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CFAP70 (cilia and flagella associated protein 70)

Written2019-01Jean Loup Huret
jean-loup.huret@atlasgeneticsoncology.org

Abstract Review on CFAP70, a poorly known gene and protein, with data on DNA, on the protein encoded, and where the gene is implicated.

Keywords CFAP70; Tetratricopeptide repeats; Cancer; Fusion gene; Axoneme; Cilia; Dynein

(Note : for Links provided by Atlas : click)

Identity

Alias_namesTTC18
tetratricopeptide repeat domain 18
Alias_symbol (synonym)FLJ25765
Other alias
HGNC (Hugo) CFAP70
LocusID (NCBI) 118491
Atlas_Id 61764
Location 10q22.1; on reverse strand  [Link to chromosome band 10q22]
Location_base_pair Starts at 73253758 and ends at 73358859 bp from pter ( according to hg19-Feb_2009)  [Mapping CFAP70.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
DNAJC9/CFAP70ECD/CFAP70CFAP70/MCU
MRPS16/CFAP70P4HA1/CFAP70

DNA/RNA

Transcription Various transcripts (see below).

Protein

Description Various isoforms have been described:
According to Vega: 3 protein coding transcripts: CFAP70-001: 3691 base pairs (bp), coding for a protein of 590 amino acids (aa); CFAP70-006: 1710bp, 498 aa; CFAP70-002: 1403bp, 361 aa
According to Uniprot: Isoform 1 (Q5T0N1-1), canonical sequence: 1,121 aa, 125,721 Da; Isoform 2 (Q5T0N1-2): 1,091 aa, 122,269 Da; Isoform 3 (Q5T0N1-3): 119 aa, 12,999 Da; Isoform 4 (Q5T0N1-6): 195 aa, 22,338 Da; Isoform 5 (Q5T0N1-7): 225 aa, 25,790 Da.
According to Ensembl: Protein ENSP00000310829: the transcript has 28 exons, 3703bp, 1121 aa, 33 domains; Protein ENSP00000347781: the transcript has 28 exons, 3691bp, 590 aa, 32 domains; Protein ENSP00000409527; the transcript has 12 exons, 1710bp, 498 aa, 23 domains; Protein ENSP00000343650: the transcript has 12 exons, 1403bp, 361 aa, 13 domains; Protein ENSP00000378334; the transcript has 9 exons, 1222bp, 179 aa, 13 domains.
Domains in the canonical sequence (Q5T0N1-1 in UniProt): 1121 aa.
there are 8 tetratricopeptide repeats (TRP): TPR 1, aa 635-668, TPR 2: aa 669-702, TPR 3 : aa 704-736, TPR 4: aa 929-962, TPR 5: aa 963-996, TPR 6: aa 1000-1033, TPR 7: aa 1035-1066 and TPR 8: aa 1068-1100. The TPR sequence contains about 34 amino acids, with a consensus sequence of small and large hydrophobic amino acids; small hydrophobic amino acids are often found at positions 8, 20, and 27, and large ones at positions 4, 7, and 24. Three-dimensional structure shows that the TPR motif contains two antiparallel α-helical subdomains (termed helix A and helix B), equivalent in length. TPR adopts a helix-turn-helix arrangement. They self-associate via a "knobs and holes" mechanism (Das et al., 1998; D'Andrea and Regan 2003; Cerveny et al., 2013; SMART).
 
  Figure 1 CFAP70 protein and domains.
Expression CFAP70 is expressed in adrenal gland, bronchus, testis, sperm flagella and in cilia of glandular cells in fallopian tube, and endometrium, according to The Human Protein Atlas.
Localisation CFAP70 localizes on the epithelial cilia and sperm flagella. It associates tightly to the ciliary axoneme (Shamoto et al., 2018).
Function Tetratricopeptide repeats are found in at least 149 proteins (PFAM). Tetratricopeptide repeat containing proteins are involved in protein-protein interactions and the assembly of multiprotein complexes, cell cycle, transcription, mitochondrial protein transport, and neurogenesis.
CFAP70 binds to the axoneme of motile cilia and flagella in close proximity to the outer dynein arms and regulates outer dynein arms activity. It is the N-terminus of CFAP70 which localizes at the base of the outer dynein arms and not the tetratricopeptide repeats. Knockdown of CFAP70 causes a reduction in ciliary motility (Shamoto et al., 2018).

Implicated in

Note Low or high expression of CFAP70 is not a prognostic indicator in any cancer tested (The Human Protein Atlas).
  
