WDR55

Summary

WDR55 (WD repeat domain 55, HGNC:25971) is a protein-coding gene on chromosome 5q31.3, encoding WD repeat-containing protein 55 (Q9H6Y2). Nucleolar protein that acts as a modulator of rRNA synthesis. It is a common-essential gene (DepMap: required in 97.7% of cancer cell lines).

Predicted to be involved in rRNA processing. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 54853 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 82 total
• Cancer dependency (DepMap): dependent in 97.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_017706

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25971
Approved symbol	WDR55
Name	WD repeat domain 55
Location	5q31.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20195, FLJ21702
Ensembl gene	ENSG00000120314
Ensembl biotype	protein_coding
OMIM	620832
Entrez	54853

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 nonsense_mediated_decay, 1 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000358337, ENST00000504897, ENST00000506393, ENST00000511232, ENST00000520764

RefSeq mRNA: 1 — MANE Select: NM_017706 NM_017706

CCDS: CCDS4235

Canonical transcript exons

ENST00000358337 — 7 exons

Exon	Start	End
ENSE00001420176	140669333	140672345
ENSE00001926778	140664904	140665103
ENSE00003511990	140668415	140668502
ENSE00003588931	140668612	140668791
ENSE00003593245	140668234	140668334
ENSE00003666909	140668891	140668990
ENSE00003668814	140669079	140669248

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 90.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.8789 / max 178.4977, expressed in 1814 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58926	12.8789	1814

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	90.28	gold quality
mucosa of transverse colon	UBERON:0004991	89.48	gold quality
lower esophagus mucosa	UBERON:0035834	87.23	gold quality
transverse colon	UBERON:0001157	86.58	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.16	gold quality
esophagus mucosa	UBERON:0002469	85.91	gold quality
stromal cell of endometrium	CL:0002255	85.63	gold quality
metanephros cortex	UBERON:0010533	85.63	gold quality
body of stomach	UBERON:0001161	85.62	gold quality
body of pancreas	UBERON:0001150	85.57	gold quality
spleen	UBERON:0002106	85.41	gold quality
sperm	CL:0000019	85.37	silver quality
blood	UBERON:0000178	85.35	gold quality
skin of leg	UBERON:0001511	85.34	gold quality
rectum	UBERON:0001052	85.17	gold quality
leukocyte	CL:0000738	84.88	gold quality
minor salivary gland	UBERON:0001830	84.87	gold quality
tendon of biceps brachii	UBERON:0008188	84.85	silver quality
monocyte	CL:0000576	84.78	gold quality
gastrocnemius	UBERON:0001388	84.75	gold quality
mucosa of stomach	UBERON:0001199	84.73	gold quality
upper lobe of left lung	UBERON:0008952	84.73	gold quality
mononuclear cell	CL:0000842	84.70	gold quality
skin of abdomen	UBERON:0001416	84.51	gold quality
small intestine	UBERON:0002108	84.40	gold quality
right lobe of liver	UBERON:0001114	84.37	gold quality
upper lobe of lung	UBERON:0008948	84.28	gold quality
esophagus	UBERON:0001043	84.13	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.13	gold quality
muscle of leg	UBERON:0001383	84.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting WDR55, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-6757-3P	99.63	66.88	1089
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-7159-3P	99.51	70.17	1920
HSA-MIR-766-3P	99.47	65.24	1811

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.7% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr55	ENSDARG00000007217
mus_musculus	Wdr55	ENSMUSG00000042660
rattus_norvegicus	Ik	ENSRNOG00000017251
drosophila_melanogaster	CG14722	FBGN0037943
caenorhabditis_elegans		WBGENE00012858

Paralogs (2): CSTF1 (ENSG00000101138), IK (ENSG00000113141)

Protein

Protein identifiers

WD repeat-containing protein 55 — Q9H6Y2 (reviewed: Q9H6Y2)

All UniProt accessions (3): D6RGJ8, Q9H6Y2, G3V1J0

UniProt curated annotations — full annotation on UniProt →

Function. Nucleolar protein that acts as a modulator of rRNA synthesis. Plays a central role during organogenesis.

Subcellular location. Nucleus. Nucleolus. Cytoplasm.

Similarity. Belongs to the WD repeat WDR55 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H6Y2-1	1	yes
Q9H6Y2-2	2

RefSeq proteins (1): NP_060176* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR017422	WDR55	Family
IPR019775	WD40_repeat_CS	Conserved_site
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR050505	WDR55/POC1	Family

Pfam: PF24796

UniProt features (57 total): strand 29, repeat 7, turn 5, modified residue 4, sequence variant 4, compositionally biased region 3, region of interest 2, chain 1, splice variant 1, helix 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7KQQ	X-RAY DIFFRACTION	1.8
9EKP	X-RAY DIFFRACTION	1.95
8FKY	ELECTRON MICROSCOPY	2.67

