IFT43 (intraflagellar transport 43)

Gene

• Entrez ID: 112752
• Gene name: Intraflagellar transport 43
• Gene symbol: IFT43
• Synonyms (NCBI Gene): C14orf179, CED3, RP81, SRTD18
• Chromosome: 14
• Chromosome location: 14q24.3
• Summary: This gene encodes a subunit of the intraflagellar transport complex A (IFT-A). IFT-A is a multiprotein complex that plays an important role in cilia assembly and maintenance by mediating retrograde ciliary transport. Mutations in this gene are a cause of

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140366557	G>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs387907107	A>G	Pathogenic	Non coding transcript variant, initiator codon variant, missense variant
rs769724508	T>A,C	Pathogenic, likely-pathogenic	Non coding transcript variant, initiator codon variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1061028	hsa-miR-1273g	CLIP-seq
MIRT1061029	hsa-miR-3136-5p	CLIP-seq
MIRT1061030	hsa-miR-4427	CLIP-seq
MIRT1061031	hsa-miR-4439	CLIP-seq
MIRT1061032	hsa-miR-4452	CLIP-seq
MIRT1061033	hsa-miR-4513	CLIP-seq
MIRT1061034	hsa-miR-563	CLIP-seq
MIRT1061035	hsa-miR-943	CLIP-seq
MIRT2246468	hsa-miR-33a	CLIP-seq
MIRT2246469	hsa-miR-33b	CLIP-seq
MIRT2246470	hsa-miR-4317	CLIP-seq
MIRT2246471	hsa-miR-4659a-3p	CLIP-seq
MIRT2246472	hsa-miR-4659b-3p	CLIP-seq
MIRT2549993	hsa-miR-520d-5p	CLIP-seq
MIRT2549994	hsa-miR-524-5p	CLIP-seq
MIRT2549995	hsa-miR-556-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25416956, 27932497, 29220510, 32296183, 32814053, 33961781
GO:0005737	Component	Cytoplasm	IEA
GO:0005814	Component	Centriole	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IDA	27932497
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	ISS
GO:0005929	Component	Cilium	NAS	27806291
GO:0005929	Component	Cilium	TAS
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0030030	Process	Cell projection organization	IEA
GO:0030991	Component	Intraciliary transport particle A	IBA
GO:0030991	Component	Intraciliary transport particle A	IDA	20889716, 27932497
GO:0030991	Component	Intraciliary transport particle A	IEA
GO:0030991	Component	Intraciliary transport particle A	IPI	27173435
GO:0034451	Component	Centriolar satellite	IDA
GO:0035721	Process	Intraciliary retrograde transport	IBA
GO:0035721	Process	Intraciliary retrograde transport	IMP	21378380
GO:0035721	Process	Intraciliary retrograde transport	NAS	27806291
GO:0036064	Component	Ciliary basal body	IDA
GO:0042995	Component	Cell projection	IEA
GO:0045171	Component	Intercellular bridge	IDA
GO:0060271	Process	Cilium assembly	IMP	21378380
GO:0060271	Process	Cilium assembly	NAS	27806291
GO:0072686	Component	Mitotic spindle	IDA
GO:0097542	Component	Ciliary tip	TAS

Other IDs

• MIM: 614068
• HGNC: 29669
• e!Ensembl: ENSG00000119650

Protein

• UniProt ID: Q96FT9
• Protein name: Intraflagellar transport protein 43 homolog
• Protein function: As a component of IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is involved in ciliogenesis (PubMed:28400947, PubMed:28973684). Involved in retrograde c
• PDB: 8BBE, 8BBG, 8FGW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15305	IFT43	63 → 193	Intraflagellar transport protein 43	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the retina, predominantly in the photoreceptor outer segment. {ECO:0000269|PubMed:28973684}.
• Sequence:

  MEDLLDLDEELRYSLATSRAKMGRRAQQESAQAENHLNGKNSSLTLTGETSSAKLPRCRQ
  GGWAGDSVKASKFRRKASEEIEDFRLRPQSLNGSDYGGDIPIIPDLEEVQEEDFVLQVAA
  PPSIQIKRVMTYRDLDNDLMKYSAIQTLDGEIDLKLLTKVLAPEHEVREDDVGWDWDHLF
  TEVSSEVLTEWDPLQTEKEDPAGQARHT

• Sequence length: 208

Pathways

Reactome:

Intraflagellar transport

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
Cranioectodermal dysplasia 3	Likely pathogenic; Pathogenic	rs201794999, rs387907107, rs777112610	RCV005005286 RCV000024093 RCV005012297	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of urinary bladder	Likely pathogenic	rs2037525325	RCV005926694	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa 81	Likely pathogenic; Pathogenic	rs201794999, rs777112610	RCV005005286 RCV005012297	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short rib-polydactyly syndrome	Pathogenic; Likely pathogenic	rs769724508, rs1555369050	RCV000851214 RCV000851215	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short-rib thoracic dysplasia 18 with polydactyly	Likely pathogenic; Pathogenic	rs201794999, rs2140102081, rs769724508, rs1555369050, rs777112610	RCV005005286 RCV001822979 RCV000578472 RCV000578473 RCV005012297	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Adrenocortical carcinoma, hereditary	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANGIOEDEMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIOPATHY	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONNECTIVE TISSUE DISEASES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Connective tissue disorder	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ 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
GLIOBLASTOMA MULTIFORME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IFT43-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Jeune thoracic dystrophy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Lung cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MIGRAINE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
URINARY BLADDER CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
URINARY BLADDER CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
URTICARIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA, FAMILIAL, 1 (disorder)	Arrhythmogenic right ventricular cardiomyopathy	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Azoospermia Nonobstructive	Nonobstructive azoospermia	Pubtator	38403804	Associate	★☆☆☆☆ Found in Text Mining only
Brachydactyly	Brachydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital pectus excavatum	Congenital Pectus Excavatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cranioectodermal dysplasia	Cranioectodermal Dysplasia	BEFREE	21378380		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cranioectodermal dysplasia	Cranioectodermal Dysplasia	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cranioectodermal Dysplasia	Craniodiaphyseal dysplasia	Pubtator	32007091	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cranioectodermal dysplasia	Cranioectodermal Dysplasia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 1	Cranioectodermal Dysplasia	BEFREE	21378380		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 1	Cranioectodermal Dysplasia	ORPHANET_DG	22791528		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 1	Cranioectodermal Dysplasia	GENOMICS_ENGLAND_DG	22791528, 26892345, 29896747		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 1	Cranioectodermal Dysplasia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 3	Cranioectodermal Dysplasia	GENOMICS_ENGLAND_DG	21378380, 22791528, 26892345, 29896747		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Craniosynostosis	Craniosynostosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cutis Laxa	Cutis Laxa	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ectodermal Dysplasia	Ectodermal Dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Familial thoracic aortic aneurysm and aortic dissection	Thoracic Aortic Aneurysm And Aortic Dissection	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hodgkin Disease	Hodgkin disease	Pubtator	10329597	Associate	★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypodontia	Hypodontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of teeth	Hypoplasia of teeth	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	26892345		★☆☆☆☆ Found in Text Mining only
LOEYS-DIETZ SYNDROME 4	Loeys-Dietz Syndrome	CLINVAR_DG	1631557, 22943793, 23824657, 24798638, 25835445, 26184463		★☆☆☆☆ Found in Text Mining only
Long narrow head	Dolichocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lymphangioma, Cystic	Cystic hygroma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microdontia (disorder)	Microdontia	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
Myopia	Myopia	BEFREE	26892345		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nephronophthisis	Nephronophthisis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polycystic Kidney Diseases	Polycystic kidney disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	GENOMICS_ENGLAND_DG	28400947		★☆☆☆☆ Found in Text Mining only
POLYDACTYLY, POSTAXIAL	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Radial polydactyly	Radial Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Degeneration	Retinal degeneration	Pubtator	28973684	Associate	★☆☆☆☆ Found in Text Mining only
RETINITIS PIGMENTOSA 81	Retinitis Pigmentosa	UNIPROT_DG	28973684		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RETINITIS PIGMENTOSA 81	Retinitis Pigmentosa	CLINVAR_DG	28973684		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rhizomelia	Rhizomelia	HPO_DG			★☆☆☆☆ Found in Text Mining only
RIENHOFF SYNDROME	Loeys-Dietz syndrome	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Short Rib-Polydactyly Syndrome	Short Rib-Polydactyly Syndrome	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY	Short Rib-Polydactyly Syndrome	GENOMICS_ENGLAND_DG	21378380, 22791528, 26892345, 28400947, 29896747		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY	Short Rib-Polydactyly Syndrome	UNIPROT_DG	28400947		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY	Short Rib-Polydactyly Syndrome	CLINVAR_DG	28400947		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Syndactyly	Syndactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Taurodontism	Taurodontism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Thoracic hypoplasia	Thoracic hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Urticaria	Urticaria	GWASCAT_DG	24236485		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ventricular Dysfunction Left	Ventricular dysfunction	Pubtator	33100131	Associate	★☆☆☆☆ Found in Text Mining only