IFT122 (intraflagellar transport 122)

Gene

• Entrez ID: 55764
• Gene name: Intraflagellar transport 122
• Gene symbol: IFT122
• Synonyms (NCBI Gene): CED, CED1, CFAP80, FAP80, SPG, WDR10, WDR10p, WDR140
• Chromosome: 3
• Chromosome location: 3q21.3-q22.1
• Summary: This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein com

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs76881473	C>T	Benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, genic downstream transcript variant
rs79187669	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Synonymous variant, coding sequence variant, 5 prime UTR variant
rs138329739	C>T	Conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, stop gained, intron variant, coding sequence variant
rs146818399	T>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, genic downstream transcript variant
rs191420441	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs267607191	T>G	Pathogenic	Coding sequence variant, missense variant
rs267607192	C>T	Pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant
rs373836204	T>C,G	Pathogenic	Synonymous variant, stop gained, 5 prime UTR variant, coding sequence variant, genic upstream transcript variant
rs376595844	G>A,C,T	Pathogenic	Genic upstream transcript variant, intron variant
rs397515567	G>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant
rs397515568	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs755005244	G>C	Pathogenic	Splice acceptor variant
rs757823317	A>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs776099605	A>C,G,T	Likely-pathogenic	Genic downstream transcript variant, downstream transcript variant, coding sequence variant, missense variant
rs781409395	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, 5 prime UTR variant
rs786205566	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs786205567	T>C	Pathogenic, likely-pathogenic	Splice donor variant
rs886041421	TA>-	Pathogenic	Frameshift variant, coding sequence variant
rs886042132	A>-	Pathogenic	Frameshift variant, intron variant, coding sequence variant
rs1185183557	C>T	Likely-pathogenic	Intron variant, stop gained, coding sequence variant
rs1559869525	G>A	Likely-pathogenic	Genic upstream transcript variant, splice donor variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018545	hsa-miR-335-5p	Microarray	18185580
MIRT2682638	hsa-miR-2355-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001843	Process	Neural tube closure	ISS
GO:0005515	Function	Protein binding	IPI	22190034, 27173435, 27932497, 28514442, 29220510, 30476139, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IDA	29220510
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	ISS
GO:0005929	Component	Cilium	NAS	27806291
GO:0005929	Component	Cilium	TAS
GO:0010172	Process	Embryonic body morphogenesis	ISS
GO:0016020	Component	Membrane	HDA	19946888
GO:0021513	Process	Spinal cord dorsal/ventral patterning	ISS
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, 29220510, 30476139
GO:0030991	Component	Intraciliary transport particle A	IEA
GO:0030991	Component	Intraciliary transport particle A	IPI	27173435
GO:0031965	Component	Nuclear membrane	IDA
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0035050	Process	Embryonic heart tube development	ISS
GO:0035115	Process	Embryonic forelimb morphogenesis	ISS
GO:0035556	Process	Intracellular signal transduction	ISS
GO:0035720	Process	Intraciliary anterograde transport	ISS
GO:0035721	Process	Intraciliary retrograde transport	IBA
GO:0035721	Process	Intraciliary retrograde transport	ISS
GO:0035721	Process	Intraciliary retrograde transport	NAS	27806291
GO:0036064	Component	Ciliary basal body	IDA	29220510
GO:0036064	Component	Ciliary basal body	IEA
GO:0042073	Process	Intraciliary transport	IEA
GO:0042073	Process	Intraciliary transport	IMP	29220510
GO:0042995	Component	Cell projection	IEA
GO:0045879	Process	Negative regulation of smoothened signaling pathway	ISS
GO:0048593	Process	Camera-type eye morphogenesis	ISS
GO:0060173	Process	Limb development	ISS
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	IMP	29220510
GO:0060271	Process	Cilium assembly	ISS
GO:0060271	Process	Cilium assembly	NAS	27806291
GO:0060971	Process	Embryonic heart tube left/right pattern formation	ISS
GO:0061512	Process	Protein localization to cilium	IBA
GO:0061512	Process	Protein localization to cilium	IEA
GO:0061512	Process	Protein localization to cilium	IMP	20889716
GO:0061512	Process	Protein localization to cilium	IMP	29220510
GO:0072594	Process	Establishment of protein localization to organelle	ISS
GO:0097542	Component	Ciliary tip	TAS
GO:0097730	Component	Non-motile cilium	IBA
GO:1905515	Process	Non-motile cilium assembly	IBA

