WDR5B

Summary

WDR5B (WD repeat domain 5B, HGNC:17826) is a protein-coding gene on chromosome 3q21.1, encoding WD repeat-containing protein 5B (Q86VZ2). Plays a role in the proliferation of retinal pigment epithelial (RPE) cells.

This intronless gene encodes a protein containing several WD40 repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, including a trp-asp at the C-terminal end. The encoded protein may mediate protein-protein interactions.

Source: NCBI Gene 54554 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 40 total
• MANE Select transcript: NM_019069

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17826
Approved symbol	WDR5B
Name	WD repeat domain 5B
Location	3q21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11287
Ensembl gene	ENSG00000196981
Ensembl biotype	protein_coding
OMIM	621240
Entrez	54554

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000330689, ENST00000920957

RefSeq mRNA: 1 — MANE Select: NM_019069 NM_019069

CCDS: CCDS3012

Canonical transcript exons

ENST00000330689 — 1 exons

Exon	Start	End
ENSE00001293682	122411846	122416062

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 83.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2142 / max 69.9609, expressed in 1686 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
44128	7.2142	1686

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	83.52	gold quality
epithelium of bronchus	UBERON:0002031	83.37	gold quality
epithelium of nasopharynx	UBERON:0001951	83.01	gold quality
right uterine tube	UBERON:0001302	82.97	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.18	gold quality
bronchus	UBERON:0002185	82.02	gold quality
hair follicle	UBERON:0002073	79.85	silver quality
diaphragm	UBERON:0001103	77.08	gold quality
islet of Langerhans	UBERON:0000006	76.57	gold quality
body of pancreas	UBERON:0001150	76.37	gold quality
corpus epididymis	UBERON:0004359	76.32	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.44	gold quality
pancreas	UBERON:0001264	75.17	gold quality
calcaneal tendon	UBERON:0003701	75.16	gold quality
tibia	UBERON:0000979	74.74	gold quality
caput epididymis	UBERON:0004358	74.68	gold quality
parotid gland	UBERON:0001831	74.44	silver quality
monocyte	CL:0000576	74.40	gold quality
leukocyte	CL:0000738	74.32	gold quality
mononuclear cell	CL:0000842	74.18	gold quality
ventricular zone	UBERON:0003053	73.88	gold quality
right lobe of liver	UBERON:0001114	73.79	gold quality
right adrenal gland	UBERON:0001233	73.62	gold quality
stromal cell of endometrium	CL:0002255	73.56	gold quality
right adrenal gland cortex	UBERON:0035827	73.53	gold quality
endometrium	UBERON:0001295	73.33	gold quality
ganglionic eminence	UBERON:0004023	73.15	gold quality
granulocyte	CL:0000094	73.14	gold quality
germinal epithelium of ovary	UBERON:0001304	73.13	gold quality
mucosa of paranasal sinus	UBERON:0005030	73.04	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	660.86
E-ANND-3	yes	3.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

90 targeting WDR5B, 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-8485	100.00	77.57	4731
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777

Literature-anchored findings (GeneRIF, showing 1)

• Initial Characterization of WDR5B Reveals a Role in the Proliferation of Retinal Pigment Epithelial Cells. (PMID:39056772)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr5	ENSDARG00000016903
mus_musculus	Wdr5b	ENSMUSG00000034379
rattus_norvegicus	Wdr5b	ENSRNOG00000002253
drosophila_melanogaster	CG10931	FBGN0034274
drosophila_melanogaster	wds	FBGN0040066

Paralogs (26): PAFAH1B1 (ENSG00000007168), SNRNP40 (ENSG00000060688), WDR62 (ENSG00000075702), WDR7 (ENSG00000091157), TBL2 (ENSG00000106638), PAK1IP1 (ENSG00000111845), WDR75 (ENSG00000115368), DCAF4 (ENSG00000119599), DAW1 (ENSG00000123977), TEP1 (ENSG00000129566), AHI1 (ENSG00000135541), WDR38 (ENSG00000136918), MAPKBP1 (ENSG00000137802), POC1B (ENSG00000139323), NEDD1 (ENSG00000139350), COP1 (ENSG00000143207), WDR17 (ENSG00000150627), WDR43 (ENSG00000163811), POC1A (ENSG00000164087), WDR88 (ENSG00000166359), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363)

Protein

Protein identifiers

WD repeat-containing protein 5B — Q86VZ2 (reviewed: Q86VZ2)

All UniProt accessions (1): Q86VZ2

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the proliferation of retinal pigment epithelial (RPE) cells. May function as a substrate receptor for CUL4-DDB1 ubiquitin E3 ligase complex.

Subunit / interactions. Probable part of a cullin-RING E3 protein ligase complex containing CUL4B-DDB1 and a substrate-recruiting component (DCAF). Interacts with CUL4B and DDB1.

Subcellular location. Nucleus.

