IFT52 (intraflagellar transport 52)

Gene

• Entrez ID: 51098
• Gene name: Intraflagellar transport 52
• Gene symbol: IFT52
• Synonyms (NCBI Gene): C20orf9, CGI-53, NGD2, NGD5
• Chromosome: 20
• Chromosome location: 20q13.12
• Summary: This gene encodes a conserved proline-rich protein that is a component of the intraflagellar transport-B (IFT-B) core complex. The encoded protein is essential for the integrity of the IFT-B core complex, and for biosynthesis and maintenance of cilia. Mut

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs748090019	C>T	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant
rs886037869	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs886037870	T>-	Likely-pathogenic, pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT003771	hsa-miR-1-3p	Microarray	15685193
MIRT003771	hsa-miR-1-3p	Microarray	15685193
MIRT1061056	hsa-miR-1827	CLIP-seq
MIRT1061057	hsa-miR-3123	CLIP-seq
MIRT1061058	hsa-miR-3612	CLIP-seq
MIRT1061059	hsa-miR-4311	CLIP-seq
MIRT1061060	hsa-miR-4433	CLIP-seq
MIRT1061061	hsa-miR-4459	CLIP-seq
MIRT1061062	hsa-miR-4695-5p	CLIP-seq
MIRT1061063	hsa-miR-4768-3p	CLIP-seq
MIRT1061064	hsa-miR-520d-5p	CLIP-seq
MIRT1061065	hsa-miR-524-5p	CLIP-seq
MIRT1061066	hsa-miR-650	CLIP-seq
MIRT2014270	hsa-miR-3144-3p	CLIP-seq
MIRT2014271	hsa-miR-3200-5p	CLIP-seq
MIRT2014272	hsa-miR-4682	CLIP-seq
MIRT2014273	hsa-miR-496	CLIP-seq
MIRT2014274	hsa-miR-875-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001841	Process	Neural tube formation	IEA
GO:0001947	Process	Heart looping	IEA
GO:0005515	Function	Protein binding	IPI	31637240
GO:0005515	Function	Protein binding	ISS
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IEA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	NAS	26980730
GO:0005929	Component	Cilium	TAS
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0009953	Process	Dorsal/ventral pattern formation	IEA
GO:0010839	Process	Negative regulation of keratinocyte proliferation	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0030992	Component	Intraciliary transport particle B	IBA
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	ISS
GO:0032391	Component	Photoreceptor connecting cilium	IDA	31637240
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0035720	Process	Intraciliary anterograde transport	IMP	27466190
GO:0035720	Process	Intraciliary anterograde transport	NAS	26980730
GO:0036064	Component	Ciliary basal body	IEA
GO:0042073	Process	Intraciliary transport	IBA
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043616	Process	Keratinocyte proliferation	IEA
GO:0044292	Component	Dendrite terminus	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IMP	27466190
GO:0060271	Process	Cilium assembly	NAS	26980730
GO:0070613	Process	Regulation of protein processing	IEA
GO:0097542	Component	Ciliary tip	IEA
GO:0097542	Component	Ciliary tip	TAS
GO:0097546	Component	Ciliary base	IDA	31637240
GO:0097546	Component	Ciliary base	IEA
GO:0097733	Component	Photoreceptor cell cilium	IEA
GO:1905515	Process	Non-motile cilium assembly	IEA

Other IDs

• MIM: 617094
• HGNC: 15901
• e!Ensembl: ENSG00000101052

Protein

• UniProt ID: Q9Y366
• Protein name: Intraflagellar transport protein 52 homolog (Protein NGD5 homolog)
• Protein function: Involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia (PubMed:27466190). Required for the antero
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09822	ABC_transp_aux	1 → 116	ABC-type uncharacterized transport system	Family

• Sequence:

