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    WDR72 WD repeat domain 72 [ Homo sapiens (human) ]

    Gene ID: 256764, updated on 2-Nov-2024

    Summary

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    Official Symbol
    WDR72provided by HGNC
    Official Full Name
    WD repeat domain 72provided by HGNC
    Primary source
    HGNC:HGNC:26790
    See related
    Ensembl:ENSG00000166415 MIM:613214; AllianceGenome:HGNC:26790
    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
    AI2A3
    Summary
    This gene encodes a protein with eight WD-40 repeats. Mutations in this gene have been associated with amelogenesis imperfecta hypomaturation type 2A3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
    Expression
    Biased expression in kidney (RPKM 35.1), thyroid (RPKM 25.6) and 3 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See WDR72 in Genome Data Viewer
    Location:
    15q21.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (53513741..53762878, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (51323311..51572387, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (53805938..54055075, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107983981 Neighboring gene uncharacterized LOC105370823 Neighboring gene long intergenic non-protein coding RNA 2490 Neighboring gene Sharpr-MPRA regulatory region 13260 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:53599743-53600942 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:53604840-53605570 Neighboring gene uncharacterized LOC105370826 Neighboring gene NANOG hESC enhancer GRCh37_chr15:53740354-53740863 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39776 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:53917398-53918006 Neighboring gene RNA, U2 small nuclear 53, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39831 Neighboring gene NANOG hESC enhancer GRCh37_chr15:54124093-54124594 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:54127299-54128498 Neighboring gene RNA, U6 small nuclear 449, pseudogene Neighboring gene uncharacterized LOC105370827 Neighboring gene unc-13 homolog C

    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 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. Mutations in the beta propeller WDR72 cause autosomal-recessive hypomaturation amelogenesis imperfecta. El-Sayed W, et al. Am J Hum Genet, 2009 Nov. PMID 19853237, Free PMC Article
    2. Hypomaturation amelogenesis imperfecta due to WDR72 mutations: a novel mutation and ultrastructural analyses of deciduous teeth. El-Sayed W, et al. Cells Tissues Organs, 2011. PMID 21196691, Free PMC Article
    3. Amelogenesis imperfecta: genotype-phenotype studies in 71 families. Wright JT, et al. Cells Tissues Organs, 2011. PMID 21597265, Free PMC Article
    4. WDR72 Mutations Associated with Amelogenesis Imperfecta and Acidosis. Zhang H, et al. J Dent Res, 2019 May. PMID 30779877, Free PMC Article
    5. Distal renal tubular acidosis caused by tryptophan-aspartate repeat domain 72 (WDR72) mutations. Rungroj N, et al. Clin Genet, 2018 Nov. PMID 30028003

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Long non-coding RNA X-Inactive Specific Transcript (XIST) interacting with USF2 promotes osteogenic differentiation of periodontal ligament stem cells through regulation of WDR72 transcription.
      Title: Long non-coding RNA X-Inactive Specific Transcript (XIST) interacting with USF2 promotes osteogenic differentiation of periodontal ligament stem cells through regulation of WDR72 transcription.
    2. Identification of the C-terminal region in Amelogenesis Imperfecta causative protein WDR72 required for Golgi localization.
      Title: Identification of the C-terminal region in Amelogenesis Imperfecta causative protein WDR72 required for Golgi localization.
    3. WDR72 mutations cause a syndromic form of AI and improve our ability to diagnose AI caused by WDR72 defects
      Title: WDR72 Mutations Associated with Amelogenesis Imperfecta and Acidosis.
    4. WDR72 mutations associated with dRTA have not been previously described. This is the first identification of pathogenic variations in WDR72 as a cause of hereditary dRTA.
      Title: Distal renal tubular acidosis caused by tryptophan-aspartate repeat domain 72 (WDR72) mutations.
    5. Based on whole exome sequencing in a large consanguineous amelogenesis imperfecta pedigree, an evidence for presence of a multi-exonic WDR72 deletion has been obtained.
      Title: Identification of the first multi-exonic WDR72 deletion in isolated amelogenesis imperfecta, and generation of a WDR72-specific copy number screening tool.
    6. WDR72 has a major role in enamel mineralization, most notably during the maturation stage, suggesting a function involving endocytic vesicle trafficking, and the removal of amelogenin proteins.
      Title: WDR72 models of structure and function: a stage-specific regulator of enamel mineralization.
    7. The rs11056571, p=1.68x10(-8); and rs2300290, p=1.09x10(-8)). rs719714 downstream of WDR72 was associated with executive functioning.
      Title: Genome-wide study identifies PTPRO and WDR72 and FOXQ1-SUMO1P1 interaction associated with neurocognitive function.
    8. Hypomaturation amelogenesis imperfecta due to WDR72 mutations: a novel mutation and ultrastructural analyses of deciduous teeth
      Title: Hypomaturation amelogenesis imperfecta due to WDR72 mutations: a novel mutation and ultrastructural analyses of deciduous teeth.
    9. the 4 recently reported SNPs,located near BNC2, SORCS1, GSC and WDR72 loci, affecting glycemic control in type 1 diabetes had no apparent effect on HbA1c in type 2 diabetes; but, for SORCS1 SNP, findings do not rule out possible relationship with HbA1c
      Title: Evaluation of four novel genetic variants affecting hemoglobin A1c levels in a population-based type 2 diabetes cohort (the HUNT2 study).
    10. A novel WDR72 dinucleotide deletion mutation (g.57,426_57,427delAT; c.1467_ 1468delAT; p.V491fsX497) was identified in both alleles of probands from Mexico and Turkey. WDR72 is a cytoplasmic protein that is critical for dental enamel formation.
      Title: Novel WDR72 mutation and cytoplasmic localization.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    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
    Amelogenesis imperfecta hypomaturation type 2A3
    MedGen: C2750771 OMIM: 613211 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    Genome-wide study identifies PTPRO and WDR72 and FOXQ1-SUMO1P1 interaction associated with neurocognitive function.
    EBI GWAS Catalog
    Joint influence of small-effect genetic variants on human longevity.
    EBI GWAS Catalog
    Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38736, MGC126663, MGC126665

