IFT88 (intraflagellar transport 88)

Gene

• Entrez ID: 8100
• Gene name: Intraflagellar transport 88
• Gene symbol: IFT88
• Synonyms (NCBI Gene): D13S1056E, DAF19, TG737, TTC10, hTg737
• Chromosome: 13
• Chromosome location: 13q12.11
• Summary: This gene encodes a member of the tetratrico peptide repeat (TPR) family. The encoded protein is involved in cilium biogenesis. Mutations of a similar gene in mouse can cause polycystic kidney disease. Several transcript variants encoding distinct isoform

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001822	Process	Kidney development	IBA
GO:0002177	Component	Manchette	ISS
GO:0005515	Function	Protein binding	IPI	25564561, 27767179, 30388400, 32296183
GO:0005730	Component	Nucleolus	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	27767179
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IDA	27623382
GO:0005814	Component	Centriole	IEA
GO:0005814	Component	Centriole	ISS
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IDA	24421332, 27727273, 28428259
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	ISS
GO:0005929	Component	Cilium	NAS	26980730
GO:0005929	Component	Cilium	TAS
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0019894	Function	Kinesin binding	IBA
GO:0030030	Process	Cell projection organization	IEA
GO:0030992	Component	Intraciliary transport particle B	IEA
GO:0030992	Component	Intraciliary transport particle B	IPI	26980730
GO:0030992	Component	Intraciliary transport particle B	ISS
GO:0031514	Component	Motile cilium	IEA
GO:0031514	Component	Motile cilium	ISS
GO:0034021	Process	Response to silicon dioxide	IEA
GO:0034451	Component	Centriolar satellite	IDA
GO:0035720	Process	Intraciliary anterograde transport	NAS	26980730
GO:0036064	Component	Ciliary basal body	IBA
GO:0036064	Component	Ciliary basal body	IDA	17604723, 27767179, 28428259, 28625565, 36606424
GO:0036064	Component	Ciliary basal body	IEA
GO:0036064	Component	Ciliary basal body	ISS
GO:0036126	Component	Sperm flagellum	ISS
GO:0042073	Process	Intraciliary transport	IBA
GO:0042995	Component	Cell projection	IEA
GO:0045171	Component	Intercellular bridge	IDA
GO:0045724	Process	Positive regulation of cilium assembly	IMP	17604723
GO:0060122	Process	Inner ear receptor cell stereocilium organization	IBA
GO:0060271	Process	Cilium assembly	ISS
GO:0060271	Process	Cilium assembly	NAS	26980730
GO:0072686	Component	Mitotic spindle	IDA
GO:0097542	Component	Ciliary tip	IEA
GO:0097542	Component	Ciliary tip	TAS
GO:0097546	Component	Ciliary base	IBA
GO:0097730	Component	Non-motile cilium	IBA
GO:0120212	Component	Sperm head-tail coupling apparatus	ISS
GO:1902017	Process	Regulation of cilium assembly	IEA
GO:1902017	Process	Regulation of cilium assembly	ISS
GO:1905515	Process	Non-motile cilium assembly	IBA
GO:2000785	Process	Regulation of autophagosome assembly	ISS

Other IDs

• MIM: 600595
• HGNC: 20606
• e!Ensembl: ENSG00000032742

Protein

• UniProt ID: Q13099
• Protein name: Intraflagellar transport protein 88 homolog (Recessive polycystic kidney disease protein Tg737 homolog) (Tetratricopeptide repeat protein 10) (TPR repeat protein 10)
• Protein function: Positively regulates primary cilium biogenesis (PubMed:17604723). Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment. {ECO:0000250|UniProtKB:Q61371, ECO:0000269|PubMed:176047
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13181	TPR_8	281 → 314	Tetratricopeptide repeat	Repeat
  PF13174	TPR_6	664 → 696	Tetratricopeptide repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the heart, brain, liver, lung, kidney, skeletal muscle and pancreas. {ECO:0000269|PubMed:7633404}.
• Sequence:

  MMQNVHLAPETDEDDLYSGYNDYNPIYDIEELENDAAFQQAVRTSHGRRPPITAKISSTA
  VTRPIATGYGSKTSLASSIGRPMTGAIQDGVTRPMTAVRAAGFTKAALRGSAFDPLSQSR
  GPASPLEAKKKDSPEEKIKQLEKEVNELVEESCIANSCGDLKLALEKAKDAGRKERVLVR
  QREQVTTPENINLDLTYSVLFNLASQYSVNEMYAEALNTYQVIVKNKMFSNAGILKMNMG
  NIYLKQRNYSKAIKFYRMALDQVPSVNKQMRIKIMQNIGVTFIQAGQYSDAINSYEHIMS
  MAPNLKAGYNLTICYFAIGDREKMKKAFQKLITVPLEIDEDKYISPSDDPHTNLVTEAIK
  NDHLRQMERERKAMAEKYIMTSAKLIAPVIETSFAAGYDWCVEVVKASQYVELANDLEIN
  KAVTYLRQKDYNQAVEILKVLEKKDSRVKSAAATNLSALYYMGKDFAQASSYADIAVNSD
  RYNPAALTNKGNTVFANGDYEKAAEFYKEALRNDSSCTEALYNIGLTYEKLNRLDEALDC
  FLKLHAILRNSAEVLYQIANIYELMENPSQAIEWLMQVVSVIPTDPQVLSKLGELYDREG
  DKSQAFQYYYESYRYFPCNIEVIEWLGAYYIDTQFWEKAIQYFERASLIQPTQVKWQLMV
  ASCFRRSGNYQKALDTYKDTHRKFPENVECLRFLVRLCTDLGLKDAQEYARKLKRLEKMK
  EIREQRIKSGRDGSGGSRGKREGSASGDSGQNYSASSKGERLSARLRALPGTNEPYESSS
  NKEIDASYVDPLGPQIERPKTAAKKRIDEDDFADEELGDDLLPE

