WDR53

Summary

WDR53 (WD repeat domain 53, HGNC:28786) is a protein-coding gene on chromosome 3q29, encoding WD repeat-containing protein 53 (Q7Z5U6).

This gene encodes a protein containing WD domains. The function of this gene is unknown.

Source: NCBI Gene 348793 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 56 total
• MANE Select transcript: NM_182627

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28786
Approved symbol	WDR53
Name	WD repeat domain 53
Location	3q29
Locus type	gene with protein product
Status	Approved
Aliases	MGC64882, MGC12928
Ensembl gene	ENSG00000185798
Ensembl biotype	protein_coding
OMIM	615110
Entrez	348793

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 32 protein_coding

ENST00000332629, ENST00000425888, ENST00000429115, ENST00000433160, ENST00000456677, ENST00000893402, ENST00000893403, ENST00000893404, ENST00000893405, ENST00000893406, ENST00000893407, ENST00000893408, ENST00000893409, ENST00000893410, ENST00000893411, ENST00000893412, ENST00000893413, ENST00000893414, ENST00000932690, ENST00000932691, ENST00000932692, ENST00000932693, ENST00000932694, ENST00000932695, ENST00000932696, ENST00000932697, ENST00000932698, ENST00000932699, ENST00000932700, ENST00000932701, ENST00000932702, ENST00000932703

RefSeq mRNA: 13 — MANE Select: NM_182627 NM_001345906, NM_001345907, NM_001345908, NM_001345909, NM_001345910, NM_001345911, NM_001345912, NM_001345913, NM_001345914, NM_001345915, NM_001345917, NM_001345918, NM_182627

CCDS: CCDS3318, CCDS87186, CCDS87187

Canonical transcript exons

ENST00000332629 — 4 exons

Exon	Start	End
ENSE00001295926	196554177	196554807
ENSE00001369722	196566877	196567307
ENSE00001431126	196568519	196568554
ENSE00003787782	196560996	196561491

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 95.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.8852 / max 64.9562, expressed in 1527 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46366	2.2141	1070
46367	1.4959	1061
46368	0.1172	23
46369	0.0418	6
46370	0.0163	4

Top tissues by expression

251 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.78	gold quality
right testis	UBERON:0004534	95.22	gold quality
testis	UBERON:0000473	94.34	gold quality
sperm	CL:0000019	91.45	gold quality
oocyte	CL:0000023	91.35	gold quality
secondary oocyte	CL:0000655	90.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.74	gold quality
granulocyte	CL:0000094	87.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.95	gold quality
pancreatic ductal cell	CL:0002079	84.14	silver quality
lower esophagus mucosa	UBERON:0035834	83.17	gold quality
islet of Langerhans	UBERON:0000006	83.12	gold quality
leukocyte	CL:0000738	82.79	gold quality
monocyte	CL:0000576	82.67	gold quality
gastrocnemius	UBERON:0001388	82.08	gold quality
muscle of leg	UBERON:0001383	81.89	gold quality
skin of leg	UBERON:0001511	81.89	gold quality
skin of abdomen	UBERON:0001416	81.27	gold quality
calcaneal tendon	UBERON:0003701	81.05	gold quality
zone of skin	UBERON:0000014	80.53	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.50	gold quality
lower esophagus muscularis layer	UBERON:0035833	80.25	gold quality
lower esophagus	UBERON:0013473	80.24	gold quality
spleen	UBERON:0002106	80.20	gold quality
stromal cell of endometrium	CL:0002255	80.11	gold quality
ventricular zone	UBERON:0003053	80.02	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	80.00	gold quality
mucosa of transverse colon	UBERON:0004991	79.82	gold quality
esophagus	UBERON:0001043	79.76	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.71	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.60

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr53	ENSDARG00000079659
mus_musculus	Wdr53	ENSMUSG00000022787
rattus_norvegicus	Wdr53	ENSRNOG00000001754

Protein

Protein identifiers

WD repeat-containing protein 53 — Q7Z5U6 (reviewed: Q7Z5U6)

All UniProt accessions (5): C9JBE7, C9JDR5, C9JJZ8, C9JQN1, Q7Z5U6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the WD repeat WDR53 family.

