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

Gene ID: 79443, updated on 5-Mar-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
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Genomic context

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Location:
3p21.31
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45917903..45995824, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45933786..46011702, complement)
105.20220307 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. A Novel Mutation in the FYCO1 Gene Causing Congenital Cataract: Case Study of a Chinese Family. Mei S, et al. Dis Markers, 2022. PMID 36061348, Free PMC Article
  3. Targeted gene sequencing of FYCO1 identified a novel mutation in a Pakistani family for autosomal recessive congenital cataract. Saleem RS, et al. Mol Genet Genomic Med, 2022 Aug. PMID 35638468, Free PMC Article
  4. Identification of a novel nonsense variant in FYCO1 gene associated with infantile cataract and cortical atrophy. Aprahamian R, et al. Ophthalmic Genet, 2021 Dec. PMID 34282983
  5. Autosomal recessive cataract (CTRCT18) in the Yakut population isolate of Eastern Siberia: a novel founder variant in the FYCO1 gene. Barashkov NA, et al. Eur J Hum Genet, 2021 Jun. PMID 33767456, Free PMC Article

See all (80) 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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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_2023_10

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

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