  MEKELRSTILFNAYKKEIFTTNNGYKSMQKKLRSNWKIQSLKDEITSEKLNGVKLWITAG
  PREKFTAAEFEILKKYLDTGGDVFVMLGEGGESRFDTNINFLLEEYGIMVNNDAVVRNVY
  HKYFHPKEALVSSGVLNREISRAAGKAVPGIIDEESSGNNAQALTFVYPFGATLSVMKPA
  VAVLSTGSVCFPLNRPILAFYHSKNQGGKLAVLGSCHMFSDQYLDKEENSKIMDVVFQWL
  TTGDIHLNQIDAEDPEISDYMMLPYTATLSKRNRECLQESDEIPRDFTTLFDLSIFQLDT
  TSFHSVIEAHEQLNVKHEPLQLIQPQFETPLPTLQPAVFPPSFRELPPPPLELFDLDETF
  SSEKARLAQITNKCTEEDLEFYVRKCGDILGVTSKLPKDQQDAKHILEHVFFQVVEFKKL
  NQEHDIDTSETAFQNNF

• Sequence length: 437

Pathways

Reactome:

Hedgehog 'off' state
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
Short rib-polydactyly syndrome	Likely pathogenic; Pathogenic	rs886037869, rs886037870	RCV000755169 RCV000755168	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short-rib thoracic dysplasia 16 with or without polydactyly	Pathogenic; Likely pathogenic	rs748090019, rs886037869, rs886037870, rs1984074001, rs1983651325, rs530999984	RCV000240043 RCV000240373 RCV000239845 RCV001263447 RCV001263448 RCV001263449	★★★★★ 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
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASPHYXIATING THORACIC DYSPLASIA JEUNE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA	—	Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ 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
GASTROINTESTINAL STROMAL TUMORS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioma susceptibility 1	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IFT52-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Jeune thoracic dystrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SHORT RIB DYSPLASIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ 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
Brachydactyly	Brachydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	26880018, 27466190, 30242358		★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathy	Pubtator	27466190	Associate	★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital anomaly of the kidney	Multicystic renal dysplasia	BEFREE	31042281		★☆☆☆☆ 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	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cranioectodermal dysplasia	Cranioectodermal Dysplasia	BEFREE	31042281		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOECTODERMAL DYSPLASIA 1	Cranioectodermal Dysplasia	ORPHANET_DG	26880018, 27466190		★☆☆☆☆ Found in Text Mining only
CRANIOECTODERMAL DYSPLASIA 1	Cranioectodermal Dysplasia	BEFREE	31042281		★☆☆☆☆ Found in Text Mining only
Craniosynostosis	Craniosynostosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★☆☆☆☆ 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
Hyperopia	Hyperopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypodontia	Hypodontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Long narrow head	Dolichocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Majewski Syndrome	Majewski Syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Microdontia (disorder)	Microdontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	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
Polydactyly	Polydactyly	GENOMICS_ENGLAND_DG	26880018		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	Pubtator	27466190	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	30242358		★☆☆☆☆ Found in Text Mining only
Rhizomelia	Rhizomelia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Saldino-Noonan Syndrome	Asphyxiating thoracic dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Short Rib-Polydactyly Syndrome	Short Rib-Polydactyly Syndrome	BEFREE	27466190		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short Rib-Polydactyly Syndrome	Short Rib-Polydactyly Syndrome	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short Rib-Polydactyly Syndrome	Short Rib-Polydactyly Syndrome	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SHORT-RIB THORACIC DYSPLASIA 16 WITH OR WITHOUT POLYDACTYLY	Short-Rib Thoracic Dysplasia With Or Without Polydactyly	UNIPROT_DG	26880018, 27466190		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SHORT-RIB THORACIC DYSPLASIA 16 WITH OR WITHOUT POLYDACTYLY	Short-Rib Thoracic Dysplasia With Or Without Polydactyly	GENOMICS_ENGLAND_DG	26880018, 30242358, 31042281		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Taurodontism	Taurodontism	HPO_DG			★☆☆☆☆ Found in Text Mining only