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:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IBA	21873635
GO:0005929	Component	Cilium	IBA	21873635
GO:0005929	Component	Cilium	TAS
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0008022	Function	Protein C-terminus binding	ISS
GO:0009953	Process	Dorsal/ventral pattern formation	IEA
GO:0030992	Component	Intraciliary transport particle B	IBA	21873635
GO:0030992	Component	Intraciliary transport particle B	ISS
GO:0031514	Component	Motile cilium	ISS
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0035720	Process	Intraciliary anterograde transport	IMP	27466190
GO:0035735	Process	Intraciliary transport involved in cilium assembly	TAS
GO:0036064	Component	Ciliary basal body	IEA
GO:0042073	Process	Intraciliary transport	IBA	21873635
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0044292	Component	Dendrite terminus	IEA
GO:0050680	Process	Negative regulation of epithelial cell proliferation	IEA
GO:0060271	Process	Cilium assembly	IBA	21873635
GO:0060271	Process	Cilium assembly	IMP	27466190
GO:0070613	Process	Regulation of protein processing	IEA
GO:0097542	Component	Ciliary tip	TAS
GO:0097546	Component	Ciliary base	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

Causal
Disease term	Disease name	dbSNP ID	References
Asphyxiating thoracic dystrophy	Saldino-Noonan Syndrome	rs137853115, rs137853025, rs1565310938, rs137853028, rs137853029, rs137853030, rs137853031, rs137853032, rs431905499, rs137853033, rs137853034, rs137853035, rs431905500, rs483352907, rs387906980, rs387906982, rs185089786, rs387907060, rs397514637, rs431905507, rs138004478, rs786205645, rs794727944, rs780539887, rs201948500, rs769975073, rs374356079, rs879255656, rs879255655, rs864622358, rs200460601, rs755883373, rs754919042, rs886039815, rs886039812, rs758522600, rs886039795, rs201037487, rs771487311, rs1043384862, rs562139820, rs771003300, rs552436294, rs943680446, rs431905497, rs368631447, rs759086770, rs775836730, rs1456300819, rs1554478948, rs1554770620, rs1554771066, rs555339053, rs896105030, rs755305630, rs771511132, rs762873763, rs764769351, rs369614706, rs371011047, rs748906528, rs1555042801, rs1555043520, rs373335226, rs1555051720, rs745870321, rs1555052524, rs901629870, rs1555054771, rs1461272672, rs780855765, rs1555060411, rs1243999036, rs1555060940, rs1555061228, rs747348765, rs1322884865, rs1555062340, rs1555063811, rs537704873, rs1386343205, rs762588952, rs1350329646, rs1555064376, rs1555066796, rs200614421, rs964711006, rs1196317554, rs747857715, rs1214801816, rs371940321, rs1555068270, rs1555071484, rs1555071503, rs776407305, rs373924400, rs1555077194, rs780600124, rs1261505725, rs200710887, rs181011657, rs1555082470, rs1453448143, rs369658526, rs766816050, rs756811136, rs368654019, rs1223907858, rs759549373, rs760214276, rs1565317399, rs1565329461, rs767846762, rs1565359085, rs751891969, rs1565390180, rs1384888093, rs1565394086, rs1565438488, rs561778796, rs373536938, rs767206815, rs371932985, rs372878677, rs1577822861, rs1327583103, rs1862810311
Brachydactyly	Brachydactyly	rs121908949, rs28937580, rs121909082, rs104894122, rs863223289, rs863223290, rs104894121, rs1587657302, rs863223292, rs74315386, rs74315387, rs28936397, rs753691079, rs121909348, rs121917852, rs121917853, rs121917854, rs121917855, rs121917859, rs121917861, rs267606873, rs267606872, rs267606985, rs267606986, rs267606987, rs267606988, rs28933082, rs397514519, rs869025613, rs869025614, rs886039878, rs1553540620, rs1057518333, rs1948841937, rs1948868228, rs1948842030, rs1948842142
Cranioectodermal dysplasia	CRANIOECTODERMAL DYSPLASIA 1, Cranioectodermal dysplasia	rs397515534, rs267607174, rs397515334, rs267607175, rs267607191, rs267607192, rs267607193, rs387906980, rs387906981, rs387907107, rs387907169, rs199952377, rs397515533, rs397515567, rs79436363, rs786205566, rs786205567, rs776099605, rs765513105, rs200140363, rs183758503, rs1553313859, rs746128772, rs1559869525, rs138329739, rs755005244, rs1185183557, rs751290509	26880018, 27466190