Induction. Up-regulated upon neural differentiation.

Similarity. Belongs to the WD repeat WDR5/wds family.

RefSeq proteins (1): NP_061942* (*=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
IPR020472	WD40_PAC1	Repeat
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR059122	Beta-prop_WDR5-like	Domain

Pfam: PF25175

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VZ2-F1	93.36	0.90

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, HAND1E47_01, chr3q21, TGGAAA_NFAT_Q4_01, GOCC_TRANSFERASE_COMPLEX, GOCC_SET1C_COMPASS_COMPLEX, GOCC_HISTONE_METHYLTRANSFERASE_COMPLEX, GOCC_METHYLTRANSFERASE_COMPLEX, GOMF_HISTONE_BINDING, MARTENS_TRETINOIN_RESPONSE_UP, GATA1_05, BARX1_TARGET_GENES, DLX4_TARGET_GENES, DLX6_TARGET_GENES, ELF2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): histone binding (GO:0042393), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), Set1C/COMPASS complex (GO:0048188)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
binding	1
intracellular membrane-bounded organelle	1
histone methyltransferase complex	1

Protein interactions and networks

STRING

1668 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR5B	ASH2L	Q9UBL3	435
WDR5B	SAMD4B	Q5PRF9	406
WDR5B	RBBP5	Q15291	404
WDR5B	FAM162A	Q96A26	377
WDR5B	MIX23	Q4VC31	376
WDR5B	SMAGP	Q0VAQ4	359
WDR5B	SEC22A	Q96IW7	351
WDR5B	FOXP4	Q8IVH2	349
WDR5B	DPY30	Q9C005	348
WDR5B	CASKIN2	Q8WXE0	343
WDR5B	ANKRD22	Q5VYY1	333
WDR5B	CNTLN	Q9NXG0	333
WDR5B	GPRC5C	Q9NQ84	332
WDR5B	FOXP2	O15409	330
WDR5B	DPH7	Q9BTV6	329

IntAct

22 interactions, top by confidence:

A	B	Type	Score
ASH2L	KMT2D	psi-mi:“MI:0914”(association)	0.890
KMT2D	RBBP5	psi-mi:“MI:0914”(association)	0.840
RBBP5	KMT2D	psi-mi:“MI:0914”(association)	0.840
CUL4B	CUL4A	psi-mi:“MI:0914”(association)	0.730
SNRNP27	UBA6	psi-mi:“MI:0914”(association)	0.530
WDR5B	TCP1	psi-mi:“MI:0914”(association)	0.530
ESR1	KMT2D	psi-mi:“MI:0914”(association)	0.520
CFTR	WDR5B	psi-mi:“MI:0915”(physical association)	0.370
WDR5B	ATP13A2	psi-mi:“MI:0915”(physical association)	0.370
WDR5B	DDB1	psi-mi:“MI:0914”(association)	0.350
NUDT9	WDR5B	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
DCAF4	IGLL5	psi-mi:“MI:0914”(association)	0.350
GPIHBP1	SAC3D1	psi-mi:“MI:0914”(association)	0.350
WDR5B	HSPA8	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (280): RPIA (Affinity Capture-MS), WDR5B (Affinity Capture-MS), WDR5B (Affinity Capture-MS), RNF220 (Affinity Capture-MS), HSF2 (Affinity Capture-MS), SEPN1 (Affinity Capture-MS), CLTCL1 (Affinity Capture-MS), ZNRF2 (Affinity Capture-MS), CCT4 (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT3 (Affinity Capture-MS), RRP12 (Affinity Capture-MS), CCT6B (Affinity Capture-MS), TCP1 (Affinity Capture-MS), CCT6A (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8RWN9, A5GFZ5, A9L985, O19137, O42602, O42603, O60762, O70152, O77676, P00516, P0C605, P19969, P31504, P31505, P31644, P35250, P41227, P47866, P51006, P53033, Q01777, Q01789, Q02029, Q02030, Q02033, Q08E50, Q13976, Q16576, Q1JQ93, Q24572, Q2KI14, Q3SWX8, Q3UX61, Q4R304, Q5FVR7, Q5MB13, Q5R654, Q5RE95, Q60748, Q60973

Diamond homologs: A1CTE6, A1DMI8, A2QVV2, B0Y7H6, B8N4F5, C4R6H3, C4YFX2, D9N129, P0CY34, P16371, P16649, P56094, Q00664, Q08274, Q09019, Q0CKB1, Q10437, Q2HJH6, Q2UM42, Q4WN25, Q5M786, Q5RE95, Q5RF51, Q5SQM0, Q6ED65, Q6PE01, Q6ZMW3, Q86VZ2, Q96DI7, Q9P4R5, Q9SY00, Q9VBC4, A8X8C6, B6QC56, B8N9H4, C0S902, C1GB49, C5FWH1, C5GVJ9, C5JD40

