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    WDFY4 WDFY family member 4 [ Homo sapiens (human) ]

    Gene ID: 57705, updated on 5-Mar-2024

    Summary

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    Official Symbol
    WDFY4provided by HGNC
    Official Full Name
    WDFY family member 4provided by HGNC
    Primary source
    HGNC:HGNC:29323
    See related
    Ensembl:ENSG00000128815 MIM:613316; AllianceGenome:HGNC:29323
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C10orf64
    Summary
    Predicted to be involved in autophagy. Predicted to act upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Predicted to act upstream of or within antigen processing and presentation and cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in lymph node (RPKM 13.1), spleen (RPKM 9.3) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q11.23
    Exon count:
    67
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (48684873..48982956)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (49534432..49832184)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (49892918..50191001)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2355 Neighboring gene mitogen-activated protein kinase 8 Neighboring gene Sharpr-MPRA regulatory region 12210 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:49607374-49608116 Neighboring gene Sharpr-MPRA regulatory region 2186 Neighboring gene Sharpr-MPRA regulatory region 5880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:49653211-49654112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:49662087-49663064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49668057-49668559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49671373-49672306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49672307-49673238 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:49674919-49675115 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:49678026-49678908 Neighboring gene Rho GTPase activating protein 22 Neighboring gene Sharpr-MPRA regulatory region 4601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49686951-49687608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49687609-49688265 Neighboring gene Sharpr-MPRA regulatory region 14185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49716013-49716998 Neighboring gene ARHGAP22 intronic transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49725473-49726106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49727221-49727810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49727811-49728398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2356 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:49741600-49742140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49750999-49751784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49763487-49763987 Neighboring gene NANOG hESC enhancer GRCh37_chr10:49782573-49783074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3331 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:49802653-49803477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49807300-49807800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49812539-49813269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3336 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:49887725-49887989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49893168-49893708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:49953319-49953863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3340 Neighboring gene ribosomal protein L13a pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3343 Neighboring gene uncharacterized LOC105378299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50105363-50106123 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:50156438-50157637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50160179-50160678 Neighboring gene leucine rich repeat containing 18 Neighboring gene uncharacterized LOC105378298 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:50219965-50220220 Neighboring gene microRNA 4294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3345 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:50264962-50265148 Neighboring gene V-set and transmembrane domain containing 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50316573-50317551

    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. Splicing variant of WDFY4 augments MDA5 signalling and the risk of clinically amyopathic dermatomyositis. Kochi Y, et al. Ann Rheum Dis, 2018 Apr. PMID 29331962
    2. An intronic variant associated with systemic lupus erythematosus changes the binding affinity of Yinyang1 to downregulate WDFY4. Zhao H, et al. Genes Immun, 2012 Oct. PMID 22972472
    3. WDFY4 polymorphisms in Chinese patients with anti-MDA5 dermatomyositis is associated with rapid progressive interstitial lung disease. Guo L, et al. Rheumatology (Oxford), 2023 Jun 1. PMID 36637178
    4. Analysis of WDFY4 rs7097397 and PHLDB1 rs7389 polymorphisms in Chinese patients with systemic lupus erythematosus. Zhai J, et al. Clin Rheumatol, 2022 Jul. PMID 35188604
    5. E26 transformation-specific-1 (ETS1) and WDFY family member 4 (WDFY4) polymorphisms in Chinese patients with rheumatoid arthritis. Zhang Y, et al. Int J Mol Sci, 2014 Feb 17. PMID 24549174, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. WDFY4 polymorphisms in Chinese patients with anti-MDA5 dermatomyositis is associated with rapid progressive interstitial lung disease.
      Title: WDFY4 polymorphisms in Chinese patients with anti-MDA5 dermatomyositis is associated with rapid progressive interstitial lung disease.
    2. Analysis of WDFY4 rs7097397 and PHLDB1 rs7389 polymorphisms in Chinese patients with systemic lupus erythematosus.
      Title: Analysis of WDFY4 rs7097397 and PHLDB1 rs7389 polymorphisms in Chinese patients with systemic lupus erythematosus.
    3. BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.
      Title: BVVL/ FL: features caused by SLC52A3 mutations; WDFY4 and TNFSF13B may be novel causative genes.
    4. We identified a variant in WDFY4 that was significantly associated with clinically amyopathic dermatomyositis (CADM). This variant had a cis-splicing quantitative trait locus effect for a truncated WDFY4isoform (tr-WDFY4), with higher expression in the risk allele.
      Title: Splicing variant of WDFY4 augments MDA5 signalling and the risk of clinically amyopathic dermatomyositis.
    5. A significantly increased risk for RA associated with the WDFY4 rs7097397 AG genotype.
      Title: E26 transformation-specific-1 (ETS1) and WDFY family member 4 (WDFY4) polymorphisms in Chinese patients with rheumatoid arthritis.
    6. rs877819 SNP in WDFY4 may be associated with systemic lupus erythematosus by reduced binding of YY1 and downregulating WDFY4 expression.
      Title: An intronic variant associated with systemic lupus erythematosus changes the binding affinity of Yinyang1 to downregulate WDFY4.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. Genetic variants in ETS1 and WDFY4 were found to be associated with systemic lupus erythematosus, in the Asian population studied.
      Title: Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.
    9. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus.
    EBI GWAS Catalog
    Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.
    EBI GWAS Catalog
    Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
    EBI GWAS Catalog
    Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D.
    EBI GWAS Catalog

