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

Summary

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

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_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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).
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	Compare labs

EBI GWAS Catalog

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

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

RH92120 (e-PCR)
- UniSTS:92676

SHGC-82811 (e-PCR)
- UniSTS:102441

RH122755 (e-PCR)
- UniSTS:134984

SHGC-147238 (e-PCR)
- UniSTS:175693

D15S1003 (e-PCR)
- UniSTS:74073

G66901 (e-PCR)
- UniSTS:166751

SHGC-107461 (e-PCR)
- UniSTS:170383

SHGC-141520 (e-PCR)
- UniSTS:172202

RH102657 (e-PCR)
- UniSTS:96991

RH102918 (e-PCR)
- UniSTS:97252

D15S170 (e-PCR)
- UniSTS:148198

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

NG_017034.2 RefSeqGene

Range

5000..250922

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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
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
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

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

53513741..53762878 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
XM_047432344.1 → XP_047288300.1 WD repeat-containing protein 72 isoform X1

UniProtKB/Swiss-Prot

Q3MJ13, Q7Z3I3, Q8N8X2
XM_047432343.1 → XP_047288299.1 WD repeat-containing protein 72 isoform X1

UniProtKB/Swiss-Prot

Q3MJ13, Q7Z3I3, Q8N8X2
XM_047432345.1 → XP_047288301.1 WD repeat-containing protein 72 isoform X3
XM_047432342.1 → XP_047288298.1 WD repeat-containing protein 72 isoform X1

UniProtKB/Swiss-Prot

Q3MJ13, Q7Z3I3, Q8N8X2
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 ...