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 21 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
Neddylation	5	13.9×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
DNA damage response	6	16.1×	1e-04
protein ubiquitination	5	10.3×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

128 predictions. Top by Δscore:

Variant	Effect	Δscore
3:122415943:A:AC	donor_gain	0.9100
3:122415944:C:CC	donor_gain	0.9100
3:122415608:A:T	acceptor_gain	0.8500
3:122415940:G:C	donor_gain	0.8300
3:122415945:T:C	donor_gain	0.8300
3:122412693:C:CT	acceptor_gain	0.7900
3:122415938:TAGG:T	donor_gain	0.7600
3:122415923:CCCTA:C	donor_loss	0.7400
3:122415924:CCT:C	donor_loss	0.7400
3:122415925:CTA:C	donor_loss	0.7400
3:122415926:TA:T	donor_loss	0.7400
3:122415927:A:AT	donor_loss	0.7400
3:122415928:C:T	donor_loss	0.7400
3:122415922:GCCCT:G	donor_loss	0.7100
3:122415929:C:A	donor_loss	0.7100
3:122414746:ATTGG:A	acceptor_gain	0.6900
3:122415458:T:TA	donor_gain	0.6800
3:122415998:GAAGC:G	donor_gain	0.6500
3:122415928:CCAGT:C	donor_gain	0.6300
3:122414739:C:CC	acceptor_gain	0.6000
3:122416002:C:CT	donor_gain	0.6000
3:122415927:A:AC	donor_gain	0.5900
3:122415928:C:CC	donor_gain	0.5900
3:122412753:ATCT:A	acceptor_gain	0.5700
3:122414738:A:C	acceptor_gain	0.5500
3:122414747:TTGGC:T	acceptor_gain	0.5500
3:122415921:AGCC:A	donor_loss	0.5500
3:122415997:CGAAG:C	donor_gain	0.5500
3:122415820:AAAG:A	donor_gain	0.5300
3:122415607:C:CT	acceptor_gain	0.5000

AlphaMissense

2152 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:122415258:A:G	W91R	0.999
3:122415258:A:T	W91R	0.999
3:122415355:A:C	S58R	0.999
3:122415355:A:T	S58R	0.999
3:122415357:T:G	S58R	0.999
3:122414949:A:G	W194R	0.998
3:122414949:A:T	W194R	0.998
3:122414971:G:C	S186R	0.998
3:122414971:G:T	S186R	0.998
3:122414973:T:G	S186R	0.998
3:122415075:A:G	W152R	0.998
3:122415075:A:T	W152R	0.998
3:122415101:C:T	G143E	0.998
3:122415104:G:C	S142W	0.998
3:122414979:A:G	S184P	0.997
3:122415020:A:T	V170D	0.997
3:122415099:A:G	S144P	0.997
3:122415105:A:G	S142P	0.997
3:122415225:A:G	S102P	0.997
3:122415231:A:G	S100P	0.997
3:122414685:A:G	W282R	0.996
3:122414685:A:T	W282R	0.996
3:122414852:A:G	L226P	0.996
3:122414947:C:A	W194C	0.996
3:122414947:C:G	W194C	0.996
3:122415073:C:A	W152C	0.996
3:122415073:C:G	W152C	0.996
3:122415201:A:G	W110R	0.996
3:122415201:A:T	W110R	0.996
3:122415227:G:T	A101D	0.996

dbSNP variants (sampled 300 via entrez): RS1000041500 (3:122411725 T>G), RS1000063567 (3:122413227 T>G), RS1000742397 (3:122411861 T>C), RS1000869933 (3:122417419 A>G), RS1001174774 (3:122411511 A>G), RS1001302243 (3:122417146 G>T), RS1001354609 (3:122416848 G>A,C,T), RS1001418364 (3:122416586 T>A,G), RS1002915388 (3:122412268 A>C), RS1003763622 (3:122415416 A>T), RS1003788066 (3:122413796 C>T), RS1003949954 (3:122413653 G>A), RS1004385373 (3:122413827 T>A), RS1004912443 (3:122415190 T>C), RS1005978996 (3:122413741 G>A)

Disease associations

OMIM: gene MIM:621240 | 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
GCST000769_5	Calcium levels	2.000000e-22

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004838	calcium measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Formaldehyde	increases expression, decreases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
butyraldehyde	decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
tebuconazole	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, increases expression	1
Acetaminophen	increases expression	1
Carbamazepine	affects expression	1
Drugs, Chinese Herbal	increases expression	1
Endosulfan	increases expression	1
Methyl Methanesulfonate	increases expression	1
Naphthoquinones	increases expression	1
Potassium Chloride	decreases expression, decreases response to substance	1
Quercetin	decreases expression	1
Selenium	decreases expression	1
Silicon Dioxide	decreases expression	1
Sodium Dodecyl Sulfate	decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	1
Dronabinol	decreases response to substance, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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