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CFAP99 (Cilia and Flagella Associated Protein 99)

Written2016-06Sinem Tunçer, Rafig Gurbanov
Department of Biological Sciences, Middle East Technical University, Ankara, Turkey

Abstract Review on CFAP99, with data on DNA, on the protein encoded, and where the gene is implicated.

Keywords CFAP99; Childhood Leukemia; Human development

(Note : for Links provided by Atlas : click)

Identity

Other aliasLOC402160
LOC441005
HGNC (Hugo) CFAP99
LocusID (NCBI) 402160
Atlas_Id 61767
Location 4p16.3 (  [Link to chromosome band 4p16]
Location_base_pair Starts at 2418945 and ends at 2462963 bp from pter ( according to hg19-Feb_2009)  [Mapping CFAP99.png]
 
  Figure 1 Cytogenetic bands within chromosome 4. The 4p16.3 is indicated by red.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DNA/RNA

 
  Figure 2 Gene neighbours of CFAP99 on chromosome 4p16.3 (NCBI Homo sapiens Annotation Release 108).
Description Orientation: Plus strand; 44.072 bases; Exon count: 15 (NCBI Homo sapiens Annotation Release 108).
Transcription Human CFAP99gene has 6 transcripts (Table 1).

Name

Transcript ID

bp

Protein

Translation ID

Biotype

CFAP99-005

ENST00000635017

2298

714aa

ENSP00000488922

Protein coding

CFAP99-006

ENST00000506607

1398

459aa

ENSP00000425050

Protein coding

CFAP99-001

ENST00000382849

2790

No protein

-

Processed transcript

CFAP99-004

ENST00000511731

927

No protein

-

Processed transcript

CFAP99-003

ENST00000514556

728

No protein

-

Processed transcript

CFAP99-002

ENST00000515732

713

No protein

-

Processed transcript


Table 1 Transcripts of human CFAP99 gene (Ensembl release 84).

Protein

Expression RNA-seq data from 32 tissues reveal that CFAP99 is expressed in testis and fallopian tube, and to a lesser degree in lung, adrenal and thyroid glands (Figure 3).
 
  Figure 3 CFAP99 tissue expression. RNA-seq data from 32 tissues are reported as mean FPKM (Fragments Per Kilobase gene model and Million reads), corresponding to mean values of the different individual samples from each tissue type.
Function Unknown
Homology The CFAP99 gene is conserved in chimpanzee, cow, mouse, rat, chicken, zebrafish, and frog (Table 2)
Species

Gene Symbol

Identity (%) Gene

Identity (%) Protein

H.sapiens

RP11-503N18.1

vs.
P.troglodytes

LOC750504

99.1

98.9

vs.
B.taurus

LOC100847979

80.5

72.9

vs.
M.musculus

Gm21446

78.7

72.9

vs.
R.norvegicus

RGD1564567

78.9

72.3

vs.
G.gallus

LOC422887

56.7

52

vs.
X.tropicalis

LOC100495334

56.2

50.2

vs.
D.rerio

LOC100534701

51.8

41.9


Table 2 Pairwise alignment of CFAP99 gene and protein sequences (in distance from human).

Implicated in

Note
  
Entity Childhood Leukemia
Note rs36086854 (minor allele A, major allele G) is a non-synonymous cSNP, a coding Single Nucleotide Polymorphism-cSNP which results in amino acid allelic variants, with an allelic frequency greater than 1 percent in population (Chen et al., 2013). The missense SNP was supposed to be associated with childhood acute lymphoblastic leukemia (ALL) (Singh, 2015).
  
  
Entity Human development
Note CFAP99 was found to be down-regulated (2.15 fold) in the fetuses of obese woman, compared with the fetuses of lean woman (Edlow et al., 2016).
  

Bibliography

Decoding the disease-associated proteins encoded in the human chromosome 4
Chen LC, Liu MY, Hsiao YC, Choong WK, Wu HY, Hsu WL, Liao PC, Sung TY, Tsai SF, Yu JS, Chen YJ
J Proteome Res 2013 Jan 4;12(1):33-44
PMID 23256888
 
Assessing the fetal effects of maternal obesity via transcriptomic analysis of cord blood: a prospective case-control study
Edlow AG, Hui L, Wick HC, Fried I, Bianchi DW
BJOG 2016 Jan;123(2):180-9
PMID 26840378
 
A Case-Only Genome-wide Association Study of Gender- and Age-specific Risk Markers for Childhood Leukemia
Singh SK
FIU Electronic Theses and Dissertations. 2015. Paper 1832; http://digitalcommons.fiu.edu/cgi/viewcontent.cgi?article=2991&context=etd
 

Citation

This paper should be referenced as such :
Tunçer S, Gurbanov R
CFAP99 (Cilia and Flagella Associated Protein 99);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/CFAP99ID61767ch4p16.html