• Sequence length: 824

Pathways

Reactome:

Hedgehog 'off' state
Intraflagellar transport
Aggrephagy

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE POLYCYSTIC KIDNEY DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, BASAL CELL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROINTESTINAL STROMAL TUMORS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IFT88-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Jeune thoracic dystrophy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
LIVER NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL OR BEHAVIOURAL DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYCYSTIC KIDNEY, AUTOSOMAL RECESSIVE	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYDACTYLY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYDACTYLY, POSTAXIAL	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet, HPO, Orphanet Disgenet, HPO, Orphanet Disgenet, HPO, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Rod-cone dystrophy	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autosomal Recessive Polycystic Kidney Disease	Polycystic kidney disease	BEFREE	10200981, 19276629, 8597639		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal Recessive Polycystic Kidney Disease	Polycystic kidney disease	CTD_human_DG	8191288, 8608416		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	26202055	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	28489570	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	22974282, 28489570, 35368955	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Basal Cell	Carcinoma	BEFREE	19701205		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Chondrosarcoma	Chondrosarcoma	BEFREE	28586053		★☆☆☆☆ Found in Text Mining only
Chronic myeloproliferative disorder	Myeloproliferative disorder	BEFREE	24658090		★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	22941275		★☆☆☆☆ Found in Text Mining only
Cleft Lip with or without Cleft Palate	Cleft Lip With Or Without Cleft Palate	BEFREE	30953423		★☆☆☆☆ Found in Text Mining only
Cleft Palate	Cleft palate	Pubtator	30953423	Associate	★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cystic kidney	Cystic Kidney Disease	BEFREE	24235270		★☆☆☆☆ Found in Text Mining only
Cystic Kidney Diseases	Cystic Kidney Disease	BEFREE	8597639		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Double Outlet Right Ventricle	Double Outlet Right Ventricle	BEFREE	30289203		★☆☆☆☆ Found in Text Mining only
Emphysema	Emphysema	Pubtator	31419013	Associate	★☆☆☆☆ Found in Text Mining only
Episodic Kinesigenic Dyskinesia 1	Episodic Kinesigenic Dyskinesia	BEFREE	19276629		★☆☆☆☆ Found in Text Mining only
Exencephaly	Anencephaly	BEFREE	22228099		★☆☆☆☆ Found in Text Mining only
Fibrocystic Breast Disease	Breast fibrocystic disease	Pubtator	26202055	Associate	★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Sarcoma	Gastrointestinal stromal tumor	CTD_human_DG	27793025		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Gastrointestinal stromal tumor	CTD_human_DG	27793025		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	37830570	Associate	★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	22974282	Associate	★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	29477141		★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Idiopathic pulmonary fibrosis	Pubtator	29477141, 35608953	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intracranial Aneurysm	Intracranial Aneurysm	BEFREE	28800037		★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	10462374, 20300861, 22974282, 27340352, 28489570, 28663060, 31662980		★☆☆☆☆ Found in Text Mining only
Liver neoplasms	Liver neoplasms	BEFREE	10462374, 22974282, 9362446		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Liver neoplasms	Liver neoplasms	CTD_human_DG	9362446		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of liver	Liver Cancer	BEFREE	20300861, 28663060		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	CTD_human_DG	9362446		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of thyroid	Thyroid cancer	BEFREE	29743590		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	26202055, 28536011, 29743590		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	10462374, 19701205, 20300861, 23246966, 27340352, 28489570, 9362446		★☆☆☆☆ Found in Text Mining only
Nephronophthisis 3	Nephronophthisis	Pubtator	39408701	Associate	★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Orofacial Cleft 1	Orofacial cleft	Pubtator	30953423	Associate	★☆☆☆☆ Found in Text Mining only
Polycystic Kidney Diseases	Polycystic kidney disease	BEFREE	11062270, 7633404		★☆☆☆☆ Found in Text Mining only
Polycystic Kidney, Autosomal Dominant	Polycystic kidney disease	BEFREE	10200981		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	CTD_human_DG	12701101		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Polydactyly	Polydactyly	BEFREE	31009951		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal Degeneration	Retinal degeneration	Pubtator	29978320	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	29978320	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	ORPHANET_DG	29978320		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis pigmentosa	Retinitis Pigmentosa	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Thyroid carcinoma	Thyroid Carcinoma	BEFREE	29743590		★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	BEFREE	29743590		★☆☆☆☆ Found in Text Mining only
Uranostaphyloschisis	Uranostaphyloschisis	BEFREE	30953423		★☆☆☆☆ Found in Text Mining only