-83878325-C-A		Tourette syndrome	Uncertain significance (Apr 27, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLITRK1	protein_coding	protein_coding	ENST00000377084	1	5185

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.957	0.0426	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.405	329	350	0.939	0.0000167	4571
Missense in Polyphen		38	88.276	0.43047		1260
Synonymous	-1.77	184	156	1.18	0.00000786	1440
Loss of Function	3.58	2	18.7	0.107	0.00000108	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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:19640509, ECO:0000269|PubMed:27273464, ECO:0000269|PubMed:27812321}.
• Disease: DISEASE: Trichotillomania (TTM) [MIM:613229]: A neuropsychiatric disorder characterized by chronic, repetitive, or compulsive hair pulling resulting in noticeable hair loss. Affected individuals may develop physical complications and often have overlapping psychological disorders, such as Gilles de la Tourette syndrome or obsessive-compulsive disorder. {ECO:0000269|PubMed:16224024, ECO:0000269|PubMed:17003809, ECO:0000269|PubMed:27812321}. Note=The disease may be caused by mutations affecting the gene represented in this entry.
• Pathway: Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Intolerance Scores

• loftool: 0.0322
• rvis_EVS: -0.85
• rvis_percentile_EVS: 11.06

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.837
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.461

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slitrk1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: axonogenesis;synapse assembly;adult behavior;multicellular organism growth;homeostatic process;positive regulation of axonogenesis;positive regulation of synapse assembly;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: extracellular region;plasma membrane;cell junction;synapse;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic density membrane
• Molecular function: protein binding