Craniosynostosis	Craniosynostosis	rs104893895, rs587777006, rs587777007, rs587777008, rs587777010, rs864321680, rs864321681, rs1057517670, rs1064794325, rs1555750816, rs1599823350
Gastrointestinal stromal tumor	Gastrointestinal Stromal Tumors, Gastrointestinal Stromal Sarcoma	rs587776653, rs74315368, rs74315369, rs587776793, rs587776794, rs587776795, rs606231209, rs121908589, rs121913685, rs121913680, rs794726675, rs587776804, rs121913517, rs121913234, rs121913512, rs267607032, rs387906780, rs201286421, rs587778661, rs587781270, rs587782243, rs74315370, rs587782703, rs786203457, rs764575966, rs786203251, rs587782604, rs200245469, rs397516836, rs786202732, rs786201161, rs786201063, rs751000085, rs869025568, rs876660642, rs876658713, rs151170408, rs878854632, rs752360961, rs121913235, rs121913521, rs121913513, rs1057519708, rs1057519710, rs121913514, rs1057519713, rs778582853, rs1060503757, rs1060502521, rs1060502543, rs898854295, rs981049067, rs916516745, rs1553887262, rs1057520032, rs1553887960, rs775143272, rs1560395607, rs1560418178, rs751904543, rs1560420761, rs1560417385, rs1560417396, rs1560417427, rs1560417438, rs1560417535, rs1560417642, rs1560417666, rs1560417673, rs1577992594, rs1577995761, rs1578003055, rs1301704156, rs1734957331	27793025
Myopia	Myopia	rs387907109, rs146936371, rs587776903, rs786205127, rs398122836, rs199624584, rs587777625, rs786205216, rs758872875, rs764211125, rs1135402746, rs765658563, rs1555941129, rs1555941116, rs199923805, rs782555528, rs1554862601, rs1586620121, rs1387950081, rs2051026773, rs1422332023
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Osteoporosis	Osteoporosis	rs72658152, rs72667023, rs587776916, rs72656370, rs768615287
Polydactyly	Polydactyly	rs1583729398, rs121917709, rs1583734240, rs121917714, rs397507422, rs398122899, rs587776959, rs386833752, rs1057518698, rs1060499558, rs755938967, rs1375768446, rs1309855392, rs1565601979, rs748321474, rs368652620, rs1562587032, rs760694987	26880018
Short rib-polydactyly syndrome	Short Rib-Polydactyly Syndrome	rs387907085, rs431905505, rs886037869, rs886037870, rs886044119, rs765513105, rs769724508, rs1555369050, rs1553324519, rs200335504, rs751222088, rs576969206, rs1037828930, rs1360128571, rs547679833, rs868310475, rs1050086118, rs1558342399, rs767206815
Short-rib thoracic dysplasia with or without polydactyly	SHORT-RIB THORACIC DYSPLASIA 16 WITH OR WITHOUT POLYDACTYLY	rs137852924, rs794726665, rs121908425, rs387906890, rs483352906, rs199689137, rs431905508, rs587777064, rs587777065, rs587777066, rs149614625, rs587777078, rs587777079, rs587777081, rs587777082, rs587777084, rs587777085, rs587777086, rs587777091, rs587777092, rs587777093, rs587777094, rs587777095, rs431905519, rs587777097, rs587777098, rs367600930, rs786205645, rs794727032, rs794727285, rs139021548, rs199947197, rs797045119, rs762081862, rs201948500, rs769975073, rs374356079, rs879255656, rs879255655, rs745930390, rs886037860, rs748090019, rs886037869, rs886037870, rs886039815, rs771487311, rs1056574154, rs771373235, rs1060505043, rs746068882, rs1555531363, rs762771340, rs765513105, rs1554460624, rs770256450, rs757499322, rs1554098663, rs79746977, rs1553516687, rs759648976, rs769651861, rs372499275, rs750338419, rs773496891, rs752878896, rs775849720, rs1362848762, rs1554053289, rs758677637, rs985064686, rs1554075284, rs769864196, rs748523193, rs755381180, rs1456300819, rs555811074, rs1261505725, rs548706733, rs371575563, rs200859699, rs770155116, rs1553359373, rs752971070, rs1554075506, rs1157065841, rs763975565, rs766663693, rs745949846, rs759125480, rs753802842, rs202024173, rs746591648, rs759150616, rs1860309810	31042281, 27466190, 26880018, 30242358

Unknown
Disease term	Disease name	Evidence	References	Source
Cranioectodermal Dysplasia	cranioectodermal dysplasia			GenCC
Diabetes	Diabetes			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Ciliopathies	Associate	27466190
Polydactyly	Associate	27466190
Short Rib Polydactyly Syndrome	Associate	27466190