SLITRK6 SLIT and NTRK like family member 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLITRK6provided by HGNC
Official Full Name: SLIT and NTRK like family member 6provided by HGNC
Primary source: HGNC:HGNC:23503
See related: Ensembl:ENSG00000184564 MIM:609681; AllianceGenome:HGNC:23503
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: DFNMYP
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. This protein functions as a regulator of neurite outgrowth required for normal hearing and vision. Mutations in this gene are a cause of myopia and deafness. [provided by RefSeq, Dec 2014]
Expression: Biased expression in urinary bladder (RPKM 12.2), salivary gland (RPKM 7.4) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

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 (85792790..85799419, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (85041234..85047862, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (86366925..86373554, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Differential expression of SLITRK6 gene as a potential therapeutic target for urothelial carcinoma in particular upper tract cancer.
Title: Differential expression of SLITRK6 gene as a potential therapeutic target for urothelial carcinoma in particular upper tract cancer.
SLITRK6 promotes the progression of lung adenocarcinoma by regulating PI3K/AKT/mTOR signaling and Warburg effect.
Title: SLITRK6 promotes the progression of lung adenocarcinoma by regulating PI3K/AKT/mTOR signaling and Warburg effect.
The role of SLITRK6 in the pathogenesis of Tourette syndrome: From the conclusion of a family-based study in the Chinese Han population.
Title: The role of SLITRK6 in the pathogenesis of Tourette syndrome: From the conclusion of a family-based study in the Chinese Han population.
Analysis of two exons of SLITRK6 gene in a Moroccan family identify a novel single deleterious mutation c.696delG, p.Trp232Cysfs*10 at homozygous state in the exon 2 of the SLITRK6, a gene reported to cause deafness and myopia in various populations.
Title: A novel mutation in SLITRK6 causes deafness and myopia in a Moroccan family.
Human cytomegalovirus downregulates SLITRK6 expression through IE2.
Title: Human cytomegalovirus downregulates SLITRK6 expression through IE2.
SLITRK6 gene nonsense mutation is associated with progressive auditory neuropathy in humans.
Title: A homozygous SLITRK6 nonsense mutation is associated with progressive auditory neuropathy in humans.
SLITRK6 plays a crucial role in the development of normal hearing as well as vision in humans and in mice and that its disruption leads to a syndrome characterized by severe myopia and deafness.
Title: SLITRK6 mutations cause myopia and deafness in humans and mice.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
High myopia-sensorineural deafness syndrome MedGen: C3806275 OMIM: 221200 GeneReviews: Deafness and Myopia Syndrome	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of irritable vs. elated mania suggests genetic differences between clinical subtypes of bipolar disorder. 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

MARC_10014-10015:996678886:1 (e-PCR)
- UniSTS:267013

RH70006 (e-PCR)
- UniSTS:69386

SLITRK6 (e-PCR)
- UniSTS:505363

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in adult locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in auditory behavior	IEA Inferred from Electronic Annotation more info
involved_in auditory receptor cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cochlea development	IEA Inferred from Electronic Annotation more info
involved_in innervation	IEA Inferred from Electronic Annotation more info
involved_in lens development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in linear vestibuloocular reflex	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in startle response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vestibulocochlear nerve development	IEA Inferred from Electronic Annotation more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: SLIT and NTRK-like protein 6

Names: 4832410J21Rik; slit and trk like gene 6

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_041801.2 RefSeqGene

Range

12265..18894

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1357

mRNA and Protein(s)

NM_032229.3 → NP_115605.2 SLIT and NTRK-like protein 6 precursor

See identical proteins and their annotated locations for NP_115605.2

Status: REVIEWED

Source sequence(s)

AL162373

Consensus CDS

CCDS41903.1

UniProtKB/Swiss-Prot

A8K9S8, Q495Q0, Q6AW93, Q9H5Y7, Q9HAA8, Q9NT60

Related

ENSP00000495507.1, ENST00000647374.2

Conserved Domains (4) summary

smart00082
Location:517 → 567

LRRCT; Leucine rich repeat C-terminal domain

sd00033
Location:94 → 113

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:411 → 471

LRR_8; Leucine rich repeat

cl26793
Location:69 → 494

PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional