CFAP53 Gene (Protein Coding)

Cilia And Flagella Associated Protein 53

GC18M050227
GIFtS:
34
This gene belongs to the CFAP53 family. It was found to be differentially expressed by the ciliated cells of frog epidermis and in skin fibroblasts from human. Mutations in this gene are associated with visceral heterotaxy-6, which implicates this gene in determination of left-right asymmetric patterning. [provided by RefSeq, Aug 2015] See more...

Aliases for CFAP53 Gene

Aliases for CFAP53 Gene

  • Cilia And Flagella Associated Protein 53 2 3 5
  • Cilia- And Flagella-Associated Protein 53 3 4
  • Coiled-Coil Domain Containing 11 2 3
  • CCDC11 3 4
  • Coiled-Coil Domain-Containing Protein 11 4
  • FLJ32743 2
  • CFAP53 5
  • HTX6 3

External Ids for CFAP53 Gene

Previous HGNC Symbols for CFAP53 Gene

  • CCDC11

Summaries for CFAP53 Gene

Entrez Gene Summary for CFAP53 Gene

  • This gene belongs to the CFAP53 family. It was found to be differentially expressed by the ciliated cells of frog epidermis and in skin fibroblasts from human. Mutations in this gene are associated with visceral heterotaxy-6, which implicates this gene in determination of left-right asymmetric patterning. [provided by RefSeq, Aug 2015]

GeneCards Summary for CFAP53 Gene

CFAP53 (Cilia And Flagella Associated Protein 53) is a Protein Coding gene. Diseases associated with CFAP53 include Heterotaxy, Visceral, 6, Autosomal and Visceral Heterotaxy.

UniProtKB/Swiss-Prot Summary for CFAP53 Gene

  • May play a role in the beating of primary cilia and thereby be involved in the establishment of organ laterality during embryogenesis.

Additional gene information for CFAP53 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CFAP53 Gene

Genomics for CFAP53 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CFAP53 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH18J050265 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 256.2 -0.8 -804 3.8 CHD2 ZBTB10 NR2C1 BRCA1 ETS1 ZNF217 POLR2A CTCF ELF1 ZIC2 CFAP53 CXXC1 MBD1 SKA1 SMAD4 lnc-CFAP53-1
GH18J050272 Promoter 0.3 EPDnew 250.4 -6.4 -6364 0.1 CFAP53 lnc-CFAP53-1 MBD1
GH18J050306 Promoter/Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 10.9 -41.6 -41577 2.1 MXD4 CEBPA MNT SMAD5 CEBPB SIN3A SAP130 RXRA KLF9 FOXA2 CFAP53 SKA1 MBD1 ENSG00000267695 ENSG00000274930 CXXC1 HSALNG0121526
GH18J050277 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 6.3 -13.4 -13395 5.4 ZSCAN16 TBP SP1 ZBTB10 BCL11A MXD4 NR2C1 MNT SMAD5 ETS1 MBD1 HSALNG0121524 lnc-CXXC1-2 SMAD4 RPL17 CXXC1 ELAC1 MEX3C CFAP53
GH18J050297 Promoter/Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 8.5 -31.7 -31651 1 ELF1 SIN3A GABPA IRF4 MAX ZBTB40 SPI1 BHLHE40 ZBTB48 HCFC1 CFAP53 ENSG00000263916 MBD1 ENSG00000267695 CXXC1 HSALNG0121526 SKA1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CFAP53 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CFAP53

Genomic Locations for CFAP53 Gene

Latest Assembly
chr18:50,227,193-50,266,495
(GRCh38/hg38)
Size:
39,303 bases
Orientation:
Minus strand

Previous Assembly
chr18:47,753,563-47,792,865
(GRCh37/hg19 by Entrez Gene)
Size:
39,303 bases
Orientation:
Minus strand

chr18:47,753,563-47,792,892
(GRCh37/hg19 by Ensembl)
Size:
39,330 bases
Orientation:
Minus strand

Genomic View for CFAP53 Gene

Genes around CFAP53 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CFAP53 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CFAP53 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CFAP53 Gene