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6Y2-F1	86.80	0.76

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 14, 354, 378, 382

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 116 (showing top): GOBP_RIBOSOME_BIOGENESIS, KIM_GASTRIC_CANCER_CHEMOSENSITIVITY, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, chr5q31, LIU_SOX4_TARGETS_DN, GOCC_NUCLEOLUS, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, DODD_NASOPHARYNGEAL_CARCINOMA_DN, LEE_BMP2_TARGETS_DN, BARX1_TARGET_GENES, CREB3L4_TARGET_GENES, DLX4_TARGET_GENES, E2F2_TARGET_GENES, ELF2_TARGET_GENES

GO Biological Process (1): rRNA processing (GO:0006364)

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

GO Cellular Component (4): nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
cellular anatomical structure	2
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
binding	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1362 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR55	LYRM2	Q9NU23	497
WDR55	ZMAT2	Q96NC0	489
WDR55	PGAP2	Q9UHJ9	468
WDR55	DDB1	Q16531	446
WDR55	WDR54	Q9H977	436
WDR55	GAK	O14976	416
WDR55	ADI1	Q9BV57	412
WDR55	HARS1	P12081	387
WDR55	THOC6	Q86W42	383
WDR55	E7EQY1	E7EQY1	382
WDR55	YAE1	Q9NRH1	381
WDR55	WDR53	Q7Z5U6	378
WDR55	R3HDM1	Q15032	374
WDR55	ZNF354B	Q96LW1	370
WDR55	DCAF1	Q9Y4B6	370

IntAct

38 interactions, top by confidence:

A	B	Type	Score
KBTBD7	METTL15	psi-mi:“MI:0914”(association)	0.730
WDR55	PES1	psi-mi:“MI:0914”(association)	0.530
CCT3	PDCD5	psi-mi:“MI:0914”(association)	0.530
CCT6A	TXNDC9	psi-mi:“MI:0914”(association)	0.530
WDR55	AP3D1	psi-mi:“MI:0914”(association)	0.530
WDR55	NPM1	psi-mi:“MI:0914”(association)	0.480
WDR55	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
CC2D2A	OFD1	psi-mi:“MI:2364”(proximity)	0.420
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
MLF2	WDR55	psi-mi:“MI:0915”(physical association)	0.400
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
Bcas2	PEX10	psi-mi:“MI:0914”(association)	0.350
FOXJ2	TCERG1	psi-mi:“MI:0914”(association)	0.350
FOXS1	DDX39A	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
NPM3	KPNA3	psi-mi:“MI:0914”(association)	0.350
SBF1	COL1A2	psi-mi:“MI:0914”(association)	0.350
HLA-A	AIP	psi-mi:“MI:0914”(association)	0.350
RB1	EIF5B	psi-mi:“MI:0914”(association)	0.350
CCT4	PDCD5	psi-mi:“MI:0914”(association)	0.350
CCT7	PDCD5	psi-mi:“MI:0914”(association)	0.350
CCT8	PDCD5	psi-mi:“MI:0914”(association)	0.350
SYT2	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
RPL19		psi-mi:“MI:0914”(association)	0.350
B4GALT2	LENG9	psi-mi:“MI:0914”(association)	0.350
MILR1	SBNO1	psi-mi:“MI:0914”(association)	0.350

BioGRID (95): WDR55 (Affinity Capture-RNA), WDR55 (Affinity Capture-RNA), PPP4R2 (Co-fractionation), WDR55 (Proximity Label-MS), WDR55 (Affinity Capture-MS), WDR55 (Affinity Capture-MS), WDR55 (Affinity Capture-MS), WDR55 (Affinity Capture-MS), WDR55 (Affinity Capture-MS), WDR55 (Affinity Capture-MS), CBWD3 (Affinity Capture-MS), MCMBP (Affinity Capture-MS), BOP1 (Affinity Capture-MS), RPL7L1 (Affinity Capture-MS), KLHDC3 (Affinity Capture-MS)

ESM2 similar proteins: A1L112, A4IHS2, A8NZM5, B2ZZS9, O00423, O80775, O95834, P93107, P97452, Q05BC3, Q0DYP5, Q13216, Q13610, Q13685, Q15269, Q1JQD2, Q2HJ56, Q32KQ2, Q32P44, Q3SZK1, Q4V8C3, Q562C2, Q58DT8, Q5BIM8, Q5F3K4, Q5R9T6, Q5RCG7, Q5RFQ3, Q5VU92, Q5XI13, Q5ZK69, Q6DRF9, Q6P6T4, Q6PFM9, Q7TNG5, Q7YR70, Q810D6, Q8BH57, Q8BHB4, Q8BU03

Diamond homologs: A1L112, A8NZM5, A8PZI1, B0D442, B2ZZS9, B3M1G0, B3P4F8, B4GMG4, B4JSW8, B4KE10, B4M4W4, B4N984, B4PU14, B4QTL6, O80775, P0CS40, P0CS41, Q0IF90, Q294Y7, Q54SA5, Q58DT8, Q5R9T6, Q6DRF9, Q8T088, Q9CX97, Q9H6Y2, O13856, Q4PA27, Q54W52, P90794, A1CJY4, A2QEV8, Q61FW2, Q6NL34, Q93794, A0CH87, A0DB19, O22468, Q6FL15, Q9VAT2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of tubulin folding intermediates by CCT/TriC	5	62.2×	1e-06
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	5	60.0×	1e-06
Prefoldin mediated transfer of substrate to CCT/TriC	5	57.9×	1e-06
Chaperonin-mediated protein folding	5	44.2×	4e-06
Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding	5	44.2×	4e-06
Association of TriC/CCT with target proteins during biosynthesis	5	43.1×	4e-06
Protein folding	5	38.2×	6e-06

