TCTN1 (tectonic family member 1)

Gene

• Entrez ID: 79600
• Gene name: Tectonic family member 1
• Gene symbol: TCTN1
• Synonyms (NCBI Gene): JBTS13, TECT1
• Chromosome: 12
• Chromosome location: 12q24.11
• Summary: This gene encodes a member of a family of secreted and transmembrane proteins. The orthologous gene in mouse functions downstream of smoothened and rab23 to modulate hedgehog signal transduction. This protein is a component of the tectonic-like complex, w

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs201894544	A>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, intron variant, missense variant
rs367543065	A>G	Pathogenic	Intron variant, splice acceptor variant
rs368907353	C>G,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, synonymous variant, stop gained
rs370336923	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, intron variant, synonymous variant, missense variant
rs730882221	A>G	Likely-pathogenic, pathogenic	Splice acceptor variant
rs751962801	C>T	Pathogenic	Stop gained, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs797046038	TAA>-	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Inframe deletion, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs797046039	G>-	Pathogenic	Non coding transcript variant, genic downstream transcript variant, splice donor variant, coding sequence variant
rs886039436	G>T	Likely-pathogenic	Splice donor variant, genic downstream transcript variant
rs886044606	A>G	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant, intron variant
rs1593376626	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant, intron variant, genic downstream transcript variant, synonymous variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT042925	hsa-miR-324-3p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001701	Process	In utero embryonic development	IEA
GO:0001841	Process	Neural tube formation	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005615	Component	Extracellular space	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0008589	Process	Regulation of smoothened signaling pathway	IEA
GO:0016020	Component	Membrane	IEA
GO:0021523	Process	Somatic motor neuron differentiation	IEA
GO:0021537	Process	Telencephalon development	IEA
GO:0021904	Process	Dorsal/ventral neural tube patterning	IEA
GO:0021956	Process	Central nervous system interneuron axonogenesis	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0035869	Component	Ciliary transition zone	IEA
GO:0036038	Component	MKS complex	IBA
GO:0036038	Component	MKS complex	IEA
GO:0036038	Component	MKS complex	ISS
GO:0042995	Component	Cell projection	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	ISS
GO:1904491	Process	Protein localization to ciliary transition zone	IBA
GO:1904491	Process	Protein localization to ciliary transition zone	IEA

Other IDs

• MIM: 609863
• HGNC: 26113
• e!Ensembl: ENSG00000204852

Protein

• UniProt ID: Q2MV58
• Protein name: Tectonic-1
• Protein function: Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Regulator of Hedgehog (Hh), req
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07773	DUF1619	78 → 387	Protein of unknown function (DUF1619)	Family

• Sequence:

  MRPRGLPPLLVVLLGCWASVSAQTDATPAVTTEGLNSTEAALATFGTFPSTRPPGTPRAP
  GPSSGPRPTPVTDVAVLCVCDLSPAQCDINCCCDPDCSSVDFSVFSACSVPVVTGDSQFC
  SQKAVIYSLNFTANPPQRVFELVDQINPSIFCIHITNYKPALSFINPEVPDENNFDTLMK
  TSDGFTLNAESYVSFTTKLDIPTAAKYEYGVPLQTSDSFLRFPSSLTSSLCTDNNPAAFL
  VNQAVKCTRKINLEQCEEIEALSMAFYSSPEILRVPDSRKKVPITVQSIVIQSLNKTLTR
  REDTDVLQPTLVNAGHFSLCVNVVLEVKYSLTYTDAGEVTKADLSFVLGTVSSVVVPLQQ
  KFEIHFLQENTQPVPLSGNPGYVVGLPLAAGFQPHKGSGIIQTTNRYGQLTILHSTTEQD
  CLALEGVRTPVLFGYTMQSGCKLRLTGALPCQLVAQKVKSLLWGQGFPDYVAPFGNSQAQ
  DMLDWVPIHFITQSFNRKDSCQLPGALVIEVKWTKYGSLLNPQAKIVNVTANLISSSFPE
  ANSGNERTILISTAVTFVDVSAPAEAGFRAPPAINARLPFNFFFPFV

• Sequence length: 587

Pathways

Reactome:

