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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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