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of telomere maintenance via telomerase	5	78.0×	5e-07
protein folding	5	11.0×	4e-03
RNA splicing	5	9.4×	8e-03
protein stabilization	6	8.5×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1749 predictions. Top by Δscore:

Variant	Effect	Δscore
5:140665009:G:GT	donor_gain	1.0000
5:140665024:G:GT	donor_gain	1.0000
5:140665081:G:GT	donor_gain	1.0000
5:140665093:G:GT	donor_gain	1.0000
5:140665093:G:T	donor_gain	1.0000
5:140665102:GT:G	donor_gain	1.0000
5:140665104:G:GG	donor_gain	1.0000
5:140668610:A:AG	acceptor_gain	1.0000
5:140668611:G:GG	acceptor_gain	1.0000
5:140668611:GT:G	acceptor_gain	1.0000
5:140668991:G:GG	donor_gain	1.0000
5:140669068:T:G	acceptor_gain	1.0000
5:140669074:TGCA:T	acceptor_loss	1.0000
5:140669077:A:AG	acceptor_gain	1.0000
5:140669077:A:G	acceptor_loss	1.0000
5:140669077:AGT:A	acceptor_gain	1.0000
5:140669077:AGTG:A	acceptor_gain	1.0000
5:140669077:AGTGG:A	acceptor_gain	1.0000
5:140669078:G:GG	acceptor_gain	1.0000
5:140669078:GT:G	acceptor_gain	1.0000
5:140669078:GTG:G	acceptor_gain	1.0000
5:140669078:GTGG:G	acceptor_gain	1.0000
5:140669078:GTGGG:G	acceptor_gain	1.0000
5:140669245:TCAGG:T	donor_loss	1.0000
5:140669246:CAGG:C	donor_loss	1.0000
5:140669247:AGG:A	donor_loss	1.0000
5:140669248:GGT:G	donor_loss	1.0000
5:140669250:T:A	donor_loss	1.0000
5:140669328:CCCA:C	acceptor_loss	1.0000
5:140669329:CCA:C	acceptor_loss	1.0000

AlphaMissense

2520 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:140669436:A:C	S312R	0.999
5:140669438:T:A	S312R	0.999
5:140669438:T:G	S312R	0.999
5:140669127:T:C	F237L	0.997
5:140669129:C:A	F237L	0.997
5:140669129:C:G	F237L	0.997
5:140669220:T:C	C268R	0.996
5:140668316:T:C	F92L	0.995
5:140668318:C:A	F92L	0.995
5:140668318:C:G	F92L	0.995
5:140668790:A:C	S187R	0.995
5:140668891:C:A	S187R	0.995
5:140668891:C:G	S187R	0.995
5:140669245:T:A	I276N	0.995
5:140669434:C:A	A311D	0.994
5:140669464:T:C	F321S	0.994
5:140665073:C:A	A54D	0.993
5:140665091:G:T	G60V	0.993
5:140668430:C:T	S103F	0.993
5:140669227:G:A	G270D	0.993
5:140669356:G:C	R285P	0.993
5:140668303:C:G	C87W	0.992
5:140668430:C:A	S103Y	0.992
5:140668656:C:A	A142D	0.992
5:140668662:G:A	G144E	0.992
5:140669335:C:A	A278D	0.992
5:140668418:T:A	L99H	0.991
5:140668429:T:C	S103P	0.991
5:140669095:C:A	A226D	0.991
5:140669245:T:G	I276S	0.991

dbSNP variants (sampled 300 via entrez): RS1000090517 (5:140668415 A>G), RS1000594583 (5:140664225 G>A), RS1000625682 (5:140663997 A>G), RS1000930483 (5:140663660 C>T), RS1001425563 (5:140663242 C>G), RS1002427074 (5:140664016 C>T), RS1002521852 (5:140663791 G>A), RS1002633256 (5:140666711 C>T), RS1002661556 (5:140670672 A>G,T), RS1003439018 (5:140665344 GATT>G), RS1003596439 (5:140671713 C>G,T), RS1003997863 (5:140665982 T>A,C,G), RS1004092548 (5:140666327 T>G), RS1004901502 (5:140669527 G>A,C), RS1006133992 (5:140670340 A>G)

Disease associations

OMIM: gene MIM:620832 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004946_157	Schizophrenia	2.000000e-08
GCST006803_54	Schizophrenia	8.000000e-07
GCST010146_22	Serum immune biomarker levels	7.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004872	inflammatory biomarker measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Allergens	increases expression	1
Arsenic	affects expression, affects methylation	1
Atrazine	decreases expression	1
Doxorubicin	decreases expression	1
Ivermectin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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