Anchoring of the basal body to the plasma membrane

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
Clear cell carcinoma of kidney	Likely pathogenic	rs760922371	RCV005937371	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Pathogenic	rs730882221	RCV000162131	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome	Likely pathogenic; Pathogenic	rs200241085, rs1165243207, rs200863258, rs2136195903, rs1398514249, rs1353535488, rs766816100, rs2136172776, rs756402483, rs748215804, rs1303964272, rs374065616, rs1475200635, rs2548754386, rs751962801, rs2067211703, rs2548929536, rs2548796089, rs2548901989, rs1456431690, rs1420275854, rs769457761, rs757348545, rs2065847886, rs2066300090, rs2066879614, rs2066579666, rs2066444872	RCV002032552 RCV003772349 RCV002543304 RCV001915855 RCV002007152 RCV001942140 RCV001879311 RCV001883240 RCV002030713 RCV001940214 RCV003108852 RCV002586667 RCV002575567 RCV002824414 RCV003765338 RCV005228001 RCV003785532 RCV003782951 RCV003808061 RCV003797294 RCV003809329 RCV003813383 RCV001856156 RCV001069111 RCV001035552 RCV001035441 RCV001035553 RCV001219098	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome 13	Pathogenic; Likely pathogenic	rs1275375836, rs200241085, rs2136171586, rs1165243207, rs1398514249, rs748215804, rs2136006298, rs730882221, rs2548832773, rs797046039, rs751962801, rs886039436, rs760922371, rs367543065, rs1593376626	RCV001335645 RCV002471121 RCV001844404 RCV001825289 RCV005002711 RCV002300621 RCV002237204 RCV000201626 RCV002471490 RCV000194752 RCV000207452 RCV003989511 RCV003984992 RCV000023788 RCV001029772	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome and related disorders	Likely pathogenic	rs200863258, rs1566003392, rs749481321, rs2067211703	RCV001844532 RCV002238589 RCV003123410 RCV003331775	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Lung cancer	Likely pathogenic; Pathogenic	rs886039436	RCV005895437	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of urinary bladder	Likely pathogenic	rs200241085	RCV005915964	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Meckel-Gruber syndrome	Likely pathogenic; Pathogenic	rs200241085, rs1165243207, rs200863258, rs2136195903, rs1398514249, rs1353535488, rs766816100, rs2136172776, rs756402483, rs748215804, rs1303964272, rs374065616, rs1475200635, rs2548754386, rs751962801, rs2067211703, rs2548929536, rs2548796089, rs2548901989, rs1456431690, rs1420275854, rs769457761, rs757348545, rs2065847886, rs2066300090, rs2066879614, rs2066579666, rs2066444872	RCV002032552 RCV003772349 RCV002543304 RCV001915855 RCV002007152 RCV001942140 RCV001879311 RCV001883240 RCV002030713 RCV001940214 RCV003108852 RCV002586667 RCV002575567 RCV002824414 RCV003765338 RCV005228001 RCV003785532 RCV003782951 RCV003808061 RCV003797294 RCV003809329 RCV003813383 RCV001856156 RCV001069111 RCV001035552 RCV001035441 RCV001035553 RCV001219098	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
TCTN1-related disorder	Likely pathogenic; Pathogenic	rs2136045792, rs2548884767, rs757348545	RCV004751032 RCV003391503 RCV003411716	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Typical Joubert syndrome MRI findings	Pathogenic	rs730882221	RCV000162131	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL DISABILITIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental disorder	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JOUBERT SYNDROME 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MECKEL SYNDROME	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ 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
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	28123172		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	28123172		★☆☆☆☆ Found in Text Mining only
Congenital cerebral hernia	Congenital Cerebral Hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	31297133	Associate	★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	21725307		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	ORPHANET_DG	21725307		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	GENOMICS_ENGLAND_DG	21725307, 22693042, 26489806, 28631893		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	CTD_human_DG	21725307		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioblastoma	Glioblastoma	BEFREE	25304031		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	25304031	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	25304031		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	25737023		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Developmental Delay	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Holoprosencephaly	Holoprosencephaly	BEFREE	28800946		★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	22693042		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Joubert syndrome	Joubert syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome 1	Joubert Syndrome	CTD_human_DG	21725307		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Joubert syndrome 1	Joubert Syndrome	ORPHANET_DG	21725307		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JOUBERT SYNDROME 13	Joubert Syndrome	GENOMICS_ENGLAND_DG	21725307, 22693042		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 13	Joubert Syndrome	CLINVAR_DG	26092869		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	26844847, 29042969		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	26310786		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	26252641		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of thyroid	Thyroid cancer	BEFREE	29042969		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	28123172		★☆☆☆☆ Found in Text Mining only
Meckel syndrome type 1	Meckel Syndrome	BEFREE	28631893		★☆☆☆☆ Found in Text Mining only
Meckel-Gruber syndrome	Meckel-Gruber Syndrome	BEFREE	28631893		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neoplasms	Neoplasms	BEFREE	31297133		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	30008857		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Occipital Encephalocele	Occipital Encephalocele	BEFREE	25118024		★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculovestibuloauditory syndrome	Oculovestibuloauditory Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oral cleft	Oral cleft	HPO_DG			★☆☆☆☆ Found in Text Mining only
OROFACIODIGITAL SYNDROME VI	Orofaciodigital syndrome	BEFREE	28631893		★☆☆☆☆ Found in Text Mining only
Orofaciodigital Syndromes	Orofaciodigital syndrome	BEFREE	28631893		★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	26844847, 29042969		★☆☆☆☆ Found in Text Mining only
Polydactyly of toes	Polydactyly Of Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	26310786		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	26310786	Associate	★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	BEFREE	25118024		★☆☆☆☆ Found in Text Mining only
Situs inversus totalis	Situs Inversus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	31297133		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	34859261	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	26252641		★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Thyroid carcinoma	Thyroid Carcinoma	BEFREE	29042969		★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	BEFREE	29042969		★☆☆☆☆ Found in Text Mining only