SLITRK6 (SLIT and NTRK like family member 6)

Gene

• Entrez ID: 84189
• Gene name: SLIT and NTRK like family member 6
• Gene symbol: SLITRK6
• Synonyms (NCBI Gene): DFNMYP
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs74591375	C>A,T	Benign-likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs587777069	G>A,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs587777070	G>T	Pathogenic	Stop gained, coding sequence variant
rs587777071	G>A	Pathogenic	Stop gained, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1369824	hsa-miR-3616-5p	CLIP-seq
MIRT1369825	hsa-miR-3647-5p	CLIP-seq
MIRT1369826	hsa-miR-4643	CLIP-seq
MIRT1369827	hsa-miR-466	CLIP-seq
MIRT1369828	hsa-miR-4789-3p	CLIP-seq
MIRT1369829	hsa-miR-573	CLIP-seq
MIRT2109777	hsa-miR-124	CLIP-seq
MIRT2109778	hsa-miR-3714	CLIP-seq
MIRT2109779	hsa-miR-3910	CLIP-seq
MIRT2109780	hsa-miR-4699-3p	CLIP-seq
MIRT2109781	hsa-miR-4798-3p	CLIP-seq
MIRT2109782	hsa-miR-506	CLIP-seq
MIRT2109783	hsa-miR-603	CLIP-seq
MIRT2109784	hsa-miR-642b	CLIP-seq
MIRT2333129	hsa-miR-1179	CLIP-seq
MIRT2109777	hsa-miR-124	CLIP-seq
MIRT2333130	hsa-miR-1251	CLIP-seq
MIRT2333131	hsa-miR-1279	CLIP-seq
MIRT2333132	hsa-miR-135a	CLIP-seq
MIRT2333133	hsa-miR-135b	CLIP-seq
MIRT2333134	hsa-miR-137	CLIP-seq
MIRT2333135	hsa-miR-150	CLIP-seq
MIRT2333136	hsa-miR-15a	CLIP-seq
MIRT2333137	hsa-miR-15b	CLIP-seq
MIRT2333138	hsa-miR-16	CLIP-seq
MIRT2333139	hsa-miR-183	CLIP-seq
MIRT2333140	hsa-miR-186	CLIP-seq
MIRT2333141	hsa-miR-195	CLIP-seq
MIRT2333142	hsa-miR-199a-3p	CLIP-seq
MIRT2333143	hsa-miR-199b-3p	CLIP-seq
MIRT2333144	hsa-miR-2052	CLIP-seq
MIRT2333145	hsa-miR-216a	CLIP-seq
MIRT2333146	hsa-miR-25	CLIP-seq
MIRT2333147	hsa-miR-27a	CLIP-seq
MIRT2333148	hsa-miR-27b	CLIP-seq
MIRT2333149	hsa-miR-300	CLIP-seq
MIRT2333150	hsa-miR-302f	CLIP-seq
MIRT2333151	hsa-miR-3120-3p	CLIP-seq
MIRT2333152	hsa-miR-3129-5p	CLIP-seq
MIRT2333153	hsa-miR-32	CLIP-seq
MIRT2333154	hsa-miR-33a	CLIP-seq
MIRT2333155	hsa-miR-33b	CLIP-seq
MIRT2333156	hsa-miR-3618	CLIP-seq
MIRT2333157	hsa-miR-363	CLIP-seq
MIRT2333158	hsa-miR-365	CLIP-seq
MIRT2333159	hsa-miR-367	CLIP-seq
MIRT2109778	hsa-miR-3714	CLIP-seq
MIRT2333160	hsa-miR-381	CLIP-seq
MIRT2109779	hsa-miR-3910	CLIP-seq
MIRT2333161	hsa-miR-3942-3p	CLIP-seq
MIRT2333162	hsa-miR-3973	CLIP-seq
MIRT2333163	hsa-miR-410	CLIP-seq
MIRT2333164	hsa-miR-424	CLIP-seq
MIRT2333165	hsa-miR-425	CLIP-seq
MIRT2333166	hsa-miR-4264	CLIP-seq
MIRT2333167	hsa-miR-4282	CLIP-seq
MIRT2333168	hsa-miR-4422	CLIP-seq
MIRT2333169	hsa-miR-450b-5p	CLIP-seq
MIRT2333170	hsa-miR-4659a-5p	CLIP-seq
MIRT2333171	hsa-miR-4659b-5p	CLIP-seq
