WDR4 WD repeat domain 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: WDR4provided by HGNC
Official Full Name: WD repeat domain 4provided by HGNC
Primary source: HGNC:HGNC:12756
See related: Ensembl:ENSG00000160193 MIM:605924; AllianceGenome:HGNC:12756
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: hWH; Wuho; MIGSB; TRM82; GAMOS6; TRMT82
Summary: This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This gene is excluded as a candidate for a form of nonsyndromic deafness (DFNB10), but is still a candidate for other disorders mapped to 21q22.3 as well as for the development of Down syndrome phenotypes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012]
Expression: Ubiquitous expression in lymph node (RPKM 3.3), appendix (RPKM 3.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (42843094..42892998, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (41231676..41281371, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (44263204..44299699, complement)

Chromosome 21 - NC_000021.9 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?

Cilia defects upon loss of WDR4 are linked to proteasomal hyperactivity and ubiquitin shortage.
Title: Cilia defects upon loss of WDR4 are linked to proteasomal hyperactivity and ubiquitin shortage.
WDR4 promotes HCC pathogenesis through N[7]-methylguanosine by regulating and interacting with METTL1.
Title: WDR4 promotes HCC pathogenesis through N(7)-methylguanosine by regulating and interacting with METTL1.
PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer therapeutic target.
Title: PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer therapeutic target.
WDR4/TRIM28 is a novel molecular target linked to lenvatinib resistance that helps retain the stem characteristics in hepatocellular carcinomas.
Title: WDR4/TRIM28 is a novel molecular target linked to lenvatinib resistance that helps retain the stem characteristics in hepatocellular carcinomas.
METTL1/WDR4-mediated tRNA m[7]G modification and mRNA translation control promote oncogenesis and doxorubicin resistance.
Title: METTL1/WDR4-mediated tRNA m(7)G modification and mRNA translation control promote oncogenesis and doxorubicin resistance.
Wdr4 promotes cerebellar development and locomotion through Arhgap17-mediated Rac1 activation.
Title: Wdr4 promotes cerebellar development and locomotion through Arhgap17-mediated Rac1 activation.
Association of RNA m[7]G Modification Gene Polymorphisms with Pediatric Glioma Risk.
Title: Association of RNA m(7)G Modification Gene Polymorphisms with Pediatric Glioma Risk.
Structural basis of regulated m[7]G tRNA modification by METTL1-WDR4.
Title: Structural basis of regulated m(7)G tRNA modification by METTL1-WDR4.
Structures and mechanisms of tRNA methylation by METTL1-WDR4.
Title: Structures and mechanisms of tRNA methylation by METTL1-WDR4.
METTL1/WDR4-mediated m(7)G tRNA modifications and m(7)G codon usage promote mRNA translation and lung cancer progression.
Title: METTL1/WDR4-mediated m(7)G tRNA modifications and m(7)G codon usage promote mRNA translation and lung cancer progression.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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
Galloway-Mowat syndrome 6 MedGen: C5193043 OMIM: 618347 GeneReviews: Not available	not available
Microcephaly, growth deficiency, seizures, and brain malformations MedGen: C5193042 OMIM: 618346 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association study of selenium concentrations. 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

A009B40 (e-PCR)
- UniSTS:11778

SHGC-156262 (e-PCR)
- UniSTS:183554

SHGC-105330 (e-PCR)
- UniSTS:167955

SHGC-58188 (e-PCR)
- UniSTS:19478

STS_CEB278 (e-PCR)
- UniSTS:255267

SHGC-147624 (e-PCR)
- UniSTS:175919

SHGC-52043 (e-PCR)
- UniSTS:70994

SHGC-58110 (e-PCR)
- UniSTS:63873

SHGC-56970 (e-PCR)
- UniSTS:34481

RH46358 (e-PCR)
- UniSTS:90076

RH98886 (e-PCR)
- UniSTS:88810

WI-13399 (e-PCR)
- UniSTS:59377

G32394 (e-PCR)
- UniSTS:116982

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables enzyme activator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables tRNA methyltransferase activator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in tRNA (guanine-N7)-methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in tRNA modification	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA modification	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of tRNA (m7G46) methyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
part_of tRNA methyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of tRNA methyltransferase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4

Names: TRM82 tRNA methyltransferase 82 homolog; WD repeat-containing protein 4; protein Wuho homolog; tRNA (guanine-N(7)-)-methyltransferase subunit WDR4

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.

mRNA and Protein(s)

NM_001260474.2 → NP_001247403.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame acceptor splice site at an internal coding exon compared to variant 1, resulting in a shorter isoform (2) missing a single aa compared to isoform 1.

