WDR48 WD repeat domain 48 [Homo sapiens (human)] - Gene

Summary

Official Symbol: WDR48provided by HGNC
Official Full Name: WD repeat domain 48provided by HGNC
Primary source: HGNC:HGNC:30914
See related: Ensembl:ENSG00000114742 MIM:612167; AllianceGenome:HGNC:30914
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: P80; UAF1; Bun62; SPG60
Summary: The protein encoded by this gene has been shown to interact with ubiquitin specific peptidase 1 (USP1), activating the deubiquitinating activity of USP1 and allowing it to remove the ubiquitin moiety from monoubiquitinated FANCD2. FANCD2 is ubiquitinated in response to DNA damage. [provided by RefSeq, Sep 2016]
Expression: Ubiquitous expression in testis (RPKM 33.3), bone marrow (RPKM 19.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p22.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (39052016..39096664)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (39064178..39108828)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (39093507..39138155)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

The UAF1-USP1 Deubiquitinase Complex Stabilizes cGAS and Facilitates Antiviral Responses.
Title: The UAF1-USP1 Deubiquitinase Complex Stabilizes cGAS and Facilitates Antiviral Responses.
USP1-WDR48 deubiquitinase complex enhances TGF-beta induced epithelial-mesenchymal transition of TNBC cells via stabilizing TAK1.
Title: USP1-WDR48 deubiquitinase complex enhances TGF-β induced epithelial-mesenchymal transition of TNBC cells via stabilizing TAK1.
ATAD5 suppresses centrosome over-duplication by regulating UAF1 and ID1.
Title: ATAD5 suppresses centrosome over-duplication by regulating UAF1 and ID1.
Structural basis of FANCD2 deubiquitination by USP1-UAF1.
Title: Structural basis of FANCD2 deubiquitination by USP1-UAF1.
The DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair.
Title: The DNA-binding activity of USP1-associated factor 1 is required for efficient RAD51-mediated homologous DNA pairing and homology-directed DNA repair.
In this report, the authors provide evidence that the previously described interaction between the viral E1 helicase and the cellular UAF1-USP1 deubiquitinating enzyme complex is required for the completion of the bidirectional theta replication of the human papilloma virus type 11 genome and the subsequent initiation of the unidirectional replication.
Title: Interaction of the Human Papillomavirus E1 Helicase with UAF1-USP1 Promotes Unidirectional Theta Replication of Viral Genomes.
There is evidence that USP1/WDR48 complex promotes cancer stem cell conservation and regulation of DNA damage repair. [REVIEW]
Title: The Role of the Complex USP1/WDR48 in Differentiation and Proliferation Processes in Cancer Stem Cells.
Our results highlight the interfaces essential for regulation of USP12 activity and show a conserved second binding of UAF1 which could be important for regulatory functions independent of USP12 activity.
Title: A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme.
These results outline a novel mechanism for the control of TBK1 activity and suggest USP1-UAF1 complex as a potential target for the prevention of viral diseases.
Title: USP1-UAF1 deubiquitinase complex stabilizes TBK1 and enhances antiviral responses.
UAF1 and WDR20 interact with USP12 at two distinct sites far from its catalytic center, allosterically activating the enzyme.
Title: Allosteric Activation of Ubiquitin-Specific Proteases by β-Propeller Proteins UAF1 and WDR20.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence. 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

D3S2895E (e-PCR)
- UniSTS:50455

G19825 (e-PCR)
- UniSTS:41508

A001Z36 (e-PCR)
- UniSTS:41509

RH48643 (e-PCR)
- UniSTS:55603

SHGC-76851 (e-PCR)
- UniSTS:31830

SHGC-76850 (e-PCR)
- UniSTS:24411

SHGC-30755 (e-PCR)
- UniSTS:49251

SHGC-153576 (e-PCR)
- UniSTS:177824

G09860 (e-PCR)
- UniSTS:31415

SHGC-76837 (e-PCR)
- UniSTS:43210

SHGC-30045 (e-PCR)
- UniSTS:40934

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables deubiquitinase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in double-strand break repair via homologous recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in embryonic organ development	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of double-strand break repair via homologous recombination	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of receptor signaling pathway via JAK-STAT	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of protein monoubiquitination	IEA Inferred from Electronic Annotation more info
involved_in seminiferous tubule development	IEA Inferred from Electronic Annotation more info
involved_in single fertilization	IEA Inferred from Electronic Annotation more info
involved_in skeletal system morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in skin development	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: WD repeat-containing protein 48