Proteins for CFAP53 Gene

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  • Protein details for CFAP53 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96M91-CFA53_HUMAN
    Recommended name:
    Cilia- and flagella-associated protein 53
    Protein Accession:
    Q96M91
    Secondary Accessions:
    • B4DXT1

    Protein attributes for CFAP53 Gene

    Size:
    514 amino acids
    Molecular mass:
    61835 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB71418.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

neXtProt entry for CFAP53 Gene

Protein Expression for CFAP53 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CFAP53 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CFAP53 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CFAP53 Gene

Domains & Families for CFAP53 Gene

Gene Families for CFAP53 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CFAP53 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CFAP53 Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain-containing protein 11 (CCD11_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96M91

UniProtKB/Swiss-Prot:

CFA53_HUMAN :
  • Belongs to the CFAP53 family.
Family:
  • Belongs to the CFAP53 family.
genes like me logo Genes that share domains with CFAP53: view

Function for CFAP53 Gene

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  6. Cell Lines for research

Molecular function for CFAP53 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the beating of primary cilia and thereby be involved in the establishment of organ laterality during embryogenesis.

Phenotypes From GWAS Catalog for CFAP53 Gene

Gene Ontology (GO) - Molecular Function for CFAP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with CFAP53: view
genes like me logo Genes that share phenotypes with CFAP53: view

Human Phenotype Ontology for CFAP53 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for CFAP53 Gene

miRTarBase miRNAs that target CFAP53

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CFAP53

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for CFAP53 Gene

Localization for CFAP53 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CFAP53 Gene

Cell projection, cilium.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CFAP53 gene
Compartment Confidence
nucleus 3
cytosol 3
extracellular 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Midbody (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CFAP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005576 extracellular region IEA --
GO:0005929 cilium IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with CFAP53: view

Pathways & Interactions for CFAP53 Gene

PathCards logo

SuperPathways for CFAP53 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CFAP53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003341 cilium movement ISS --
GO:0007275 multicellular organism development IEA --
GO:0007368 determination of left/right symmetry IMP 26531781
GO:0060271 cilium assembly IEA --
GO:0060287 epithelial cilium movement involved in determination of left/right asymmetry ISS --
genes like me logo Genes that share ontologies with CFAP53: view

No data available for Pathways by source and SIGNOR curated interactions for CFAP53 Gene

Drugs & Compounds for CFAP53 Gene

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No Compound Related Data Available

Transcripts for CFAP53 Gene

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mRNA/cDNA for CFAP53 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CFAP53

Alternative Splicing Database (ASD) splice patterns (SP) for CFAP53 Gene

No ASD Table

Relevant External Links for CFAP53 Gene

GeneLoc Exon Structure for
CFAP53

Expression for CFAP53 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CFAP53 Gene

mRNA expression in normal human tissues for CFAP53 Gene
mRNA expression by GTEx for CFAP53 Gene

Protein differential expression in normal tissues from HIPED for CFAP53 Gene

This gene is overexpressed in Urine (32.7), Islet of Langerhans (15.3), Heart (7.4), and Cerebrospinal fluid (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CFAP53 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CFAP53

mRNA Expression by UniProt/SwissProt for CFAP53 Gene:

Q96M91-CFA53_HUMAN
Tissue specificity: Expressed in skin fibroblasts (at protein level).

Phenotype-based relationships between genes and organs from Gene ORGANizer for CFAP53 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • lymphatic
  • nervous
  • reproductive
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • head
Thorax:
  • heart
Abdomen:
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
Pelvis:
  • uterus
General:
  • blood
  • blood vessel
genes like me logo Genes that share expression patterns with CFAP53: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES for CFAP53 Gene

Orthologs for CFAP53 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CFAP53 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CCDC11 30 31
  • 99.81 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CCDC11 30 31
  • 87.16 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CCDC11 31
  • 81 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ccdc11 30
  • 78.8 (n)
Mouse
(Mus musculus)
 Mammalia Ccdc11 30 31
  • 78.1 (n)
 OneToOne
Cfap53 17
Platypus
(Ornithorhynchus anatinus)
 Mammalia CCDC11 31
  • 48 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CCDC11 31
  • 46 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CCDC11 31
  • 34 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia ccdc11 30
  • 52.37 (n)
Zebrafish
(Danio rerio)
 Actinopterygii LOC101883738 30
  • 49.01 (n)
ccdc11 31
  • 31 (a)
 OneToOne
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 41 (a)
 OneToOne
Species where no ortholog for CFAP53 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CFAP53 Gene

