CNTN6 (contactin 6)

Gene

• Entrez ID: 27255
• Gene name: Contactin 6
• Gene symbol: CNTN6
• Synonyms (NCBI Gene): NB3
• Chromosome: 3
• Chromosome location: 3p26.3
• Summary: The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connectio

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs773080572	C>A	Likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, 5 prime UTR variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT901723	hsa-miR-3160-5p	CLIP-seq
MIRT901724	hsa-miR-607	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0007155	Process	Cell adhesion	IEA
GO:0007155	Process	Cell adhesion	TAS	9486763
GO:0007156	Process	Homophilic cell adhesion via plasma membrane adhesion molecules	IBA
GO:0007219	Process	Notch signaling pathway	IEA
GO:0007411	Process	Axon guidance	IBA
GO:0007417	Process	Central nervous system development	TAS	9486763
GO:0016020	Component	Membrane	IEA
GO:0030424	Component	Axon	IBA
GO:0042734	Component	Presynaptic membrane	IEA
GO:0045202	Component	Synapse	IBA
GO:0045747	Process	Positive regulation of Notch signaling pathway	IEA
GO:0050808	Process	Synapse organization	IBA
GO:0070593	Process	Dendrite self-avoidance	IBA
GO:0098552	Component	Side of membrane	IEA
GO:0098632	Function	Cell-cell adhesion mediator activity	IBA
GO:0098688	Component	Parallel fiber to Purkinje cell synapse	IEA
GO:0098793	Component	Presynapse	IEA

Other IDs

• MIM: 607220
• HGNC: 2176
• e!Ensembl: ENSG00000134115

Protein

• UniProt ID: Q9UQ52
• Protein name: Contactin-6 (Neural recognition molecule NB-3) (hNB-3)
• Protein function: Contactins mediate cell surface interactions during nervous system development. Participates in oligodendrocytes generation by acting as a ligand of NOTCH1. Its association with NOTCH1 promotes NOTCH1 activation through the released notch intrac
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13927	Ig_3	25 → 104		Domain
  PF13927	Ig_3	124 → 200		Domain
  PF13927	Ig_3	226 → 301		Domain
  PF07679	I-set	318 → 403	Immunoglobulin I-set domain	Domain
  PF07679	I-set	408 → 496	Immunoglobulin I-set domain	Domain
  PF13927	Ig_3	501 → 580		Domain
  PF00041	fn3	599 → 687	Fibronectin type III domain	Domain
  PF00041	fn3	804 → 891	Fibronectin type III domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in nervous system. Highly expressed in cerebellum. Expressed at intermediate level in thalamus, subthalamic nucleus. Weakly expressed in corpus callosum, caudate nucleus and spinal cord.
• Sequence:

  MRLLWKLVILLPLINSSAGDGLLSRPIFTQEPHDVIFPLDLSKSEVILNCAANGYPSPHY
  RWKQNGTDIDFTMSYHYRLDGGSLAINSPHTDQDIGMYQCLATNLLGTILSRKAKLQFAY
  IEDFETKTRSTVSVREGQGVVLLCGPPPHFGDLSYAWTFNDNPLYVQEDNRRFVSQETGN
  LYIAKVEPSDVGNYTCFITNKEAQRSVQGPPTPLVQRTDGVMGEYEPKIEVRFPETIQAA
  KDSSVKLECFALGNPVPDISWRRLDGSPLPGKVKYSKSQAILEIPNFQQEDEGFYECIAS
  NLRGRNLAKGQLIFYAPPEWEQKIQNTHLSIYDNLLWECKASGKPNPWYTWLKNGERLNP
  EERIQIENGTLIITMLNVSDSGVYQCAAENKYQIIYANAELRVLASAPDFSKSPVKKKSF
  VQVGGDIVIGCKPNAFPRAAISWKRGTETLRQSKRIFLLEDGSLKIYNITRSDAGSYTCI
  ATNQFGTAKNTGSLIVKERTVITVPPSKMDVTVGESIVLPCQVSHDPSIEVVFVWFFNGD
  VIDLKKGVAHFERIGGESVGDLMIRNIQLHHSGKYLCTVQTTLESLSAVADIIVRGPPGP
  PEDVQVEDISSTTSQLSWRAGPDNNSPIQIFTIQTRTPFSVGWQAVATVPEILNGKTYNA
  TVVGLSPWVEYEFRVVAGNSIGIGEPSEPSELLRTKASVPVVAPVNIHGGGGSRSELVIT
  WESIPEELQNGEGFGYIIMFRPVGSTTWSKEKVSSVESSRFVYRNESIIPLSPFEVKVGV
  YNNEGEGSLSTVTIVYSGEDEPQLAPRGTSLQSFSASEMEVSWNAIAWNRNTGRVLGYEV
  LYWTDDSKESMIGKIRVSGNVTTKNITGLKANTIYFASVRAYNTAGTGPSSPPVNVTTKK
  SPPSQPPANIAWKLTNSKLCLNWEHVKTMENESEVLGYKILYRQNRQSKTHILETNNTSA
  ELLVPFEEDYLIEIRTVSDGGDGSSSEEIRIPKMSSLSSRGIQFLEPSTHFLSIVIVIFH
  CFAIQPLI

• Sequence length: 1028

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
Autism spectrum disorder	Likely pathogenic	rs1336350265	RCV002465064	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autistic behavior	Likely pathogenic	rs773080572	RCV000663360	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, ADENOID CYSTIC	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CNTN6-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	ClinGen	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTANEOUS MASTOCYTOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GILLES DE LA TOURETTE SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR HYPOTENSION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenoid Cystic Carcinoma	Adenocarcinoma	CTD_human_DG	23685749		★☆☆☆☆ Found in Text Mining only
Anorexia Nervosa	Anorexia	BEFREE	28064060		★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	BEFREE	28064060		★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	27166760	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	27166760, 28064060, 30836150		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic behavior	Autism	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autistic Disorder	Autism	Pubtator	27166760	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	BEFREE	31098770		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	22205951		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar disorder	Pubtator	22205951	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	BEFREE	28064060		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	19509545		★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophy 2	Cone-rod dystrophy	BEFREE	30156464		★☆☆☆☆ Found in Text Mining only
Corneal dystrophy and perceptive deafness	Corneal dystrophy	Pubtator	27166760	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	31518906	Associate	★☆☆☆☆ Found in Text Mining only
Differentiated Thyroid Gland Carcinoma	Thyroid Carcinoma	BEFREE	23015367		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	29983269		★☆☆☆☆ Found in Text Mining only
Gilles de la Tourette syndrome	Tourette Syndrome	BEFREE	28641109		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Developmental Delay	BEFREE	29327201, 31518906		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	19300444		★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington disease	Pubtator	33049985	Associate	★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	BEFREE	19300444		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	28064060, 29327201, 31518906, 31678775		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	31518906, 31678775	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	24871463	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	24871463		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	28064060, 29327201, 30836150, 31678775		★☆☆☆☆ Found in Text Mining only
PARKINSON DISEASE 2, AUTOSOMAL RECESSIVE JUVENILE	Parkinson Disease	BEFREE	26864383		★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychotic disorders	Pubtator	38340697	Associate	★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	28064060, 29983269		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Tourette Syndrome	Tourette syndrome	Pubtator	28641109	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Trisomy	Trisomy	Pubtator	25223409	Associate	★☆☆☆☆ Found in Text Mining only
X-linked hydrocephalus syndrome	Hydrocephalus Syndrome, X-Linked	BEFREE	19300444		★☆☆☆☆ Found in Text Mining only