Source sequence(s)

AP001628, AP001629

UniProtKB/Swiss-Prot

P57081

Conserved Domains (3) summary

COG2319
Location:25 → 231

WD40; WD40 repeat [General function prediction only]

sd00039
Location:65 → 102

7WD40; WD40 repeat [structural motif]

cl02567
Location:20 → 299

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_001260475.2 → NP_001247404.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3

See identical proteins and their annotated locations for NP_001247404.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate donor splice site at an exon in the 5' region compared to variant 1, resulting in translation initiation from an in-frame downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 4-6 encode the same isoform.

Source sequence(s)

AP001628, AP001629

UniProtKB/Swiss-Prot

P57081

Conserved Domains (2) summary

sd00039
Location:3 → 38

7WD40; WD40 repeat [structural motif]

cl25539
Location:4 → 154

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_001260476.2 → NP_001247405.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3

See identical proteins and their annotated locations for NP_001247405.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses alternate donor splice sites at the 5' terminal exon and at another exon in the 5' region compared to variant 1, resulting in translation initiation from an in-frame downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 4-6 encode the same isoform.

Source sequence(s)

AP001628, AP001629

UniProtKB/Swiss-Prot

P57081

Related

ENST00000476326.5

Conserved Domains (2) summary

sd00039
Location:3 → 38

7WD40; WD40 repeat [structural motif]

cl25539
Location:4 → 154

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_001260477.2 → NP_001247406.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 3

See identical proteins and their annotated locations for NP_001247406.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains an alternate 5' terminal exon and uses an alternate donor splice site at an exon in the 5' region compared to variant 1, resulting in translation initiation from an in-frame downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1. Variants 4-6 encode the same isoform.

Source sequence(s)

AP001628, AP001629

UniProtKB/Swiss-Prot

P57081

Related

ENST00000492742.5

Conserved Domains (2) summary

sd00039
Location:3 → 38

7WD40; WD40 repeat [structural motif]

cl25539
Location:4 → 154

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_018669.6 → NP_061139.2 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 1

See identical proteins and their annotated locations for NP_061139.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 2 both encode the same isoform.

Source sequence(s)

AP001628, AP001629

Consensus CDS

CCDS13691.1

UniProtKB/Swiss-Prot

A8KA58, B2RCA3, B4DNQ7, D3DSK3, P57081, Q9BVM5, Q9HCR3

Related

ENSP00000381266.2, ENST00000398208.3

Conserved Domains (2) summary

sd00039
Location:65 → 102

7WD40; WD40 repeat [structural motif]

cl29593
Location:20 → 300

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_033661.5 → NP_387510.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform 1

See identical proteins and their annotated locations for NP_387510.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AJ243912, AK298015, DC303088

Consensus CDS

CCDS13691.1

UniProtKB/Swiss-Prot

A8KA58, B2RCA3, B4DNQ7, D3DSK3, P57081, Q9BVM5, Q9HCR3

Related

ENSP00000328671.2, ENST00000330317.6

Conserved Domains (2) summary

sd00039
Location:65 → 102

7WD40; WD40 repeat [structural motif]

cl29593
Location:20 → 300

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_048535.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate donor splice site at the 5' terminal exon compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF (with a strong Kozak signal) that is predicted to interfere with the translation of the longest ORF; translation of the upstream ORF renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AJ243913, AK298015, BC006341

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_000021.9 Reference GRCh38.p14 Primary Assembly

Range

42843094..42892998 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017028264.2 → XP_016883753.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2
XM_011529433.2 → XP_011527735.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X1

Conserved Domains (3) summary

COG2319
Location:23 → 227

WD40; WD40 repeat [General function prediction only]

sd00039
Location:6 → 55

7WD40; WD40 repeat [structural motif]

cl02567
Location:139 → 296

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_024452048.2 → XP_024307816.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

Conserved Domains (2) summary

sd00039
Location:3 → 38

7WD40; WD40 repeat [structural motif]

cl25539
Location:4 → 154

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_024452047.2 → XP_024307815.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3

Conserved Domains (2) summary

sd00039
Location:3 → 38

7WD40; WD40 repeat [structural motif]

cl25539
Location:4 → 154

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_017028263.2 → XP_016883752.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060945.1 Alternate T2T-CHM13v2.0

Range

41231676..41281371 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054324315.1 → XP_054180290.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X1
XM_054324317.1 → XP_054180292.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2
XM_054324319.1 → XP_054180294.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3
XM_054324318.1 → XP_054180293.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X3
XM_054324316.1 → XP_054180291.1 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 isoform X2