Entity Breast adenocarcinoma
Note The fusion gene DNAJC9/CFAP70 (10q22-10q22) has been found in breast adenocarcinoma (Gao et al. 2018).
The fusion gene CFAP70/ MCU (10q22-10q22) has been found in a breast cancer cell line (Klijn et al. 2015).
  
  
Entity Uterus corpus adenocarcinoma
Note The fusion gene P4HA1/CFAP70 (10q22-10q22) has been found in uterus corpus adenocarcinoma (Hu et al. 2018).
  
  
Entity Lung squamous cell carcinoma
Note The fusion gene ECD/CFAP70 (10q22-10q22) has been found in lung squamous cell carcinoma (Yoshihara et al. 2015).
  
  
Entity Thyroid adenocarcinoma
Note The fusion gene MRPS16/CFAP70 (10q22-10q22) has been found in thyroid adenocarcinoma (Yoshihara et al. 2015).
  

Bibliography

Tetratricopeptide repeat motifs in the world of bacterial pathogens: role in virulence mechanisms
Cerveny L, Straskova A, Dankova V, Hartlova A, Ceckova M, Staud F, Stulik J
Infect Immun 2013 Mar;81(3):629-35
PMID 23264049
 
TPR proteins: the versatile helix
D'Andrea LD, Regan L
Trends Biochem Sci 2003 Dec;28(12):655-62
PMID 14659697
 
The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions
Das AK, Cohen PW, Barford D
EMBO J 1998 Mar 2;17(5):1192-9
PMID 9482716
 
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L
Cell Rep 2018 Apr 3;23(1):227-238
PMID 29617662
 
TumorFusions: an integrative resource for cancer-associated transcript fusions
Hu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K, Lang FM, Martinez-Ledesma E, Lee SH, Zheng S, Verhaak RGW
Nucleic Acids Res 2018 Jan 4;46(D1):D1144-D1149
PMID 29099951
 
A comprehensive transcriptional portrait of human cancer cell lines
Klijn C, Durinck S, Stawiski EW, Haverty PM, Jiang Z, Liu H, Degenhardt J, Mayba O, Gnad F, Liu J, Pau G, Reeder J, Cao Y, Mukhyala K, Selvaraj SK, Yu M, Zynda GJ, Brauer MJ, Wu TD, Gentleman RC, Manning G, Yauch RL, Bourgon R, Stokoe D, Modrusan Z, Neve RM, de Sauvage FJ, Settleman J, Seshagiri S, Zhang Z
Nat Biotechnol 2015 Mar;33(3):306-12
PMID 25485619
 
CFAP70 Is a Novel Axoneme-Binding Protein That Localizes at the Base of the Outer Dynein Arm and Regulates Ciliary Motility
Shamoto N, Narita K, Kubo T, Oda T, Takeda S
Cells 2018 Aug 29;7(9)
PMID 30158508
 
The landscape and therapeutic relevance of cancer-associated transcript fusions
Yoshihara K, Wang Q, Torres-Garcia W, Zheng S, Vegesna R, Kim H, Verhaak RG
Oncogene 2015 Sep 10;34(37):4845-54
PMID 25500544
 

Citation

This paper should be referenced as such :
Huret JL
CFAP70 (cilia and flagella associated protein 70);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/CFAP70ID61764ch10q22.html


