IFT74 (intraflagellar transport 74)

Gene

• Entrez ID: 80173
• Gene name: Intraflagellar transport 74
• Gene symbol: IFT74
• Synonyms (NCBI Gene): BBS22, CCDC2, CMG-1, CMG1, JBTS40, SPGF58
• Chromosome: 9
• Chromosome location: 9p21.2
• Summary: This gene encodes a core intraflagellar transport (IFT) protein which belongs to a multi-protein complex involved in the transport of ciliary proteins along axonemal microtubules. IFT proteins are found at the base of the cilium as well as inside the cili

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs200699377	G>T	Pathogenic	Splice acceptor variant, 3 prime UTR variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT027044	hsa-miR-103a-3p	Sequencing	20371350
MIRT031787	hsa-miR-16-5p	Sequencing	20371350
MIRT709600	hsa-miR-590-3p	HITS-CLIP	19536157
MIRT709599	hsa-miR-6828-3p	HITS-CLIP	19536157
MIRT709598	hsa-miR-6071	HITS-CLIP	19536157
MIRT709597	hsa-miR-544a	HITS-CLIP	19536157
MIRT709596	hsa-miR-6738-3p	HITS-CLIP	19536157
MIRT324839	hsa-miR-15a-5p	HITS-CLIP	22473208
MIRT324840	hsa-miR-15b-5p	HITS-CLIP	22473208
MIRT031787	hsa-miR-16-5p	HITS-CLIP	22473208
MIRT324841	hsa-miR-195-5p	HITS-CLIP	22473208
MIRT709600	hsa-miR-590-3p	HITS-CLIP	19536157
MIRT709599	hsa-miR-6828-3p	HITS-CLIP	19536157
MIRT709598	hsa-miR-6071	HITS-CLIP	19536157
MIRT709597	hsa-miR-544a	HITS-CLIP	19536157
MIRT709596	hsa-miR-6738-3p	HITS-CLIP	19536157
MIRT1061078	hsa-miR-1303	CLIP-seq
MIRT1061079	hsa-miR-4276	CLIP-seq
MIRT1061080	hsa-miR-1185	CLIP-seq
MIRT1061081	hsa-miR-129-5p	CLIP-seq
MIRT1061078	hsa-miR-1303	CLIP-seq
MIRT1061082	hsa-miR-15a	CLIP-seq
MIRT1061083	hsa-miR-15b	CLIP-seq
MIRT1061084	hsa-miR-16	CLIP-seq
MIRT1061085	hsa-miR-195	CLIP-seq
MIRT1061086	hsa-miR-3679-5p	CLIP-seq
MIRT1061087	hsa-miR-424	CLIP-seq
MIRT1061088	hsa-miR-451b	CLIP-seq
MIRT1061089	hsa-miR-4524	CLIP-seq
MIRT1061090	hsa-miR-497	CLIP-seq
MIRT1061091	hsa-miR-503	CLIP-seq
MIRT1061092	hsa-miR-646	CLIP-seq
MIRT1061080	hsa-miR-1185	CLIP-seq
MIRT1061078	hsa-miR-1303	CLIP-seq
MIRT1061082	hsa-miR-15a	CLIP-seq
MIRT1061083	hsa-miR-15b	CLIP-seq
MIRT1061084	hsa-miR-16	CLIP-seq
MIRT2246483	hsa-miR-181a	CLIP-seq
MIRT2246484	hsa-miR-181b	CLIP-seq
MIRT2246485	hsa-miR-181c	CLIP-seq
MIRT2246486	hsa-miR-181d	CLIP-seq
MIRT1061085	hsa-miR-195	CLIP-seq
MIRT1061086	hsa-miR-3679-5p	CLIP-seq
MIRT1061087	hsa-miR-424	CLIP-seq
MIRT2246487	hsa-miR-4262	CLIP-seq
MIRT1061088	hsa-miR-451b	CLIP-seq
MIRT1061089	hsa-miR-4524	CLIP-seq
MIRT1061090	hsa-miR-497	CLIP-seq
MIRT1061091	hsa-miR-503	CLIP-seq
MIRT2246488	hsa-miR-543	CLIP-seq
MIRT1061092	hsa-miR-646	CLIP-seq
MIRT2246483	hsa-miR-181a	CLIP-seq
MIRT2246484	hsa-miR-181b	CLIP-seq
MIRT2246485	hsa-miR-181c	CLIP-seq
MIRT2246486	hsa-miR-181d	CLIP-seq
MIRT2389280	hsa-miR-331-5p	CLIP-seq
MIRT2246487	hsa-miR-4262	CLIP-seq
MIRT2246488	hsa-miR-543	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001669	Component	Acrosomal vesicle	IEA
GO:0003334	Process	Keratinocyte development	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	28428259, 28625565, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005813	Component	Centrosome	IEA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	NAS	26980730
GO:0005929	Component	Cilium	TAS
GO:0007219	Process	Notch signaling pathway	IEA
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0007507	Process	Heart development	IEA
GO:0008544	Process	Epidermis development	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:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031514	Component	Motile cilium	IEA
GO:0031514	Component	Motile cilium	ISS
GO:0033630	Process	Positive regulation of cell adhesion mediated by integrin	IEA
GO:0035720	Process	Intraciliary anterograde transport	NAS	26980730
GO:0035735	Process	Intraciliary transport involved in cilium assembly	IBA
GO:0035735	Process	Intraciliary transport involved in cilium assembly	IMP	23990561
GO:0042073	Process	Intraciliary transport	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043616	Process	Keratinocyte proliferation	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048487	Function	Beta-tubulin binding	IBA
GO:0048487	Function	Beta-tubulin binding	IDA	23990561
GO:0048487	Function	Beta-tubulin binding	IEA
GO:0050680	Process	Negative regulation of epithelial cell proliferation	IEA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	IMP	23990561
GO:0060271	Process	Cilium assembly	NAS	26980730
GO:0097542	Component	Ciliary tip	TAS
GO:1905515	Process	Non-motile cilium assembly	IEA