    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

    • FLJ17416, FLJ36288, FLJ45748, KIAA1607, MGC40604, MGC45899

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in CD8-positive, alpha-beta T cell activation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in antigen processing and presentation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to virus IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    WD repeat- and FYVE domain-containing protein 4

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001370153.1 → NP_001357082.1  WD repeat- and FYVE domain-containing protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC035139, AC068898

    2. NM_001370154.1 → NP_001357083.1  WD repeat- and FYVE domain-containing protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC068898, BC034937
      Consensus CDS
      CCDS91241.1
      Related
      ENSP00000354141.2, ENST00000360890.6

    3. NM_001394531.1 → NP_001381460.1  WD repeat- and FYVE domain-containing protein 4 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC035139, AC060234, AC068898
      Consensus CDS
      CCDS44385.1
      UniProtKB/Swiss-Prot
      B9ZVP2, Q6ZS81, Q86WZ4, Q8N4A3, Q8TEN7, Q96BE1, Q9H7H8, Q9HCG5
      Related
      ENSP00000320563.5, ENST00000325239.12
      Conserved Domains (4) summary
      cd01201
      Location:2388 → 2512
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:2937 → 2980
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2540 → 2821
      Beach; Beige/BEACH domain
      cl29593
      Location:2902 → 3100
      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. NM_020945.2 → NP_065996.1  WD repeat- and FYVE domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_065996.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC035139, AC060234, AC068898
      Consensus CDS
      CCDS44385.1
      UniProtKB/Swiss-Prot
      B9ZVP2, Q6ZS81, Q86WZ4, Q8N4A3, Q8TEN7, Q96BE1, Q9H7H8, Q9HCG5
      Conserved Domains (4) summary
      cd01201
      Location:2388 → 2512
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:2937 → 2980
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2540 → 2821
      Beach; Beige/BEACH domain
      cl29593
      Location:2902 → 3100
      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: 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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      48684873..48982956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011539988.3 → XP_011538290.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011538290.1

      UniProtKB/Swiss-Prot
      B9ZVP2, Q6ZS81, Q86WZ4, Q8N4A3, Q8TEN7, Q96BE1, Q9H7H8, Q9HCG5
      Conserved Domains (4) summary
      cd01201
      Location:2388 → 2512
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:2937 → 2980
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2540 → 2821
      Beach; Beige/BEACH domain
      cl29593
      Location:2902 → 3100
      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_017016463.2 → XP_016871952.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B9ZVP2, Q6ZS81, Q86WZ4, Q8N4A3, Q8TEN7, Q96BE1, Q9H7H8, Q9HCG5
      Conserved Domains (4) summary
      cd01201
      Location:2388 → 2512
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      sd00039
      Location:2937 → 2980
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2540 → 2821
      Beach; Beige/BEACH domain
      cl29593
      Location:2902 → 3100
      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 ...

    3. XM_011539986.4 → XP_011538288.3  WD repeat- and FYVE domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B9ZVP2, Q6ZS81, Q86WZ4, Q8N4A3, Q8TEN7, Q96BE1, Q9H7H8, Q9HCG5

    4. XM_011539987.3 → XP_011538289.3  WD repeat- and FYVE domain-containing protein 4 isoform X4

    5. XM_011539990.4 → XP_011538292.2  WD repeat- and FYVE domain-containing protein 4 isoform X5

    6. XM_011539991.4 → XP_011538293.2  WD repeat- and FYVE domain-containing protein 4 isoform X6

      UniProtKB/TrEMBL
      A0A1W7HCV9

    7. XM_011539992.3 → XP_011538294.2  WD repeat- and FYVE domain-containing protein 4 isoform X7

    8. XM_047425565.1 → XP_047281521.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B9ZVP2, Q6ZS81, Q86WZ4, Q8N4A3, Q8TEN7, Q96BE1, Q9H7H8, Q9HCG5

    9. XM_047425566.1 → XP_047281522.1  WD repeat- and FYVE domain-containing protein 4 isoform X2

    10. XM_017016464.1 → XP_016871953.1  WD repeat- and FYVE domain-containing protein 4 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      49534432..49832184
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366425.1 → XP_054222400.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    2. XM_054366430.1 → XP_054222405.1  WD repeat- and FYVE domain-containing protein 4 isoform X11

    3. XM_054366432.1 → XP_054222407.1  WD repeat- and FYVE domain-containing protein 4 isoform X12

    4. XM_054366429.1 → XP_054222404.1  WD repeat- and FYVE domain-containing protein 4 isoform X10

    5. XM_054366424.1 → XP_054222399.1  WD repeat- and FYVE domain-containing protein 4 isoform X9

    6. XM_054366423.1 → XP_054222398.1  WD repeat- and FYVE domain-containing protein 4 isoform X8

    7. XM_054366426.1 → XP_054222401.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    8. XM_054366427.1 → XP_054222402.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    9. XM_054366428.1 → XP_054222403.1  WD repeat- and FYVE domain-containing protein 4 isoform X2

    10. XM_054366431.1 → XP_054222406.1  WD repeat- and FYVE domain-containing protein 4 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZS81.3 GenPept UniProtKB/Swiss-Prot:Q6ZS81

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