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    FYCO1 FYVE and coiled-coil domain autophagy adaptor 1 [ Homo sapiens (human) ]

    Gene ID: 79443, updated on 9-Dec-2024

    Summary

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    Official Symbol
    FYCO1provided by HGNC
    Official Full Name
    FYVE and coiled-coil domain autophagy adaptor 1provided by HGNC
    Primary source
    HGNC:HGNC:14673
    See related
    Ensembl:ENSG00000163820 MIM:607182; AllianceGenome:HGNC:14673
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CATC2; RUFY3; ZFYVE7; CTRCT18
    Summary
    The gene encodes a Rab7 adapter protein that is implicated in the microtubule transport of autophagosomes. The encoded protein contains a RUN domain, a 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), the autophagosome marker LC3, and the kinesin KIF5. Mutations in this gene are associated with inclusion body myositis (IBM) and autosomal recessive congenital cataracts (CATC2). [provided by RefSeq, Aug 2020]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Ubiquitous expression in heart (RPKM 22.7), endometrium (RPKM 12.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FYCO1 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45917903..45995824, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45933786..46011702, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45959395..46037316, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene leucine zipper transcription factor like 1 Neighboring gene CCR9 promoter region Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4 Neighboring gene C-C motif chemokine receptor 9 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:45956761-45957960 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:45979037-45980236 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45989039-45989208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19787 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009167-46009806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009807-46010446 Neighboring gene Sharpr-MPRA regulatory region 2695 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46029541-46030041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46034569-46035069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46037115-46037614 Neighboring gene uncharacterized LOC105377063 Neighboring gene nuclear receptor binding factor 2 pseudogene 2 Neighboring gene X-C motif chemokine receptor 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. FYCO1 regulates migration, invasion, and invadopodia formation in HeLa cells through CDC42/N-WASP/Arp2/3 signaling pathway. Sun X, et al. Biochem Cell Biol, 2022 Dec 1. PMID 36342046
    2. FYCO1: linking autophagosomes to microtubule plus end-directing molecular motors. Pankiv S, et al. Autophagy, 2010 May. PMID 20364109
    3. Mutations in FYCO1 cause autosomal-recessive congenital cataracts. Chen J, et al. Am J Hum Genet, 2011 Jun 10. PMID 21636066, Free PMC Article
    4. Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis. Güttsches AK, et al. Ann Neurol, 2017 Feb. PMID 28009083, Free PMC Article
    5. Genetics in inclusion body myositis. Rothwell S, et al. Curr Opin Rheumatol, 2017 Nov. PMID 28777108, Free PMC Article

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FYCO1 regulates migration, invasion, and invadopodia formation in HeLa cells through CDC42/N-WASP/Arp2/3 signaling pathway.
      Title: FYCO1 regulates migration, invasion, and invadopodia formation in HeLa cells through CDC42/N-WASP/Arp2/3 signaling pathway.
    2. A Novel Mutation in the FYCO1 Gene Causing Congenital Cataract: Case Study of a Chinese Family.
      Title: A Novel Mutation in the FYCO1 Gene Causing Congenital Cataract: Case Study of a Chinese Family.
    3. Targeted gene sequencing of FYCO1 identified a novel mutation in a Pakistani family for autosomal recessive congenital cataract.
      Title: Targeted gene sequencing of FYCO1 identified a novel mutation in a Pakistani family for autosomal recessive congenital cataract.
    4. Nlp promotes autophagy through facilitating the interaction of Rab7 and FYCO1.
      Title: Nlp promotes autophagy through facilitating the interaction of Rab7 and FYCO1.
    5. Autosomal recessive cataract (CTRCT18) in the Yakut population isolate of Eastern Siberia: a novel founder variant in the FYCO1 gene.
      Title: Autosomal recessive cataract (CTRCT18) in the Yakut population isolate of Eastern Siberia: a novel founder variant in the FYCO1 gene.
    6. Identification of a novel nonsense variant in FYCO1 gene associated with infantile cataract and cortical atrophy.
      Title: Identification of a novel nonsense variant in FYCO1 gene associated with infantile cataract and cortical atrophy.
    7. Lung expression of genes putatively involved in SARS-CoV-2 infection is modulated in cis by germline variants.
      Title: Lung expression of genes putatively involved in SARS-CoV-2 infection is modulated in cis by germline variants.
    8. Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases.
      Title: Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases.
    9. FYCO1 regulates accumulation of post-mitotic midbodies by mediating LC3-dependent midbody degradation
      Title: FYCO1 regulates accumulation of post-mitotic midbodies by mediating LC3-dependent midbody degradation.
    10. FYCO1 and MAP1LC3A interact through a novel binding mode that involves Atg8-family proteins
      Title: Structural basis of FYCO1 and MAP1LC3A interaction reveals a novel binding mode for Atg8-family proteins.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Cataract 18
    MedGen: C1864908 OMIM: 610019 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ13335, MGC126517, MGC126519, DKFZp779K1152