MIRT2333172	hsa-miR-4666-3p	CLIP-seq
MIRT2333173	hsa-miR-4684-5p	CLIP-seq
MIRT2333174	hsa-miR-4696	CLIP-seq
MIRT2333175	hsa-miR-4698	CLIP-seq
MIRT2109780	hsa-miR-4699-3p	CLIP-seq
MIRT2333176	hsa-miR-4699-5p	CLIP-seq
MIRT2333177	hsa-miR-4713-5p	CLIP-seq
MIRT2333178	hsa-miR-4729	CLIP-seq
MIRT2333179	hsa-miR-4731-3p	CLIP-seq
MIRT2333180	hsa-miR-4797-3p	CLIP-seq
MIRT2109781	hsa-miR-4798-3p	CLIP-seq
MIRT2333181	hsa-miR-4801	CLIP-seq
MIRT2333182	hsa-miR-497	CLIP-seq
MIRT2109782	hsa-miR-506	CLIP-seq
MIRT2333183	hsa-miR-507	CLIP-seq
MIRT2333184	hsa-miR-513a-5p	CLIP-seq
MIRT2333185	hsa-miR-520d-5p	CLIP-seq
MIRT2333186	hsa-miR-520g	CLIP-seq
MIRT2333187	hsa-miR-520h	CLIP-seq
MIRT2333188	hsa-miR-524-5p	CLIP-seq
MIRT2333189	hsa-miR-532-3p	CLIP-seq
MIRT2333190	hsa-miR-554	CLIP-seq
MIRT2333191	hsa-miR-557	CLIP-seq
MIRT2333192	hsa-miR-561	CLIP-seq
MIRT2333193	hsa-miR-584	CLIP-seq
MIRT2109783	hsa-miR-603	CLIP-seq
MIRT2333194	hsa-miR-606	CLIP-seq
MIRT2333195	hsa-miR-624	CLIP-seq
MIRT2333196	hsa-miR-630	CLIP-seq
MIRT2109784	hsa-miR-642b	CLIP-seq
MIRT2333197	hsa-miR-656	CLIP-seq
MIRT2333198	hsa-miR-922	CLIP-seq
MIRT2333199	hsa-miR-92a	CLIP-seq
MIRT2333200	hsa-miR-92b	CLIP-seq
MIRT2333201	hsa-miR-934	CLIP-seq
MIRT2333202	hsa-miR-936	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001964	Process	Startle response	IEA
GO:0002088	Process	Lens development in camera-type eye	IEA
GO:0002093	Process	Auditory receptor cell morphogenesis	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	23543054
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0007409	Process	Axonogenesis	IBA
GO:0007409	Process	Axonogenesis	IEA
GO:0007416	Process	Synapse assembly	IEA
GO:0007416	Process	Synapse assembly	IMP	23543054
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007605	Process	Sensory perception of sound	IEA
GO:0008344	Process	Adult locomotory behavior	IEA
GO:0009986	Component	Cell surface	IDA	23543054
GO:0016020	Component	Membrane	IEA
GO:0021562	Process	Vestibulocochlear nerve development	IEA
GO:0031223	Process	Auditory behavior	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042472	Process	Inner ear morphogenesis	IEA
GO:0043010	Process	Camera-type eye development	IEA
GO:0048812	Process	Neuron projection morphogenesis	IEA
GO:0051965	Process	Positive regulation of synapse assembly	IBA
GO:0051965	Process	Positive regulation of synapse assembly	IEA
GO:0060005	Process	Vestibular reflex	IEA
GO:0060007	Process	Linear vestibuloocular reflex	IEA
GO:0060384	Process	Innervation	IEA
GO:0071944	Component	Cell periphery	IEA
GO:0090102	Process	Cochlea development	IEA

