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Aliases for FYCO1 Gene

Aliases for FYCO1 Gene

  • FYVE And Coiled-Coil Domain Containing 1 2 3 5
  • Zinc Finger FYVE Domain-Containing Protein 7 3 4
  • ZFYVE7 3 4
  • FYVE And Coiled-Coil Domain-Containing Protein 1 3
  • RUN And FYVE Domain Containing 3 3
  • CTRCT18 3
  • CATC2 3
  • RUFY3 3

External Ids for FYCO1 Gene

Previous GeneCards Identifiers for FYCO1 Gene

  • GC03M045200
  • GC03M045778
  • GC03M045919

Summaries for FYCO1 Gene

Entrez Gene Summary for FYCO1 Gene

  • This gene encodes a protein that contains a RUN domain, FYVE-type zinc finger domain and Golgi dynamics (GOLD) domain. The encoded protein plays a role in microtubule plus end-directed transport of autophagic vesicles through interactions with the small GTPase Rab7, phosphatidylinositol-3-phosphate (PI3P) and the autophagosome marker LC3. Mutations in this gene are a cause of autosomal recessive congenital cataract-2 (CATC2). [provided by RefSeq, Dec 2011]

GeneCards Summary for FYCO1 Gene

FYCO1 (FYVE And Coiled-Coil Domain Containing 1) is a Protein Coding gene. Diseases associated with FYCO1 include Cataract 18, Autosomal Recessive and Early-Onset Nuclear Cataract. GO annotations related to this gene include nucleotide binding. An important paralog of this gene is EEA1.

UniProtKB/Swiss-Prot for FYCO1 Gene

  • May mediate microtubule plus end-directed vesicle transport.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FYCO1 Gene

Genomics for FYCO1 Gene

Regulatory Elements for FYCO1 Gene

Enhancers for FYCO1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G045991 1.8 FANTOM5 ENCODE dbSUPER 15.5 +1.9 1870 5.3 HDGF PKNOX1 CREB3L1 AGO1 WRNIP1 ARID4B SIN3A YY1 SLC30A9 ZNF766 CXCR6 FYCO1 CCR1 CCDC12 SACM1L CCR5 CCR2
GH03G046106 2 FANTOM5 Ensembl ENCODE dbSUPER 13.5 -115.8 -115821 9.6 HDGF PKNOX1 ATF1 FOXA2 WRNIP1 ELK1 ZNF207 FOS DEK JUNB CCR1 CCRL2 CXCR6 FYCO1 CCR2 CCR5 LIMD1 XCR1 CCR3 SACM1L
GH03G045983 1.8 FANTOM5 Ensembl ENCODE dbSUPER 14.7 +8.8 8845 6.2 FOXA2 SIN3A ZNF48 YY1 CBX5 FOS NFYC JUNB TBX21 ZNF592 CXCR6 CCRL2 FYCO1 LZTFL1 CCR2 CCR5 CCR1 CCR3
GH03G046088 1.9 FANTOM5 Ensembl ENCODE dbSUPER 13.5 -99.5 -99477 13.4 HDGF TBP PKNOX1 TBL1XR1 WRNIP1 BMI1 RAD21 EGR1 ZNF143 FOS CCR1 CCRL2 CXCR6 FYCO1 CCR5 LOC102724297 CCR2 CCR3 CCDC12 LIMD1
GH03G045914 1.4 Ensembl ENCODE dbSUPER 18.1 +80.3 80250 2.3 PKNOX1 TBL1XR1 WRNIP1 ZFP64 BMI1 EGR1 ZNF207 FOS RELB ETV6 FYCO1 CXCR6 LZTFL1 ENSG00000201635
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FYCO1 on UCSC Golden Path with GeneCards custom track

Promoters for FYCO1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000151798 424 1601 HDGF PKNOX1 CREB3L1 AGO1 WRNIP1 ARID4B SIN3A YY1 SLC30A9 ZNF766

Genomic Location for FYCO1 Gene

Chromosome:
3
Start:
45,917,899 bp from pter
End:
45,995,824 bp from pter
Size:
77,926 bases
Orientation:
Minus strand

Genomic View for FYCO1 Gene

Genes around FYCO1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FYCO1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FYCO1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FYCO1 Gene

Proteins for FYCO1 Gene

  • Protein details for FYCO1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQS8-FYCO1_HUMAN
    Recommended name:
    FYVE and coiled-coil domain-containing protein 1
    Protein Accession:
    Q9BQS8
    Secondary Accessions:
    • B7ZKT7
    • Q3MJE6
    • Q86T41
    • Q86TB1
    • Q8TEF9
    • Q96IV5
    • Q9H8P9

