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WDFY3 WD repeat and FYVE domain containing 3 [ Homo sapiens (human) ]

Gene ID: 23001, updated on 10-Dec-2019

Summary

Official Symbol
WDFY3provided by HGNC
Official Full Name
WD repeat and FYVE domain containing 3provided by HGNC
Primary source
HGNC:HGNC:20751
See related
Ensembl:ENSG00000163625 MIM:617485
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
ALFY; BCHS; MCPH18; ZFYVE25
Summary
This gene encodes a phosphatidylinositol 3-phosphate-binding protein that functions as a master conductor for aggregate clearance by autophagy. This protein shuttles from the nuclear membrane to colocalize with aggregated proteins, where it complexes with other autophagic components to achieve macroautophagy-mediated clearance of these aggregated proteins. However, it is not necessary for starvation-induced macroautophagy. [provided by RefSeq, May 2010]
Expression
Ubiquitous expression in kidney (RPKM 8.6), brain (RPKM 8.1) and 25 other tissues See more
Orthologs

Genomic context

See WDFY3 in Genome Data Viewer
Location:
4q21.23
Exon count:
74
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (84669547..84966690, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (85590690..85887544, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723338 Neighboring gene ribosomal protein L3 pseudogene 13 Neighboring gene CDP-diacylglycerol synthase 1 Neighboring gene RNA, 7SL, cytoplasmic 552, pseudogene Neighboring gene RNA, U6 small nuclear 469, pseudogene Neighboring gene WDFY3 antisense RNA 2 Neighboring gene RN7SK pseudogene 48 Neighboring gene quinone oxidoreductase-like protein 2 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0993, MGC16461

Gene Ontology Provided by GOA

Function Evidence Code Pubs
1-phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
PubMed 
beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
aggrephagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with Atg12-Atg5-Atg16 complex IDA
Inferred from Direct Assay
more info
PubMed 
PML body IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with autophagosome IDA
Inferred from Direct Assay
more info
PubMed 
autophagosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
axon IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
extrinsic component of autophagosome membrane IEA
Inferred from Electronic Annotation
more info
 
extrinsic component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
inclusion body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear envelope IDA
Inferred from Direct Assay
more info
PubMed 
nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
perikaryon IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
WD repeat and FYVE domain-containing protein 3
Names
autophagy-linked FYVE protein

NCBI Reference Sequences (RefSeq)

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_046917.1 RefSeqGene

    Range
    4702..301845
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014991.5NP_055806.2  WD repeat and FYVE domain-containing protein 3

    See identical proteins and their annotated locations for NP_055806.2

    Status: REVIEWED

    Source sequence(s)
    AB023210, AC108021, AF538685, AI393222, AI962188
    Consensus CDS
    CCDS3609.1
    UniProtKB/Swiss-Prot
    Q8IZQ1
    UniProtKB/TrEMBL
    A0A024RDI0
    Related
    ENSP00000295888.4, ENST00000295888.8
    Conserved Domains (7) summary
    smart01026
    Location:26952976
    Beach; Beige/BEACH domain
    COG2319
    Location:30443247
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25342657
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34493513
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14341554
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30843125
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30843246
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    84669547..84966690 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531759.2XP_011530061.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011530061.1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. XM_017007909.1XP_016863398.1  WD repeat and FYVE domain-containing protein 3 isoform X7

  3. XM_011531763.3XP_011530065.1  WD repeat and FYVE domain-containing protein 3 isoform X4

    See identical proteins and their annotated locations for XP_011530065.1

    UniProtKB/Swiss-Prot
    Q8IZQ1
    UniProtKB/TrEMBL
    A0A024RDI0
    Conserved Domains (7) summary
    smart01026
    Location:26952976
    Beach; Beige/BEACH domain
    COG2319
    Location:30443247
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25342657
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34493513
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14341554
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30843125
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30843246
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. XM_011531760.3XP_011530062.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011530062.1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. XM_011531764.3XP_011530066.1  WD repeat and FYVE domain-containing protein 3 isoform X5

    Conserved Domains (7) summary
    smart01026
    Location:26852966
    Beach; Beige/BEACH domain
    COG2319
    Location:30343237
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25242647
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34393503
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14241544
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30743115
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30743236
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  6. XM_011531761.3XP_011530063.1  WD repeat and FYVE domain-containing protein 3 isoform X2

    Conserved Domains (7) summary
    smart01026
    Location:26982979
    Beach; Beige/BEACH domain
    COG2319
    Location:30473250
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25372660
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34523516
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30873128
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30873249
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  7. XM_011531757.3XP_011530059.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011530059.1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  8. XM_005262858.5XP_005262915.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005262915.1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  9. XM_017007908.2XP_016863397.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  10. XM_017007907.2XP_016863396.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  11. XM_017007906.2XP_016863395.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    Conserved Domains (7) summary
    smart01026
    Location:27132994
    Beach; Beige/BEACH domain
    COG2319
    Location:30623265
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25522675
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34673531
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:31023143
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:31023264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  12. XM_011531765.3XP_011530067.1  WD repeat and FYVE domain-containing protein 3 isoform X6

    UniProtKB/Swiss-Prot
    Q8IZQ1
    Conserved Domains (7) summary
    smart01026
    Location:26782959
    Beach; Beige/BEACH domain
    COG2319
    Location:30273230
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25172640
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34323496
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14341554
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30673108
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30673229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  13. XM_011531762.3XP_011530064.1  WD repeat and FYVE domain-containing protein 3 isoform X3

    Conserved Domains (7) summary
    smart01026
    Location:26962977
    Beach; Beige/BEACH domain
    COG2319
    Location:30453248
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34503514
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30853126
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30853247
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  14. XM_011531766.2XP_011530068.1  WD repeat and FYVE domain-containing protein 3 isoform X8

    Conserved Domains (2) summary
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    cl22861
    Location:12091268
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  15. XM_011531767.2XP_011530069.1  WD repeat and FYVE domain-containing protein 3 isoform X9

    Conserved Domains (2) summary
    pfam15787
    Location:14521572
    DUF4704; Domain of unknown function (DUF4704)
    cl22861
    Location:12091268
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_178583.2: Suppressed sequence

    Description
    NM_178583.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  2. NM_178585.2: Suppressed sequence

    Description
    NM_178585.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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