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in plus-end-directed vesicle transport along microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in plus-end-directed vesicle transport along microtubule IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    FYVE and coiled-coil domain-containing protein 1
    Names
    FYVE and coiled-coil domain containing 1
    RUN and FYVE domain containing 3
    zinc finger FYVE domain-containing protein 7

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_031955.1 RefSeqGene

      Range
      5001..82922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001386421.1 → NP_001373350.1  FYVE and coiled-coil domain-containing protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Consensus CDS
      CCDS2734.1
      UniProtKB/Swiss-Prot
      B7ZKT7, Q3MJE6, Q86T41, Q86TB1, Q8TEF9, Q96IV5, Q9BQS8, Q9H8P9
      Conserved Domains (5) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1419 → 1464
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 164
      RUN; RUN domain

    2. NM_001386422.1 → NP_001373351.1  FYVE and coiled-coil domain-containing protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Consensus CDS
      CCDS2734.1
      UniProtKB/Swiss-Prot
      B7ZKT7, Q3MJE6, Q86T41, Q86TB1, Q8TEF9, Q96IV5, Q9BQS8, Q9H8P9
      Conserved Domains (5) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1419 → 1464
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 164
      RUN; RUN domain

    3. NM_001386423.1 → NP_001373352.1  FYVE and coiled-coil domain-containing protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (5) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1418 → 1463
      GOLD_2; Golgi-dynamics membrane-trafficking
      cd17698
      Location:7 → 164
      RUN_FYCO1; RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins

    4. NM_001386424.1 → NP_001373353.1  FYVE and coiled-coil domain-containing protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (4) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      cl02689
      Location:59 → 164
      RUN; RUN domain

    5. NM_001386425.1 → NP_001373354.1  FYVE and coiled-coil domain-containing protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (4) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      cl02689
      Location:59 → 164
      RUN; RUN domain

    6. NM_001386426.1 → NP_001373355.1  FYVE and coiled-coil domain-containing protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (5) summary
      PRK11281
      Location:938 → 1124
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:203 → 1010
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1130 → 1187
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1379 → 1424
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:19 → 124
      RUN; RUN domain

    7. NM_001386427.1 → NP_001373356.1  FYVE and coiled-coil domain-containing protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (5) summary
      PRK11281
      Location:930 → 1116
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:195 → 1002
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1122 → 1179
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1371 → 1416
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 124
      RUN; RUN domain

    8. NM_001386428.1 → NP_001373357.1  FYVE and coiled-coil domain-containing protein 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (4) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      cl02689
      Location:59 → 164
      RUN; RUN domain

    9. NM_001386429.1 → NP_001373358.1  FYVE and coiled-coil domain-containing protein 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (4) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      cd17698
      Location:7 → 164
      RUN_FYCO1; RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins

    10. NM_001386430.1 → NP_001373359.1  FYVE and coiled-coil domain-containing protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Conserved Domains (4) summary
      PRK11281
      Location:778 → 964
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:43 → 850
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:970 → 1027
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1219 → 1264
      GOLD_2; Golgi-dynamics membrane-trafficking

    11. NM_024513.4 → NP_078789.2  FYVE and coiled-coil domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_078789.2

      Status: REVIEWED

      Source sequence(s)
      AC099782, BC101468, DB134257
      Consensus CDS
      CCDS2734.1
      UniProtKB/Swiss-Prot
      B7ZKT7, Q3MJE6, Q86T41, Q86TB1, Q8TEF9, Q96IV5, Q9BQS8, Q9H8P9
      Related
      ENSP00000296137.2, ENST00000296137.7
      Conserved Domains (5) summary
      PRK11281
      Location:978 → 1164
      PRK11281; mechanosensitive channel MscK
      TIGR02168
      Location:243 → 1050
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15726
      Location:1170 → 1227
      FYVE_FYCO1; FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins
      pfam13897
      Location:1419 → 1464
      GOLD_2; Golgi-dynamics membrane-trafficking
      cl02689
      Location:59 → 164
      RUN; RUN domain

    RNA

    1. NR_170107.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC099782

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      45917903..45995824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448902.1 → XP_047304858.1  FYVE and coiled-coil domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B7ZKT7, Q3MJE6, Q86T41, Q86TB1, Q8TEF9, Q96IV5, Q9BQS8, Q9H8P9

    2. XM_047448903.1 → XP_047304859.1  FYVE and coiled-coil domain-containing protein 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      45933786..46011702 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347841.1 → XP_054203816.1  FYVE and coiled-coil domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      B7ZKT7, Q3MJE6, Q86T41, Q86TB1, Q8TEF9, Q96IV5, Q9BQS8, Q9H8P9

    2. XM_054347842.1 → XP_054203817.1  FYVE and coiled-coil domain-containing protein 1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQS8.3 GenPept UniProtKB/Swiss-Prot:Q9BQS8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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