ENSEMBL:
Gene Tree for CFAP53 (if available)
TreeFam:
Gene Tree for CFAP53 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CFAP53: view image

Paralogs for CFAP53 Gene

Pseudogenes.org Pseudogenes for CFAP53 Gene

genes like me logo Genes that share paralogs with CFAP53: view

No data available for Paralogs for CFAP53 Gene

Variants for CFAP53 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CFAP53 Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
957789 Uncertain Significance: Heterotaxy, visceral, 6, autosomal 50,243,080(-) A/G
NM_145020.5(CFAP53):c.1033T>C (p.Tyr345His) 		MISSENSE
959683 Uncertain Significance: Heterotaxy, visceral, 6, autosomal 50,262,036(-) C/T
NM_145020.5(CFAP53):c.253G>A (p.Asp85Asn) 		MISSENSE
960150 Uncertain Significance: Heterotaxy, visceral, 6, autosomal 50,251,489(-) G/A
NM_145020.5(CFAP53):c.769C>T (p.Arg257Cys) 		MISSENSE
964003 Uncertain Significance: Heterotaxy, visceral, 6, autosomal 50,242,930(-) A/C
NM_145020.5(CFAP53):c.1183T>G (p.Cys395Gly) 		MISSENSE
969306 Uncertain Significance: Heterotaxy, visceral, 6, autosomal; none provided 50,243,012(-) G/T
NM_145020.5(CFAP53):c.1101C>A (p.Asp367Glu) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CFAP53 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CFAP53 Gene

Variant ID Type Subtype PubMed ID
esv3416788 CNV insertion 20981092
nsv1057599 CNV gain 25217958
nsv576889 CNV loss 21841781

Variation tolerance for CFAP53 Gene

Residual Variation Intolerance Score: 75.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.09; 92.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CFAP53 Gene

Human Gene Mutation Database (HGMD)
CFAP53
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CFAP53

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CFAP53 Gene

Disorders for CFAP53 Gene

MalaCards: The human disease database

(17) MalaCards diseases for CFAP53 Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
heterotaxy, visceral, 6, autosomal
  • htx6
visceral heterotaxy
  • heterotaxia
dextrocardia with situs inversus
  • situs inversus totalis
dextrocardia
  • heart predominantly in right hemithorax
heterotaxy
  • heterotaxia
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CFA53_HUMAN
  • Heterotaxy, visceral, 6, autosomal (HTX6) [MIM:614779]: A form of visceral heterotaxy, a complex disorder due to disruption of the normal left-right asymmetry of the thoracoabdominal organs. Visceral heterotaxy or situs ambiguus results in randomization of the placement of visceral organs, including the heart, lungs, liver, spleen, and stomach. The organs are oriented randomly with respect to the left-right axis and with respect to one another. It can be associated with a variety of congenital defects including cardiac malformations. HTX6 clinical features are situs inversus totalis and severe complex cardiac malformations including unbalanced atrioventricular canal defects, transposition of the great arteries with severe pulmonary stenosis, right aortic arch, abnormal systemic venous return and total anomalous pulmonary venous drainage. {ECO:0000269 PubMed:22577226, ECO:0000269 PubMed:26531781}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for CFAP53

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CFAP53: view

No data available for Genatlas for CFAP53 Gene

Publications for CFAP53 Gene

  1. A human laterality disorder associated with recessive CCDC11 mutation. (PMID: 22577226) Perles Z … Elpeleg O (Journal of medical genetics 2012) 2 3 4 74
  2. A Zebrafish Loss-of-Function Model for Human CFAP53 Mutations Reveals Its Specific Role in Laterality Organ Function. (PMID: 26531781) Noël ES … Bakkers J (Human mutation 2016) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. (PMID: 32814053) Haenig C … Wanker EE (Cell reports 2020) 3

ExternalLinks

View latest publications for CFAP53 gene in Mastermind

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