Other IDs

• MIM: 606045
• HGNC: 13556
• e!Ensembl: ENSG00000163913

Protein

• UniProt ID: Q9HBG6
• Protein name: Intraflagellar transport protein 122 homolog (WD repeat-containing protein 10) (WD repeat-containing protein 140)
• Protein function: As a component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is required in ciliogenesis and ciliary protein trafficking (PubMed:27932497, PubMed
• PDB: 8BBE, 8BBF, 8BBG, 8FGW, 8FH3
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00400	WD40	43 → 81	WD domain, G-beta repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Expressed in many tissues. Predominant expression in testis and pituitary. {ECO:0000269|PubMed:11242542}.
• Sequence:

  MRAVLTWRDKAEHCINDIAFKPDGTQLILAAGSRLLVYDTSDGTLLQPLKGHKDTVYCVA
  YAKDGKRFASGSADKSVIIWTSKLEGILKYTHNDAIQCVSYNPITHQLASCSSSDFGLWS
  PEQKSVSKHKSSSKIICCSWTNDGQYLALGMFNGIISIRNKNGEEKVKIERPGGSLSPIW
  SICWNPSSRWESFWMNRENEDAEDVIVNRYIQEIPSTLKSAVYSSQGSEAEEEEPEEEDD
  SPRDDNLEERNDILAVADWGQKVSFYQLSGKQIGKDRALNFDPCCISYFTKGEYILLGGS
  DKQVSLFTKDGVRLGTVGEQNSWVWTCQAKPDSNYVVVGCQDGTISFYQLIFSTVHGLYK
  DRYAYRDSMTDVIVQHLITEQKVRIKCKELVKKIAIYRNRLAIQLPEKILIYELYSEDLS
  DMHYRVKEKIIKKFECNLLVVCANHIILCQEKRLQCLSFSGVKEREWQMESLIRYIKVIG
  GPPGREGLLVGLKNGQILKIFVDNLFAIVLLKQATAVRCLDMSASRKKLAVVDENDTCLV
  YDIDTKELLFQEPNANSVAWNTQCEDMLCFSGGGYLNIKASTFPVHRQKLQGFVVGYNGS
  KIFCLHVFSISAVEVPQSAPMYQYLDRKLFKEAYQIACLGVTDTDWRELAMEALEGLDFE
  TAKKAFIRVQDLRYLELISSIEERKKRGETNNDLFLADVFSYQGKFHEAAKLYKRSGHEN
  LALEMYTDLCMFEYAKDFLGSGDPKETKMLITKQADWARNIKEPKAAVEMYISAGEHVKA
  IEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGYAAETYLKMGDLKSLVQL
  HVETQRWDEAFALGEKHPEFKDDIYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQ
  LTNNAVAESRFNDAAYYYWMLSMQCLDIAQDPAQKDTMLGKFYHFQRLAELYHGYHAIHR
  HTEDPFSVHRPETLFNISRFLLHSLPKDTPSGISKVKILFTLAKQSKALGAYRLARHAYD
  KLRGLYIPARFQKSIELGTLTIRAKPFHDSEELVPLCYRCSTNNPLLNNLGNVCINCRQP
  FIFSASSYDVLHLVEFYLEEGITDEEAISLIDLEVLRPKRDDRQLEIANNSSQILRLVET
  KDSIGDEDPFTAKLSFEQGGSEFVPVVVSRLVLRSMSRRDVLIKRWPPPLRWQYFRSLLP
  DASITMCPSCFQMFHSEDYELLVLQHGCCPYCRRCKDDPGP

• Sequence length: 1241

Pathways

Reactome:

Hedgehog 'off' state
Intraflagellar transport

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Cranioectodermal dysplasia	Pathogenic	rs786205567	RCV000256473
Cranioectodermal dysplasia 1	Likely pathogenic; Pathogenic	rs372483083, rs2081339145, rs1559868433, rs1299632365, rs2108740086, rs1039467525, rs2108311256, rs2108101855, rs2108328020, rs369346055, rs786205566, rs786205567, rs2532710574, rs770590297, rs267607191, rs267607192, rs267607193, rs746129224, rs2531429983, rs2076139894, rs764222986, rs763755540, rs2531375175, rs905675504, rs2532967754, rs1300189424, rs2532525678, rs951629848, rs2531458645, rs2532968237, rs1377926916, rs1559941008, rs2077995074, rs2531744619, rs776099605, rs1559869525, rs138329739, rs755005244, rs1185183557, rs397515567, rs2077955754, rs372355939, rs2074912574, rs2083230922	RCV001535931 RCV001536093 RCV001783466 RCV001783467 RCV001797987 RCV001867450 RCV001972294 RCV002023959 RCV002249079 RCV003075682 RCV003989481 RCV004527368 RCV002664317 RCV002574933 RCV000004898 RCV000004899 RCV000004901 RCV002635923 RCV002819414 RCV002856848 RCV002850900 RCV002890405 RCV002881756 RCV002944096 RCV003010300 RCV003030742 RCV003502761 RCV003503122 RCV003503971 RCV003612484 RCV003612768 RCV003611270 RCV003612354 RCV003612424 RCV005230338 RCV000705197 RCV000705716 RCV002477685 RCV002500985 RCV000055971 RCV001281142 RCV001281141 RCV001261959 RCV001263242
IFT122-related disorder	Likely pathogenic; Pathogenic	rs1559868433, rs1240946692, rs138329739	RCV003416445 RCV003391305 RCV003392543
Rod-cone dystrophy	Likely pathogenic	rs2084588345	RCV001376272

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Uncertain significance; Conflicting classifications of pathogenicity	rs535606113, rs138793724	RCV005926462 RCV005897588
Colon adenocarcinoma	Conflicting classifications of pathogenicity	rs138793724	RCV005897587
Colorectal cancer	Conflicting classifications of pathogenicity	rs138793724	RCV005897590
Connective tissue disorder	Conflicting classifications of pathogenicity; Uncertain significance; Benign; Likely benign	rs202074599, rs371325633, rs2081968039, rs746556063, rs749670705, rs555281580, rs557159295, rs769527595, rs777023612, rs150550701, rs76881473, rs200606803, rs61744639, rs138793724, rs61744218, rs150174636, rs9836202, rs116819033, rs141626835, rs61741773, rs146874343, rs538635135	RCV002277032 RCV002278758 RCV002278759 RCV002278760 RCV002278761 RCV002278762 RCV002278763 RCV002278765 RCV002278766 RCV002277342 RCV002277380 RCV002278283 RCV002278313 RCV002278530 RCV002278533 RCV002278531 RCV002278535 RCV002278532 RCV002278534 RCV002279461 RCV002279596 RCV002279611
Familial cancer of breast	Conflicting classifications of pathogenicity	rs138793724	RCV005897586
Gastric cancer	Uncertain significance	rs769712676	RCV005923895
Hepatocellular carcinoma	Benign; Conflicting classifications of pathogenicity	rs2285354, rs138793724	RCV005889815 RCV005897589
Microcephaly	Likely benign	rs149029829	RCV001252861
Ovarian serous cystadenocarcinoma	Likely benign; Benign	rs149872501, rs111668739	RCV005918896 RCV005897593
Sarcoma	Conflicting classifications of pathogenicity	rs138793724, rs768782991	RCV005897591 RCV005913878
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs138793724	RCV005897592
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs111668739	RCV005897594
Uveal melanoma	Conflicting classifications of pathogenicity; Benign	rs200915373, rs2285354	RCV005925604 RCV005889816

Associations from Text Mining
Disease Name	Relationship Type	References
Camurati Engelmann Syndrome	Stimulate	40204055
Cranioectodermal Dysplasia	Associate	20493458, 32007091