Names: USP1 associated factor 1; WD repeat endosomal protein; testicular tissue protein Li 224

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_051663.1 RefSeqGene

Range

5031..49679

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001303402.2 → NP_001290331.1 WD repeat-containing protein 48 isoform 2

See identical proteins and their annotated locations for NP_001290331.1

Status: REVIEWED

Source sequence(s)

AB040882

UniProtKB/Swiss-Prot

Q8TAF3

Conserved Domains (3) summary

cd00200
Location:3 → 204

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 ...

sd00039
Location:38 → 78

7WD40; WD40 repeat [structural motif]

pfam11816
Location:427 → 591

DUF3337; Domain of unknown function (DUF3337)
NM_001303403.2 → NP_001290332.1 WD repeat-containing protein 48 isoform 3

See identical proteins and their annotated locations for NP_001290332.1

Status: REVIEWED

Source sequence(s)

AB040882

UniProtKB/Swiss-Prot

Q8TAF3

Conserved Domains (3) summary

cd00200
Location:30 → 277

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 ...

sd00039
Location:35 → 73

7WD40; WD40 repeat [structural motif]

pfam11816
Location:500 → 664

DUF3337; Domain of unknown function (DUF3337)
NM_001346225.2 → NP_001333154.1 WD repeat-containing protein 48 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes the longest isoform (4).

Source sequence(s)

AC123903, AC138124

Conserved Domains (3) summary

cd00200
Location:30 → 324

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 ...

sd00039
Location:35 → 73

7WD40; WD40 repeat [structural motif]

pfam11816
Location:547 → 711

DUF3337; Domain of unknown function (DUF3337)
NM_001346226.2 → NP_001333155.1 WD repeat-containing protein 48 isoform 5

Status: REVIEWED

Source sequence(s)

AC123903, AC138124

Conserved Domains (3) summary

cd00200
Location:17 → 229

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 ...

sd00039
Location:22 → 58

7WD40; WD40 repeat [structural motif]

pfam11816
Location:452 → 616

DUF3337; Domain of unknown function (DUF3337)
NM_001346227.2 → NP_001333156.1 WD repeat-containing protein 48 isoform 6

Status: REVIEWED

Source sequence(s)

AC123903, AC138124

UniProtKB/Swiss-Prot

Q8TAF3

Conserved Domains (3) summary

sd00039
Location:2 → 32

7WD40; WD40 repeat [structural motif]

pfam11816
Location:334 → 498

DUF3337; Domain of unknown function (DUF3337)

cl29593
Location:5 → 111

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 ...
NM_001346228.2 → NP_001333157.1 WD repeat-containing protein 48 isoform 7

Status: REVIEWED

Source sequence(s)

AC123903, AC138124

UniProtKB/Swiss-Prot

Q8TAF3

Conserved Domains (3) summary

cd00200
Location:4 → 216

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 ...

sd00039
Location:9 → 45

7WD40; WD40 repeat [structural motif]

pfam11816
Location:439 → 603

DUF3337; Domain of unknown function (DUF3337)
NM_020839.4 → NP_065890.1 WD repeat-containing protein 48 isoform 1

See identical proteins and their annotated locations for NP_065890.1

Status: REVIEWED

Source sequence(s)

AB040882

Consensus CDS

CCDS33738.1

UniProtKB/Swiss-Prot

B4DM86, B4DQI2, B4DY84, Q63HJ2, Q658Y1, Q8N3Z1, Q8TAF3, Q9NSK8, Q9P279

UniProtKB/TrEMBL

A0A024R2L1, A0A140VJZ7

Related

ENSP00000307491.5, ENST00000302313.10

Conserved Domains (3) summary

cd00200
Location:30 → 286

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 ...

sd00039
Location:35 → 73

7WD40; WD40 repeat [structural motif]

pfam11816
Location:509 → 673

DUF3337; Domain of unknown function (DUF3337)

RNA

NR_144399.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

BC037168, DA414095

Related

ENST00000420940.6
NR_144400.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC123903, AC138124
NR_144401.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC123903, AC138124

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

39052016..39096664

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005265346.5 → XP_005265403.1 WD repeat-containing protein 48 isoform X1

Conserved Domains (4) summary

COG2319
Location:29 → 328

WD40; WD40 repeat [General function prediction only]

cd00200
Location:30 → 286

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 ...

pfam11816
Location:509 → 647

DUF3337; Domain of unknown function (DUF3337)

sd00039
Location:35 → 73

7WD40; WD40 repeat [structural motif]