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

Gene ID: 256764, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (53513741..53762878, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (51323311..51572387, complement)
105.20220307 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
  • 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. WDR72 Mutations Associated with Amelogenesis Imperfecta and Acidosis. Zhang H, et al. J Dent Res, 2019 May. PMID 30779877, Free PMC Article
  2. Distal renal tubular acidosis caused by tryptophan-aspartate repeat domain 72 (WDR72) mutations. Rungroj N, et al. Clin Genet, 2018 Nov. PMID 30028003
  3. Identification of the first multi-exonic WDR72 deletion in isolated amelogenesis imperfecta, and generation of a WDR72-specific copy number screening tool. Hentschel J, et al. Gene, 2016 Sep 15. PMID 27259663
  4. A Novel Homozygous WDR72 Mutation in Two Siblings with Amelogenesis Imperfecta and Mild Short Stature. Kuechler A, et al. Mol Syndromol, 2012 Nov. PMID 23293580, Free PMC Article
  5. Target gene analyses of 39 amelogenesis imperfecta kindreds. Chan HC, et al. Eur J Oral Sci, 2011 Dec. PMID 22243262, Free PMC Article

See all (30) 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
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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)

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

  • FLJ38736, MGC126663, MGC126665

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in enamel mineralization IEA
Inferred from Electronic Annotation
more info
  
involved_in extracellular matrix disassembly IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to plasma membrane IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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

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