TCTN3 (tectonic family member 3)

Gene

• Entrez ID: 26123
• Gene name: Tectonic family member 3
• Gene symbol: TCTN3
• Synonyms (NCBI Gene): C10orf61, JBTS18, OFD4, TECT3
• Chromosome: 10
• Chromosome location: 10q24.1
• Summary: This gene encodes a member of the tectonic gene family which functions in Hedgehog signal transduction and development of the neural tube. Mutations in this gene have been associated with Orofaciodigital Syndrome IV and Joubert Syndrom 18. Alternatively s

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs181107730	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs201367852	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, synonymous variant
rs387907273	G>A	Pathogenic	Coding sequence variant, stop gained
rs745688122	C>T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant, initiator codon variant
rs764091969	G>A,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs768525869	AG>-	Pathogenic	Coding sequence variant, frameshift variant
rs781327291	GACTTACCTGTATAGA>-	Likely-pathogenic	Coding sequence variant, intron variant, splice donor variant
rs793888507	CT>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs793888508	C>A,T	Pathogenic	Stop gained, coding sequence variant, intron variant, missense variant
rs1589613893	ATCCTGG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1589623689	C>T	Pathogenic	Splice acceptor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT042807	hsa-miR-339-5p	CLASH	23622248
MIRT1416826	hsa-miR-1252	CLIP-seq
MIRT1416827	hsa-miR-205	CLIP-seq
MIRT1416828	hsa-miR-300	CLIP-seq
MIRT1416829	hsa-miR-381	CLIP-seq
MIRT1416830	hsa-miR-3929	CLIP-seq
MIRT1416831	hsa-miR-4297	CLIP-seq
MIRT1416832	hsa-miR-4419b	CLIP-seq
MIRT1416833	hsa-miR-4476	CLIP-seq
MIRT1416834	hsa-miR-4478	CLIP-seq
MIRT1416835	hsa-miR-4666-3p	CLIP-seq
MIRT1416836	hsa-miR-4803	CLIP-seq
MIRT1416837	hsa-miR-624	CLIP-seq
MIRT1416838	hsa-miR-935	CLIP-seq
MIRT2125019	hsa-miR-139-5p	CLIP-seq
MIRT2125020	hsa-miR-198	CLIP-seq
MIRT2125021	hsa-miR-3134	CLIP-seq
MIRT2125022	hsa-miR-3909	CLIP-seq
MIRT2125023	hsa-miR-4268	CLIP-seq
MIRT2125024	hsa-miR-4328	CLIP-seq
MIRT2125025	hsa-miR-4530	CLIP-seq
MIRT2125026	hsa-miR-455-3p	CLIP-seq
MIRT2125027	hsa-miR-4652-3p	CLIP-seq
MIRT2125024	hsa-miR-4328	CLIP-seq
MIRT2640394	hsa-miR-3920	CLIP-seq
MIRT2640395	hsa-miR-4668-5p	CLIP-seq
MIRT2640396	hsa-miR-548a-3p	CLIP-seq
MIRT2640397	hsa-miR-548e	CLIP-seq
MIRT2640398	hsa-miR-548f	CLIP-seq
MIRT2640399	hsa-miR-759	CLIP-seq
MIRT2640394	hsa-miR-3920	CLIP-seq
MIRT2640395	hsa-miR-4668-5p	CLIP-seq
MIRT2640396	hsa-miR-548a-3p	CLIP-seq
MIRT2640397	hsa-miR-548e	CLIP-seq
MIRT2640398	hsa-miR-548f	CLIP-seq
MIRT2640399	hsa-miR-759	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005634	Component	Nucleus	IDA	17464193
GO:0006915	Process	Apoptotic process	IEA
GO:0007224	Process	Smoothened signaling pathway	IBA
GO:0007224	Process	Smoothened signaling pathway	IMP	22883145
GO:0016020	Component	Membrane	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0043065	Process	Positive regulation of apoptotic process	IDA	17464193
GO:0060170	Component	Ciliary membrane	TAS
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	ISS

Other IDs

• MIM: 613847
• HGNC: 24519
• e!Ensembl: ENSG00000119977

Protein

• UniProt ID: Q6NUS6
• Protein name: Tectonic-3
• Protein function: Part of the tectonic-like complex which is required for tissue-specific ciliogenesis and may regulate ciliary membrane composition (By similarity). May be involved in apoptosis regulation. Necessary for signal transduction through the sonic hedg
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07773	DUF1619	90 → 390	Protein of unknown function (DUF1619)	Family

• Sequence:

  MRTPQLALLQVFFLVFPDGVRPQPSSSPSGAVPTSLELQRGTDGGTLQSPSEATATRPAV
  PGLPTVVPTLVTPSAPGNRTVDLFPVLPICVCDLTPGACDINCCCDRDCYLLHPRTVFSF
  CLPGSVRSSSWVCVDNSVIFRSNSPFPSRVFMDSNGIRQFCVHVNNSNLNYFQKLQKVNA
  TNFQALAAEFGGESFTSTFQTQSPPSFYRAGDPILTYFPKWSVISLLRQPAGVGAGGLCA
  ESNPAGFLESKSTTCTRFFKNLASSCTLDSALNAASYYNFTVLKVPRSMTDPQNMEFQVP
  VILTSQANAPLLAGNTCQNVVSQVTYEIETNGTFGIQKVSVSLGQTNLTVEPGASLQQHF
  ILRFRAFQQSTAASLTSPRSGNPGYIVGKPLLALTDDISYSMTLLQSQGNGSCSVKRHEV
  QFGVNAISGCKLRLKKADCSHLQQEIYQTLHGRPRPEYVAIFGNADPAQKGGWTRILNRH
  CSISAINCTSCCLIPVSLEIQVLWAYVGLLSNPQAHVSGVRFLYQCQSIQDSQQVTEVSL
  TTLVNFVDITQKPQPPRGQPKMDWKWPFDFFPFKVAFSRGVFSQKCSVSPILILCLLLLG
  VLNLETM