RefSeq proteins (13): NP_001332835, NP_001332836, NP_001332837, NP_001332838, NP_001332839, NP_001332840, NP_001332841, NP_001332842, NP_001332843, NP_001332844, NP_001332846, NP_001332847, NP_872433* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR019775	WD40_repeat_CS	Conserved_site
IPR024977	Apc4-like_WD40_dom	Domain
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR042453	WDR53	Family

Pfam: PF00400, PF12894

UniProt features (13 total): repeat 7, compositionally biased region 2, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5U6-F1	85.20	0.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, TGCGCANK_UNKNOWN, GATA1_01, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP, AACTTT_UNKNOWN, ELK1_01, AP2GAMMA_01, ATGGYGGA_UNKNOWN, AP2ALPHA_01, MTF1_Q4, ARID5B_TARGET_GENES, ARNT2_TARGET_GENES, GSE13547_CTRL_VS_ANTI_IGM_STIM_ZFX_KO_BCELL_2H_DN, CEBPZ_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

1014 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR53	SMCO1	Q147U7	751
WDR53	UBXN7	O94888	736
WDR53	FBXO45	P0C2W1	727
WDR53	PIGZ	Q86VD9	670
WDR53	NCBP2	P52298	649
WDR53	DYNLT2B	Q8WW35	643
WDR53	SENP5	Q96HI0	627
WDR53	PCYT1A	P49585	626
WDR53	ZDHHC19	Q8WVZ1	612
WDR53	RNF168	Q8IYW5	590
WDR53	BDH1	Q02338	588
WDR53	CEP19	Q96LK0	583
WDR53	TM4SF19	Q96DZ7	582
WDR53	CFAP44	Q96MT7	526
WDR53	DNAJC30	Q96LL9	482

IntAct

4 interactions, top by confidence:

A	B	Type	Score
WDR53	BLVRA	psi-mi:“MI:0914”(association)	0.530
WDR53	NACAD	psi-mi:“MI:0914”(association)	0.350
WDR53	DDB2	psi-mi:“MI:0914”(association)	0.350

BioGRID (233): BBS1 (Affinity Capture-MS), RSAD1 (Affinity Capture-MS), EEF1A2 (Affinity Capture-MS), RSAD1 (Affinity Capture-MS), EEF1A2 (Affinity Capture-MS), NACAD (Affinity Capture-MS), BLVRA (Affinity Capture-MS), WDR53 (Two-hybrid), EEF1A2 (Affinity Capture-MS), BBS1 (Affinity Capture-MS), MOCOS (Affinity Capture-MS), BLVRA (Affinity Capture-MS), RSAD1 (Affinity Capture-MS), RPL36AL (Affinity Capture-MS), DDB2 (Affinity Capture-MS)

ESM2 similar proteins: A2AKB9, A2RRH5, A2RUS2, O43379, O60336, P58742, Q08BB3, Q0VBY8, Q148I1, Q15334, Q3MHH0, Q3SZD4, Q3U3T8, Q499N3, Q4R3J7, Q4VBE8, Q5FW06, Q5QP82, Q5RCX2, Q5T6F0, Q5U4D9, Q5U4F6, Q5VW00, Q5ZJL7, Q63ZP7, Q6AX81, Q6AY87, Q6NS57, Q6NWH1, Q6P1M3, Q6P809, Q7Z5U6, Q80Y17, Q86W42, Q8AVS9, Q8BGW4, Q8BGZ3, Q8C5V5, Q8HXL3, Q8K4K5

Diamond homologs: Q32KQ2, Q5XGE2, Q6NUD0, Q7Z5U6, Q7ZXZ2, Q9DB94, B8N9H4, Q2UGU1, Q9FKT5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

56 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

732 predictions. Top by Δscore:

Variant	Effect	Δscore
3:196554814:A:C	acceptor_gain	0.9900
3:196568515:ATAC:A	donor_loss	0.9900
3:196568516:TAC:T	donor_loss	0.9900
3:196568517:ACCT:A	donor_loss	0.9900
3:196561097:T:A	donor_gain	0.9800
3:196569136:T:TA	acceptor_gain	0.9800
3:196567190:CCA:C	donor_gain	0.9700
3:196567192:A:AC	donor_gain	0.9700
3:196568475:G:C	donor_gain	0.9700
3:196561490:CT:C	acceptor_gain	0.9600
3:196567151:AT:A	donor_gain	0.9600
3:196554810:T:C	acceptor_gain	0.9500
3:196554813:C:CT	acceptor_gain	0.9500
3:196554807:CCTT:C	acceptor_gain	0.9400
3:196568526:T:TA	donor_gain	0.9400
3:196568553:A:AC	donor_gain	0.9400
3:196554810:T:TC	acceptor_gain	0.9300
3:196568471:CGAAG:C	donor_gain	0.9300
3:196554807:CCT:C	acceptor_loss	0.9200
3:196554808:CTTT:C	acceptor_loss	0.9200
3:196554809:T:G	acceptor_loss	0.9200
3:196567184:CAG:C	donor_gain	0.9200
3:196567186:G:C	donor_gain	0.9200
3:196568555:A:T	donor_gain	0.9200
3:196569133:ACCT:A	acceptor_gain	0.9200
3:196561279:T:C	acceptor_gain	0.9100
3:196568803:G:GG	donor_gain	0.9100
3:196560990:CATCA:C	donor_loss	0.9000
3:196560991:ATCAC:A	donor_loss	0.9000
3:196560992:TCACC:T	donor_loss	0.9000

AlphaMissense

2332 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:196554798:A:G	W164R	0.998
3:196554798:A:T	W164R	0.998
3:196561059:G:C	C139W	0.998
3:196561016:A:G	S154P	0.997
3:196561147:G:T	A110D	0.997
3:196561044:A:C	F144L	0.996
3:196561044:A:T	F144L	0.996
3:196561046:A:G	F144L	0.996
3:196554623:C:G	R222P	0.995
3:196554644:C:T	G215D	0.995
3:196554649:A:C	S213R	0.995
3:196554649:A:T	S213R	0.995
3:196554651:T:G	S213R	0.995
3:196561009:C:T	G156E	0.995
3:196561060:C:T	C139Y	0.995
3:196561061:A:G	C139R	0.995
3:196554689:G:T	A200D	0.994
3:196554512:C:T	G259E	0.993
3:196554648:A:G	C214R	0.993
3:196561021:A:G	L152P	0.993
3:196561045:A:G	F144S	0.993
3:196561141:G:T	A112D	0.993
3:196554626:A:T	V221D	0.992
3:196561003:T:A	D158V	0.992
3:196561004:C:G	D158H	0.992
3:196554257:G:T	A344D	0.991
3:196561010:C:G	G156R	0.991
3:196561010:C:T	G156R	0.991
3:196561021:A:C	L152R	0.991
3:196554642:C:G	A216P	0.990

dbSNP variants (sampled 300 via entrez): RS1000212234 (3:196563754 T>G), RS1000301780 (3:196557417 G>A,T), RS1000339568 (3:196566668 C>T), RS1000662036 (3:196558478 A>G), RS1000683710 (3:196562409 C>G), RS1000809736 (3:196560323 A>C,G), RS1000878622 (3:196566500 G>A,C), RS1001078206 (3:196565351 G>A,C), RS1001148739 (3:196560039 G>A), RS1001149058 (3:196554984 C>A,G,T), RS1001289064 (3:196556930 G>A), RS1001784251 (3:196568561 A>C), RS1001940338 (3:196567671 A>C,G), RS1002159087 (3:196559214 T>C), RS1002233559 (3:196560743 T>C)

Disease associations

OMIM: gene MIM:615110 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009798_34	Asthma	4.000000e-12

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
pirinixic acid	increases activity, increases expression, affects binding	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
Sunitinib	increases expression	1
Cisplatin	increases expression	1
Quercetin	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases expression	1
Cadmium Chloride	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.