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in ameloblast differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in enamel mineralization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in extracellular matrix disassembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in microtubule polymerization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein import IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of pH IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ruffle organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tubulin complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    WD repeat-containing protein 72

    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_017034.2 RefSeqGene

      Range
      5000..250922
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001277176.2 → NP_001264105.1  WD repeat-containing protein 72 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains multiple differences, compared to variant 1, including the lack of multiple 5' coding exons. It represents use of an internal promoter. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC066614, AK310211, CK299278, DA748816
      Consensus CDS
      CCDS73730.1
      UniProtKB/TrEMBL
      A0A087WTC3
      Related
      ENSP00000477754.1, ENST00000614174.4

    2. NM_182758.4 → NP_877435.3  WD repeat-containing protein 72 isoform a

      See identical proteins and their annotated locations for NP_877435.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC066611, AC066614, AK096055, BC101614, BX537884, CK299278
      Consensus CDS
      CCDS10151.1
      UniProtKB/Swiss-Prot
      Q3MJ13, Q7Z3I3, Q8N8X2
      UniProtKB/TrEMBL
      H0YLX4
      Related
      ENSP00000353699.5, ENST00000360509.10
      Conserved Domains (3) summary
      COG2319
      Location:404 → 596
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:20 → 60
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:404 → 595
      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 ...

    RNA

    1. NR_102334.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC066611, AC066614, BC101614, BX648571, CK299278

    2. NR_102335.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains multiple differences, compared to variant 1, including the lack of multiple 5' exons. It represents use of an internal promoter. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC066614, AK310211, CK299278
      Related
      ENST00000567224.1

    3. NR_102336.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC066614, CK299278, DA736178

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      53513741..53762878 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521436.3 → XP_011519738.1  WD repeat-containing protein 72 isoform X2

      UniProtKB/TrEMBL
      H0YLX4
      Conserved Domains (3) summary
      COG2319
      Location:404 → 590
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:20 → 60
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:404 → 589
      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_047432344.1 → XP_047288300.1  WD repeat-containing protein 72 isoform X1

      UniProtKB/Swiss-Prot
      Q3MJ13, Q7Z3I3, Q8N8X2

    3. XM_047432343.1 → XP_047288299.1  WD repeat-containing protein 72 isoform X1

      UniProtKB/Swiss-Prot
      Q3MJ13, Q7Z3I3, Q8N8X2

    4. XM_047432345.1 → XP_047288301.1  WD repeat-containing protein 72 isoform X3

    5. XM_047432342.1 → XP_047288298.1  WD repeat-containing protein 72 isoform X1

      UniProtKB/Swiss-Prot
      Q3MJ13, Q7Z3I3, Q8N8X2

    6. XM_017022061.2 → XP_016877550.1  WD repeat-containing protein 72 isoform X1

      UniProtKB/Swiss-Prot
      Q3MJ13, Q7Z3I3, Q8N8X2
      UniProtKB/TrEMBL
      H0YLX4
      Conserved Domains (3) summary
      COG2319
      Location:404 → 596
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:20 → 60
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:404 → 595
      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 ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      51323311..51572387 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377676.1 → XP_054233651.1  WD repeat-containing protein 72 isoform X3

    2. XM_054377675.1 → XP_054233650.1  WD repeat-containing protein 72 isoform X2

    3. XM_054377672.1 → XP_054233647.1  WD repeat-containing protein 72 isoform X1

    4. XM_054377673.1 → XP_054233648.1  WD repeat-containing protein 72 isoform X1

    5. XM_054377671.1 → XP_054233646.1  WD repeat-containing protein 72 isoform X1

    6. XM_054377674.1 → XP_054233649.1  WD repeat-containing protein 72 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3MJ13.2 GenPept UniProtKB/Swiss-Prot:Q3MJ13

    Gene LinkOut

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

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