External links

Nomenclature
HGNC (Hugo)CFAP70   30726
Cards
Atlas61764
Entrez_Gene (NCBI)CFAP70  118491  cilia and flagella associated protein 70
AliasesTTC18
GeneCards (Weizmann)CFAP70
Ensembl hg19 (Hinxton)ENSG00000156042 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000156042 [Gene_View]  ENSG00000156042 [Sequence]  chr10:73253758-73358859 [Contig_View]  CFAP70 [Vega]
ICGC DataPortalENSG00000156042
TCGA cBioPortalCFAP70
AceView (NCBI)CFAP70
Genatlas (Paris)CFAP70
WikiGenes118491
SOURCE (Princeton)CFAP70
Genetics Home Reference (NIH)CFAP70
Genomic and cartography
GoldenPath hg38 (UCSC)CFAP70  -     chr10:73253758-73358859 -  10q22.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CFAP70  -     10q22.2   [Description]    (hg19-Feb_2009)
EnsemblCFAP70 - 10q22.2 [CytoView hg19]  CFAP70 - 10q22.2 [CytoView hg38]
Mapping of homologs : NCBICFAP70 [Mapview hg19]  CFAP70 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AF435958 AF435959 AI458159 AK022235 AK098631
RefSeq transcript (Entrez)NM_001350933 NM_001350934 NM_145170
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CFAP70
Cluster EST : UnigeneHs.720588 [ NCBI ]
CGAP (NCI)Hs.720588
Alternative Splicing GalleryENSG00000156042
Gene ExpressionCFAP70 [ NCBI-GEO ]   CFAP70 [ EBI - ARRAY_EXPRESS ]   CFAP70 [ SEEK ]   CFAP70 [ MEM ]
Gene Expression Viewer (FireBrowse)CFAP70 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)118491
GTEX Portal (Tissue expression)CFAP70
Human Protein AtlasENSG00000156042-CFAP70 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ5T0N1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ5T0N1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ5T0N1
Splice isoforms : SwissVarQ5T0N1
PhosPhoSitePlusQ5T0N1
Domaine pattern : Prosite (Expaxy)TPR (PS50005)    TPR_REGION (PS50293)   
Domains : Interpro (EBI)TPR-contain_dom    TPR-like_helical_dom    TPR_repeat   
Domain families : Pfam (Sanger)TPR_8 (PF13181)   
Domain families : Pfam (NCBI)pfam13181   
Domain families : Smart (EMBL)TPR (SM00028)  
Conserved Domain (NCBI)CFAP70
DMDM Disease mutations118491
Blocks (Seattle)CFAP70
SuperfamilyQ5T0N1
Human Protein Atlas [tissue]ENSG00000156042-CFAP70 [tissue]
Peptide AtlasQ5T0N1
HPRD15583
IPIIPI00217938   IPI00902826   IPI00956282   IPI00478343   IPI00513680   
Protein Interaction databases
DIP (DOE-UCLA)Q5T0N1
IntAct (EBI)Q5T0N1
FunCoupENSG00000156042
BioGRIDCFAP70
STRING (EMBL)CFAP70
ZODIACCFAP70
Ontologies - Pathways
QuickGOQ5T0N1
Ontology : AmiGOmolecular_function  cilium  biological_process  extracellular exosome  
Ontology : EGO-EBImolecular_function  cilium  biological_process  extracellular exosome  
NDEx NetworkCFAP70
Atlas of Cancer Signalling NetworkCFAP70
Wikipedia pathwaysCFAP70
Orthology - Evolution
OrthoDB118491
GeneTree (enSembl)ENSG00000156042
Phylogenetic Trees/Animal Genes : TreeFamCFAP70
HOGENOMQ5T0N1
Homologs : HomoloGeneCFAP70
Homology/Alignments : Family Browser (UCSC)CFAP70
Gene fusions - Rearrangements
Fusion : QuiverCFAP70
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCFAP70 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CFAP70
dbVarCFAP70
ClinVarCFAP70
1000_GenomesCFAP70 
Exome Variant ServerCFAP70
ExAC (Exome Aggregation Consortium)ENSG00000156042
GNOMAD BrowserENSG00000156042
Varsome BrowserCFAP70
Genetic variants : HAPMAP118491
Genomic Variants (DGV)CFAP70 [DGVbeta]
DECIPHERCFAP70 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCFAP70 
Mutations
ICGC Data PortalCFAP70 
TCGA Data PortalCFAP70 
Broad Tumor PortalCFAP70
OASIS PortalCFAP70 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDCFAP70
BioMutasearch CFAP70
DgiDB (Drug Gene Interaction Database)CFAP70
DoCM (Curated mutations)CFAP70 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CFAP70 (select a term)
intoGenCFAP70
Cancer3DCFAP70(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
DisGeNETCFAP70
MedgenCFAP70
Genetic Testing Registry CFAP70
NextProtQ5T0N1 [Medical]
TSGene118491
GENETestsCFAP70
Target ValidationCFAP70
Huge Navigator CFAP70 [HugePedia]
snp3D : Map Gene to Disease118491
BioCentury BCIQCFAP70
ClinGenCFAP70
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD118491
Chemical/Pharm GKB GenePA134881300
Clinical trialCFAP70
Miscellaneous
canSAR (ICR)CFAP70 (select the gene name)
DataMed IndexCFAP70
Probes
Litterature
PubMed5 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCFAP70
EVEXCFAP70
GoPubMedCFAP70
iHOPCFAP70
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Jan 17 18:51:32 CET 2019

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jlhuret@AtlasGeneticsOncology.org.