• Sequence length: 607

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
Ciliopathy	Likely pathogenic; Pathogenic	rs763132585	RCV005361864	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome 18	Likely pathogenic; Pathogenic	rs1224169161, rs553175533, rs779729881, rs755903123, rs777263669, rs761798713, rs793888508, rs749018985, rs1276774121, rs763132585, rs2139744863, rs373479905, rs2139731384, rs2139749042, rs1221992171, rs2492752964, rs1046385111, rs2492748621, rs750644251, rs763557318, rs2492761413, rs764091969, rs747710152, rs1157302392, rs745688122, rs2492753291, rs2492760878, rs2492743120, rs2097955017, rs1262446492, rs2492761440, rs2492740075, rs1174698466, rs2492790282, rs1202783767, rs387907273, rs768525869, rs1566074908, rs1589613893	RCV001379433 RCV001882726 RCV001896023 RCV001974853 RCV002029922 RCV001898313 RCV001914436 RCV001963032 RCV002007223 RCV002007314 RCV002007409 RCV001941559 RCV001988259 RCV001967151 RCV002043471 RCV002289211 RCV002468883 RCV002634078 RCV002654910 RCV002612326 RCV003104650 RCV002517029 RCV002829115 RCV002863360 RCV002889728 RCV000201547 RCV003007542 RCV003029406 RCV003059382 RCV003050185 RCV003784362 RCV003792379 RCV003806525 RCV003806615 RCV003798618 RCV003807623 RCV003812783 RCV001852611 RCV002513274 RCV000030715 RCV002535034 RCV000804457	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome and related disorders	Likely pathogenic; Pathogenic	rs1224169161, rs755903123, rs761798713, rs793888508, rs373479905, rs745688122, rs2097949677	RCV003987855 RCV005432863 RCV004782815 RCV003492701 RCV003323961 RCV004782310 RCV003988538	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Orofacial-digital syndrome IV	Likely pathogenic; Pathogenic	rs1224169161, rs553175533, rs779729881, rs755903123, rs777263669, rs761798713, rs793888508, rs749018985, rs1276774121, rs763132585, rs2139744863, rs373479905, rs2139731384, rs2139749042, rs1221992171, rs1046385111, rs2492748621, rs750644251, rs763557318, rs2492761413, rs764091969, rs747710152, rs1157302392, rs745688122, rs2492753291, rs2492760878, rs2492743120, rs2097955017, rs1262446492, rs2492761440, rs2492740075, rs1174698466, rs2492790282, rs1202783767, rs2139738553, rs387907273, rs793888507, rs768525869, rs1566074908, rs1589613893, rs1589623689, rs2097923913	RCV001379433 RCV001882726 RCV001896023 RCV001974853 RCV002029922 RCV001898313 RCV001914436 RCV001963032 RCV002007223 RCV002007314 RCV002007409 RCV001941559 RCV001988259 RCV001967151 RCV002043471 RCV002571430 RCV002634078 RCV002654910 RCV002612326 RCV003104650 RCV000190630 RCV002829115 RCV002863360 RCV002889728 RCV000796275 RCV003007542 RCV003029406 RCV003059382 RCV003050185 RCV003784362 RCV003792379 RCV003806525 RCV003806615 RCV003798618 RCV003807623 RCV003812783 RCV000030710 RCV000030712 RCV000030713 RCV000030714 RCV002535034 RCV000804457 RCV001007403 RCV001197442	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
TCTN3-related disorder	Pathogenic; Likely pathogenic	rs761798713, rs373479905, rs1566074908	RCV003401841 RCV004538683 RCV004535803	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CILIOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIVERTICULAR DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Long QT syndrome	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MECKEL SYNDROME	—	CTD, Orphanet CTD, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MECKEL-GRUBER SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME 4	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME IV	—	ClinVar, HPO ClinVar, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME TYPE 4	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME TYPE 6	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME VI	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acquired Kyphoscoliosis	Acquired Kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Acquired porencephaly	Acquired Porencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Addison Disease	Addison`s Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anus, Imperforate	Imperforate anus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Bilateral Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Bone Diseases Developmental	Bone disease	Pubtator	22883145	Associate	★☆☆☆☆ Found in Text Mining only
Bone Diseases, Developmental	Bone Disease	BEFREE	22883145		★☆☆☆☆ Found in Text Mining only
Brachydactyly	Brachydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	22883145	Associate	★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral cortical hemiatrophy	Cerebral cortical hemiatrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Choanal Atresia	Choanal Atresia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	22883145, 23972372		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ciliopathies	Ciliopathy	Pubtator	22883145, 36039988	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clinodactyly	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital absence of kidneys syndrome	Renal agenesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital atresia of rectum	Congenital Atresia Of Rectum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Camptodactyly	Congenital Camptodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Heart Defects	Congenital heart defects	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of lung	Pulmonary hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital kyphoscoliosis	Congenital kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital pectus excavatum	Congenital Pectus Excavatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Exophthalmos	Proptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	22883145, 25118024		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	GENOMICS_ENGLAND_DG	22883145, 25118024		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hamartoma	Hamartoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	33098376	Associate	★☆☆☆☆ Found in Text Mining only
Holoprosencephaly	Holoprosencephaly	BEFREE	28800946		★☆☆☆☆ Found in Text Mining only
Horseshoe Kidney	Horseshoe Kidney	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypothalamic hamartomas	Hypothalamic Hamartomas	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	25118024		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 18	Joubert Syndrome	UNIPROT_DG	22883145		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 18	Joubert Syndrome	GENOMICS_ENGLAND_DG	22883145, 25118024		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 18	Joubert Syndrome	CLINVAR_DG	26092869		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Kidney Diseases Cystic	Kidney disease	Pubtator	22883145	Associate	★☆☆☆☆ Found in Text Mining only
Laryngomalacia	Laryngomalacia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micromelia	Micromelia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Monorchism	Monorchism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural Tube Defect	BEFREE	29725084		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Orofaciodigital syndrome 4	Orofaciodigital syndrome	BEFREE	22883145, 25118024		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 4	Orofaciodigital syndrome	GENOMICS_ENGLAND_DG	22883145, 25118024		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 4	Orofaciodigital syndrome	CLINVAR_DG	22883145		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 4	Orofaciodigital syndrome	ORPHANET_DG	22883145		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 4	Orofaciodigital syndrome	Pubtator	36039988	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome 4	Orofaciodigital syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome type 4	Orofaciodigital Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital syndrome type 6	Orofaciodigital Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME VI	Orofaciodigital syndrome	ORPHANET_DG	22883145		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Orofaciodigital Syndromes	Orofaciodigital syndrome	Pubtator	22883145, 36039988	Associate	★☆☆☆☆ Found in Text Mining only
Osteofibrous Dysplasia	Osteofibrous dysplasia	Pubtator	22883145	Associate	★☆☆☆☆ Found in Text Mining only
Osteofibrous Dysplasia	Osteofibrous Dysplasia	BEFREE	23972372		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	GENOMICS_ENGLAND_DG	22883145		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	Pubtator	33098376	Associate	★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly of toes	Polydactyly Of Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly preaxial type 1	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
POLYDACTYLY, POSTAXIAL	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Porencephalic cyst	Porencephalic cyst	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★☆☆☆☆ Found in Text Mining only
Radial polydactyly	Radial Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Short Rib-Polydactyly Syndrome	Short Rib-Polydactyly Syndrome	BEFREE	22883145		★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Subcortical cerebral atrophy	Subcortical cerebral atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Submucous cleft of hard palate	Submucosal cleft palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly	Syndactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly of the toes	Syndactyly Of The Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ulnar polydactyly of fingers	Postaxial hand polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only