    Protein attributes for FYCO1 Gene

    Size:
    1478 amino acids
    Molecular mass:
    166983 Da
    Quaternary structure:
    • Can form homodimers. Interacts (via C-terminus) with MAP1LC3B. Interacts with RAB7A; the interaction with RAB7A induces FYCO1 recruitment to late endosomal/lysosomal compartments. Interacts with MAP1LC3B (By similarity).
    SequenceCaution:
    • Sequence=AAH07218.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14559.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB84991.1; Type=Frameshift; Positions=1402; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for FYCO1 Gene

    Alternative splice isoforms for FYCO1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FYCO1 Gene

Post-translational modifications for FYCO1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FYCO1 Gene

No data available for DME Specific Peptides for FYCO1 Gene

Domains & Families for FYCO1 Gene

Gene Families for FYCO1 Gene

Suggested Antigen Peptide Sequences for FYCO1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FYCO1: view

No data available for UniProtKB/Swiss-Prot for FYCO1 Gene

Function for FYCO1 Gene

Molecular function for FYCO1 Gene

UniProtKB/Swiss-Prot Function:
May mediate microtubule plus end-directed vesicle transport.

Gene Ontology (GO) - Molecular Function for FYCO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 20100911
GO:0044183 protein binding involved in protein folding IBA --
GO:0046872 metal ion binding IEA --
GO:0051082 unfolded protein binding IBA --
genes like me logo Genes that share ontologies with FYCO1: view
genes like me logo Genes that share phenotypes with FYCO1: view

Human Phenotype Ontology for FYCO1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for FYCO1 Gene

Localization for FYCO1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FYCO1 Gene

Cytoplasmic vesicle, autophagosome. Endosome. Lysosome. Note=Localizes to the external but not to the internal membrane of autophagosomes, and upon autophagosome/late endosome/lysosome fusion, it stays on the external surface of autolysosomes.

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 FYCO1 gene
Compartment Confidence
lysosome 5
endosome 5
golgi apparatus 4
cytosol 3
nucleus 2
cytoskeleton 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for FYCO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA,IDA 20100911
GO:0005768 endosome IEA --
GO:0005770 late endosome IDA 20100911
GO:0005776 autophagosome IEA,IDA 20100911
GO:0005794 Golgi apparatus IDA --
genes like me logo Genes that share ontologies with FYCO1: view

Pathways & Interactions for FYCO1 Gene

SuperPathways for FYCO1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for FYCO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006458 de novo protein folding IBA --
GO:0006810 transport IEA --
GO:0061077 chaperone-mediated protein folding IBA --
GO:0072383 plus-end-directed vesicle transport along microtubule IMP 20100911
GO:1901098 positive regulation of autophagosome maturation IMP 26468287
genes like me logo Genes that share ontologies with FYCO1: view

No data available for Pathways by source and SIGNOR curated interactions for FYCO1 Gene

Drugs & Compounds for FYCO1 Gene

No Compound Related Data Available

Transcripts for FYCO1 Gene

Unigene Clusters for FYCO1 Gene

FYVE and coiled-coil domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FYCO1 Gene

No ASD Table

Relevant External Links for FYCO1 Gene

GeneLoc Exon Structure for
FYCO1
ECgene alternative splicing isoforms for
FYCO1

Expression for FYCO1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FYCO1 Gene

mRNA differential expression in normal tissues according to GTEx for FYCO1 Gene

This gene is overexpressed in Muscle - Skeletal (x6.9).

Protein differential expression in normal tissues from HIPED for FYCO1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (6.4) and Gallbladder (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FYCO1 Gene



Protein tissue co-expression partners for FYCO1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of FYCO1 Gene:

FYCO1

SOURCE GeneReport for Unigene cluster for FYCO1 Gene:

Hs.200227

mRNA Expression by UniProt/SwissProt for FYCO1 Gene:

Q9BQS8-FYCO1_HUMAN
Tissue specificity: Expressed in heart and skeletal muscle.