Other IDs

• MIM: 608040
• HGNC: 21424
• e!Ensembl: ENSG00000096872

Protein

• UniProt ID: Q96LB3
• Protein name: Intraflagellar transport protein 74 homolog (Capillary morphogenesis gene 1 protein) (CMG-1) (Coiled-coil domain-containing protein 2)
• Protein function: Component of the intraflagellar transport (IFT) complex B: together with IFT81, forms a tubulin-binding module that specifically mediates transport of tubulin within the cilium (PubMed:23990561). Binds beta-tubulin via its basic region (PubMed:2
• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in adult and fetal kidney and expressed at lower level in adult heart, placenta, lung, liver and pancreas, and in fetal heart, lung and liver. Little to no expression was detected in adult brain and skeletal muscle or
• Sequence:

  MASNHKSSAARPVSRGGVGLTGRPPSGIRPLSGNIRVATAMPPGTARPGSRGCPIGTGGV
  LSSQIKVAHRPVTQQGLTGMKTGTKGPQRQILDKSYYLGLLRSKISELTTEVNKLQKGIE
  MYNQENSVYLSYEKRAETLAVEIKELQGQLADYNMLVDKLNTNTEMEEVMNDYNMLKAQN
  DRETQSLDVIFTERQAKEKQIRSVEEEIEQEKQATDDIIKNMSFENQVKYLEMKTTNEKL
  LQELDTLQQQLDSQNMKKESLEAEIAHSQVKQEAVLLHEKLYELESHRDQMIAEDKSIGS
  PMEEREKLLKQIKDDNQEIASMERQLTDTKEKINQFIEEIRQLDMDLEEHQGEMNQKYKE
  LKKREEHMDTFIETFEETKNQELKRKAQIEANIVALLEHCSRNINRIEQISSITNQELKM
  MQDDLNFKSTEVQKSQSTAQNLTSDIQRLQLDLQKMELLESKMTEEQHSLKSKIKQMTTD
  LEIYNDLPALKSSGEEKIKKLHQERMILSTHRNAFKKIMEKQNIEYEALKTQLQENETHS
  QLTNLERKWQHLEQNNFAMKEFIATKSQESDYQPIKKNVTKQIAEYNKTIVDALHSTSGN
  

• Sequence length: 600

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
Acute myeloid leukemia	Likely pathogenic	rs201953338	RCV005926993	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bardet-Biedl syndrome	Likely pathogenic; Pathogenic	rs150219690	RCV005361704	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bardet-Biedl syndrome 22	Pathogenic; Likely pathogenic	rs2131541114, rs1391036863, rs200699377	RCV001554330 RCV005254118 RCV000240867	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
IFT74-related disorder	Likely pathogenic; Pathogenic	rs150219690, rs377639405, rs766986213, rs200556379, rs201953338, rs1391036863, rs1334193252, rs200699377, rs1350359379	RCV004743566 RCV003923391 RCV004744563 RCV003434569 RCV003420542 RCV004725329 RCV004725404 RCV003409371 RCV004741699	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Jeune thoracic dystrophy	Likely pathogenic	rs759662469	RCV000515865	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome 40	Likely pathogenic; Pathogenic	rs150219690, rs2131480409, rs2131540908, rs751583919, rs1056125920, rs2131642498, rs1391036863	RCV001731252 RCV001731253 RCV001731254 RCV001731255 RCV001731256 RCV002248338 RCV003147778	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Multiple Morphological Anomalies of Sperm Flagella (MMAF)	Pathogenic	rs2131525662	RCV001420509	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 58	Pathogenic	rs2131525662	RCV001732114	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTISM SPECTRUM DISORDER	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIARY MOTILITY DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CILIOPATHY	—	ClinGen, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL ABSENCE OF PART OF BRAIN	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HYPOPLASIA OF PART OF BRAIN	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYDRANENCEPHALY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Joubert syndrome	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LISSENCEPHALY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACROGYRIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJEWSKI SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALE INFERTILITY DUE TO LARGE-HEADED MULTIFLAGELLAR POLYPLOID SPERMATOZOA	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALE INFERTILITY WITH LARGE-HEADED, MULTIFLAGELLAR, POLYPLOID SPERMATOZOA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROGYRIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY CILIARY DYSKINESIA	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Short-rib thoracic dysplasia 6 with or without polydactyly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Uncertain significance	ClinVar	★★☆☆☆ 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
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	17383054		★☆☆☆☆ Found in Text Mining only
Bardet-Biedl Syndrome	Bardet-Biedl Syndrome	BEFREE	27486776		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
BARDET-BIEDL SYNDROME 20	Bardet-Biedl Syndrome	GENOMICS_ENGLAND_DG	27486776		★☆☆☆☆ Found in Text Mining only
BARDET-BIEDL SYNDROME 20	Bardet-Biedl Syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	35564499	Associate	★☆☆☆☆ Found in Text Mining only
Bronchiectasis	Bronchiectasis	Pubtator	37555648	Associate	★☆☆☆☆ Found in Text Mining only
Ciliary Motility Disorders	Ciliary dyskinesia	Pubtator	37555648	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ciliopathies	Ciliopathy	Pubtator	33875766, 37555648	Associate	★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	Pubtator	31881747	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	17166276	Associate	★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	37555648	Associate	★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	32144365	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	Pubtator	32144365	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oligospermia	Oligospermia	BEFREE	31004481		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	GWASDB_DG	19571808		★☆☆☆☆ Found in Text Mining only