Other IDs

• MIM: 609681
• HGNC: 23503
• e!Ensembl: ENSG00000184564

Protein

• UniProt ID: Q9H5Y7
• Protein name: SLIT and NTRK-like protein 6
• Protein function: Regulator of neurite outgrowth required for normal hearing and vision.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13855	LRR_8	143 → 195	Leucine rich repeat	Repeat
  PF13855	LRR_8	364 → 423	Leucine rich repeat	Repeat
  PF13855	LRR_8	411 → 471	Leucine rich repeat	Repeat
  PF13855	LRR_8	459 → 518	Leucine rich repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: In adult brain, highly expressed in putamen with no expression in cerebral cortex. Expressed in adult and fetal lung and fetal liver. Also expressed at high levels in some brain tumors including medulloblastomas and primitive neuroecto
• Sequence:

  MKLWIHLFYSSLLACISLHSQTPVLSSRGSCDSLCNCEEKDGTMLINCEAKGIKMVSEIS
  VPPSRPFQLSLLNNGLTMLHTNDFSGLTNAISIHLGFNNIADIEIGAFNGLGLLKQLHIN
  HNSLEILKEDTFHGLENLEFLQADNNFITVIEPSAFSKLNRLKVLILNDNAIESLPPNIF
  RFVPLTHLDLRGNQLQTLPYVGFLEHIGRILDLQLEDNKWACNCDLLQLKTWLENMPPQS
  IIGDVVCNSPPFFKGSILSRLKKESICPTPPVYEEHEDPSGSLHLAATSSINDSRMSTKT
  TSILKLPTKAPGLIPYITKPSTQLPGPYCPIPCNCKVLSPSGLLIHCQERNIESLSDLRP
  PPQNPRKLILAGNIIHSLMKSDLVEYFTLEMLHLGNNRIEVLEEGSFMNLTRLQKLYLNG
  NHLTKLSKGMFLGLHNLEYLYLEYNAIKEILPGTFNPMPKLKVLYLNNNLLQVLPPHIFS
  GVPLTKVNLKTNQFTHLPVSNILDDLDLLTQIDLEDNPWDCSCDLVGLQQWIQKLSKNTV
  TDDILCTSPGHLDKKELKALNSEILCPGLVNNPSMPTQTSYLMVTTPATTTNTADTILRS
  LTDAVPLSVLILGLLIMFITIVFCAAGIVVLVLHRRRRYKKKQVDEQMRDNSPVHLQYSM
  YGHKTTHHTTERPSASLYEQHMVSPMVHVYRSPSFGPKHLEEEEERNEKEGSDAKHLQRS
  LLEQENHSPLTGSNMKYKTTNQSTEFLSFQDASSLYRNILEKERELQQLGITEYLRKNIA
  QLQPDMEAHYPGAHEELKLMETLMYSRPRKVLVEQTKNEYFELKANLHAEPDYLEVLEQQ
  T

• Sequence length: 841

Pathways

KEGG:

Cell adhesion molecules

Reactome:

Receptor-type tyrosine-protein phosphatases

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Global developmental delay	Pathogenic	rs2501107669	RCV001255410	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
High myopia-sensorineural deafness syndrome	Likely pathogenic; Pathogenic	rs587777069, rs587777070, rs587777071	RCV000074448 RCV000074449 RCV000074450	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SLITRK6-related disorder	Likely pathogenic; Pathogenic	rs2501106009, rs587777069	RCV003397863 RCV003407451	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTOSOMAL RECESSIVE ISOLATED SENSORINEURAL DEAFNESS TYPE DFNB	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast ductal adenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL RECESSIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GESTATIONAL DIABETES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing impairment	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
HEARING LOSS, AUTOSOMAL RECESSIVE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEWY BODY DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MARSHALL SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Auditory neuropathy	Auditory Neuropathy	BEFREE	23946138		★☆☆☆☆ Found in Text Mining only
Auditory neuropathy	Auditory neuropathy	Pubtator	23946138	Associate	★☆☆☆☆ Found in Text Mining only
Autosomal recessive non-syndromic sensorineural deafness type DFNB	Non-Syndromic Sensorineural Deafness	Orphanet			★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	33187236	Associate	★☆☆☆☆ Found in Text Mining only
DEAFNESS AND MYOPIA	DEAFNESS AND MYOPIA	CLINGEN_DG	19936227, 23543054, 23946138		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA	DEAFNESS AND MYOPIA	ORPHANET_DG	23543054		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA	DEAFNESS AND MYOPIA	BEFREE	29551497		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA	DEAFNESS AND MYOPIA	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA	DEAFNESS AND MYOPIA	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS AND MYOPIA	DEAFNESS AND MYOPIA	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing Loss	Hearing loss	Pubtator	23946138	Associate	★☆☆☆☆ Found in Text Mining only
High myopia-sensorineural deafness syndrome	High Myopia-Sensorineural Deafness Syndrome	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	BEFREE	23543054		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	23946138	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	14557068		★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	27530937		★☆☆☆☆ Found in Text Mining only
Profound hearing impairment	Hearing Impairment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	30361509	Associate	★☆☆☆☆ Found in Text Mining only
Respiratory Tract Infections	Respiratory system infectious disease	Pubtator	26317352	Associate	★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	27530937		★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	BEFREE	23543054, 23946138		★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Urothelial Carcinoma	Urothelial Carcinoma	BEFREE	26317352, 30844889		★☆☆☆☆ Found in Text Mining only