External links

Nomenclature
HGNC (Hugo)CFAP99   51180
Cards
AtlasCFAP99ID61767ch4p16
Entrez_Gene (NCBI)CFAP99  402160  cilia and flagella associated protein 99
Aliases
GeneCards (Weizmann)CFAP99
Ensembl hg19 (Hinxton)ENSG00000249428 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000249428 [Gene_View]  chr4:2418945-2462963 [Contig_View]  CFAP99 [Vega]
ICGC DataPortalENSG00000249428
TCGA cBioPortalCFAP99
AceView (NCBI)CFAP99
Genatlas (Paris)CFAP99
WikiGenes402160
SOURCE (Princeton)CFAP99
Genetics Home Reference (NIH)CFAP99
Genomic and cartography
GoldenPath hg38 (UCSC)CFAP99  -     chr4:2418945-2462963 +  4p16.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CFAP99  -     4p16.3   [Description]    (hg19-Feb_2009)
EnsemblCFAP99 - 4p16.3 [CytoView hg19]  CFAP99 - 4p16.3 [CytoView hg38]
Mapping of homologs : NCBICFAP99 [Mapview hg19]  CFAP99 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK126028 BC010180
RefSeq transcript (Entrez)NM_001193282
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CFAP99
Cluster EST : UnigeneHs.443116 [ NCBI ]
CGAP (NCI)Hs.443116
Alternative Splicing GalleryENSG00000249428
Gene ExpressionCFAP99 [ NCBI-GEO ]   CFAP99 [ EBI - ARRAY_EXPRESS ]   CFAP99 [ SEEK ]   CFAP99 [ MEM ]
Gene Expression Viewer (FireBrowse)CFAP99 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)402160
GTEX Portal (Tissue expression)CFAP99
Human Protein AtlasENSG00000249428-CFAP99 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtD6REC4   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtD6REC4  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProD6REC4
Splice isoforms : SwissVarD6REC4
PhosPhoSitePlusD6REC4
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)CFAP99
DMDM Disease mutations402160
Blocks (Seattle)CFAP99
SuperfamilyD6REC4
Human Protein Atlas [tissue]ENSG00000249428-CFAP99 [tissue]
Peptide AtlasD6REC4
IPIIPI00888587   
Protein Interaction databases
DIP (DOE-UCLA)D6REC4
IntAct (EBI)D6REC4
FunCoupENSG00000249428
BioGRIDCFAP99
STRING (EMBL)CFAP99
ZODIACCFAP99
Ontologies - Pathways
QuickGOD6REC4
Ontology : AmiGOcell projection  
Ontology : EGO-EBIcell projection  
NDEx NetworkCFAP99
Atlas of Cancer Signalling NetworkCFAP99
Wikipedia pathwaysCFAP99
Orthology - Evolution
OrthoDB402160
GeneTree (enSembl)ENSG00000249428
Phylogenetic Trees/Animal Genes : TreeFamCFAP99
HOVERGEND6REC4
HOGENOMD6REC4
Homologs : HomoloGeneCFAP99
Homology/Alignments : Family Browser (UCSC)CFAP99
Gene fusions - Rearrangements
Tumor Fusion PortalCFAP99
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCFAP99 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CFAP99
dbVarCFAP99
ClinVarCFAP99
1000_GenomesCFAP99 
Exome Variant ServerCFAP99
ExAC (Exome Aggregation Consortium)ENSG00000249428
GNOMAD BrowserENSG00000249428
Genetic variants : HAPMAP402160
Genomic Variants (DGV)CFAP99 [DGVbeta]
DECIPHERCFAP99 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCFAP99 
Mutations
ICGC Data PortalCFAP99 
TCGA Data PortalCFAP99 
Broad Tumor PortalCFAP99
OASIS PortalCFAP99 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDCFAP99
BioMutasearch CFAP99
DgiDB (Drug Gene Interaction Database)CFAP99
DoCM (Curated mutations)CFAP99 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CFAP99 (select a term)
intoGenCFAP99
Cancer3DCFAP99(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
DisGeNETCFAP99
MedgenCFAP99
Genetic Testing Registry CFAP99
NextProtD6REC4 [Medical]
TSGene402160
GENETestsCFAP99
Target ValidationCFAP99
Huge Navigator CFAP99 [HugePedia]
snp3D : Map Gene to Disease402160
BioCentury BCIQCFAP99
ClinGenCFAP99
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD402160
Chemical/Pharm GKB GenePA166123677
Clinical trialCFAP99
Miscellaneous
canSAR (ICR)CFAP99 (select the gene name)
Probes
Litterature
PubMed1 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCFAP99
EVEXCFAP99
GoPubMedCFAP99
iHOPCFAP99
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:46:55 CET 2017

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