Evidence on tissue expression from TISSUES for FYCO1 Gene

  • Heart(4.4)
  • Muscle(4.4)
  • Liver(4.2)
  • Lung(4.2)
  • Skin(4.2)
  • Spleen(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FYCO1 Gene

Germ Layers:
  • ectoderm
Systems:
  • nervous
Organs:
Head and neck:
  • eye
  • head
genes like me logo Genes that share expression patterns with FYCO1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for FYCO1 Gene

Orthologs for FYCO1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for FYCO1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FYCO1 35 34
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia FYCO1 34 35
  • 84.18 (n)
cow
(Bos Taurus)
Mammalia FYCO1 34 35
  • 83.53 (n)
rat
(Rattus norvegicus)
Mammalia Fyco1 34
  • 80.32 (n)
mouse
(Mus musculus)
Mammalia Fyco1 34 16 35
  • 79.81 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia FYCO1 35
  • 62 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia FYCO1 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves FYCO1 34 35
  • 62.58 (n)
lizard
(Anolis carolinensis)
Reptilia FYCO1 35
  • 52 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC565649 34
  • 50.62 (n)
FYCO1 (2 of 2) 35
  • 38 (a)
OneToMany
fyco1a 35
  • 38 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG4030 35
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rabn-5 35
  • 17 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PIB1 37
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 18 (a)
OneToMany
Species where no ortholog for FYCO1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • 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 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for FYCO1 Gene

ENSEMBL:
Gene Tree for FYCO1 (if available)
TreeFam:
Gene Tree for FYCO1 (if available)

Paralogs for FYCO1 Gene

Paralogs for FYCO1 Gene

genes like me logo Genes that share paralogs with FYCO1: view

Variants for FYCO1 Gene

Sequence variations from dbSNP and Humsavar for FYCO1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs387906965 Pathogenic, Cataract 18 (CTRCT18) [MIM:610019] 45,931,195(-) CAGCC(C/T)GATCC nc-transcript-variant, reference, missense
rs387906963 Pathogenic 45,968,289(-) TGGCA(C/T)AGGAG nc-transcript-variant, reference, stop-gained
rs387906964 Pathogenic 45,967,128(-) AGAGC(C/T)AGTGC nc-transcript-variant, reference, stop-gained
rs387906966 Pathogenic 45,967,788(-) AGCTG(C/T)AGTTC nc-transcript-variant, reference, stop-gained
rs111480321 Likely benign 45,921,574(+) CAACG(C/T)CTCGG nc-transcript-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for FYCO1 Gene

Variant ID Type Subtype PubMed ID
esv2725227 CNV deletion 23290073
esv2759145 CNV loss 17122850
nsv476148 CNV novel sequence insertion 20440878
nsv834678 CNV gain 17160897

Variation tolerance for FYCO1 Gene

Residual Variation Intolerance Score: 97.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 17.25; 98.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FYCO1 Gene

Human Gene Mutation Database (HGMD)
FYCO1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FYCO1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FYCO1 Gene

Disorders for FYCO1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for FYCO1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cataract 18, autosomal recessive
  • cataract 18
early-onset nuclear cataract
cataract 44
  • ctrct44
- elite association - COSMIC cancer census association via MalaCards
Search FYCO1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FYCO1_HUMAN
  • Cataract 18 (CTRCT18) [MIM:610019]: An opacification of the crystalline lens of the eye becoming evident at birth or in infancy. It frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. {ECO:0000269 PubMed:21636066}. Note=The disease is caused by mutations affecting the gene represented in this entry. Pathogenic mutations in FYCO1 can affect intracellular transport of autophagocytic vesicles from the perinuclear area to the periphery, leading to an accumulation of large numbers of vesicles and hence loss of lens transparency (PubMed:21636066). {ECO:0000269 PubMed:21636066}.

Relevant External Links for FYCO1

Genetic Association Database (GAD)
FYCO1
Human Genome Epidemiology (HuGE) Navigator
FYCO1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
FYCO1
genes like me logo Genes that share disorders with FYCO1: view

No data available for Genatlas for FYCO1 Gene

Publications for FYCO1 Gene

  1. The transcriptional map of the common eliminated region 1 (C3CER1) in 3p21.3. (PMID: 11896456) Kiss H. … Dumanski J.P. (Eur. J. Hum. Genet. 2002) 2 3 4 64
  2. Autophagy promotes primary ciliogenesis by removing OFD1 from centriolar satellites. (PMID: 24089205) Tang Z. … Zhong Q. (Nature 2013) 3 4 64
  3. Mutations in FYCO1 cause autosomal-recessive congenital cataracts. (PMID: 21636066) Chen J. … Hejtmancik J.F. (Am. J. Hum. Genet. 2011) 3 4 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport. (PMID: 20100911) Pankiv S. … Johansen T. (J. Cell Biol. 2010) 3 4 64

Products for FYCO1 Gene

Sources for FYCO1 Gene

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