CFAP99 (Cilia and Flagella Associated Protein 99)

2016-06-01 Sinem Tunçer , Rafig Gurbanov Affiliation

Department of Biological Sciences, Middle East Technical University, Ankara, Turkey

Identity

HGNC

CFAP99

LOCATION

4p16.3 (

IMAGE

LEGEND

Figure 1 Cytogenetic bands within chromosome 4. The 4p16.3 is indicated by red.

LOCUSID

402160

ALIAS

LOC402160,LOC441005

Abstract

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

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).

Proteins

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

Entity name

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 name

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

Pubmed ID	Last Year	Title	Authors
23256888	2013	Decoding the disease-associated proteins encoded in the human chromosome 4.	Chen LC et al
26840378	2016	Assessing the fetal effects of maternal obesity via transcriptomic analysis of cord blood: a prospective case-control study.	Edlow AG et al

Other Information

Locus ID:

NCBI: 402160
HGNC: 51180
Ensembl: ENSG00000206113

Variants:

dbSNP: 402160
ClinVar: 402160
TCGA: ENSG00000206113
COSMIC: CFAP99

RNA/Proteins

Gene ID	Transcript ID	Uniprot
ENSG00000206113	ENST00000506607	A0A499FIZ3
ENSG00000206113	ENST00000635017	A0A0U1RQC7

Expression (GTEx)

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

Citation

Sinem Tunçer ; Rafig Gurbanov

CFAP99 (Cilia and Flagella Associated Protein 99)

Atlas Genet Cytogenet Oncol Haematol. 2016-06-01

Online version: http://atlasgeneticsoncology.org/gene/61767/cfap99