WDR88

Summary

WDR88 (WD repeat domain 88, HGNC:26999) is a protein-coding gene on chromosome 19q13.11, encoding WD repeat-containing protein 88 (Q6ZMY6).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 72 total
• MANE Select transcript: NM_173479

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26999
Approved symbol	WDR88
Name	WD repeat domain 88
Location	19q13.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000166359
Ensembl biotype	protein_coding
Entrez	126248

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000355868, ENST00000361680, ENST00000592765

RefSeq mRNA: 1 — MANE Select: NM_173479 NM_173479

CCDS: CCDS12429

Canonical transcript exons

ENST00000355868 — 11 exons

Exon	Start	End
ENSE00001102408	33151181	33151310
ENSE00001102409	33148772	33148910
ENSE00001102414	33137677	33137787
ENSE00001235450	33172348	33172440
ENSE00001235458	33164197	33164265
ENSE00001235462	33160414	33160496
ENSE00001235470	33156355	33156542
ENSE00001235484	33147645	33147708
ENSE00001235491	33144844	33144932
ENSE00002759772	33132114	33132445
ENSE00003500325	33175396	33175799

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 87.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0179 / max 18.9456, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175076	0.0101	3
175077	0.0078	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.24	gold quality
sperm	CL:0000019	82.62	silver quality
left testis	UBERON:0004533	74.14	gold quality
right testis	UBERON:0004534	73.85	gold quality
testis	UBERON:0000473	72.16	gold quality
prefrontal cortex	UBERON:0000451	60.82	gold quality
smooth muscle tissue	UBERON:0001135	60.81	gold quality
right uterine tube	UBERON:0001302	60.13	gold quality
islet of Langerhans	UBERON:0000006	59.93	gold quality
vermiform appendix	UBERON:0001154	59.56	gold quality
monocyte	CL:0000576	59.53	gold quality
leukocyte	CL:0000738	59.18	gold quality
granulocyte	CL:0000094	59.08	gold quality
apex of heart	UBERON:0002098	58.77	gold quality
cortical plate	UBERON:0005343	58.02	gold quality
ganglionic eminence	UBERON:0004023	57.85	gold quality
lymph node	UBERON:0000029	57.37	gold quality
gastrocnemius	UBERON:0001388	57.20	gold quality
muscle of leg	UBERON:0001383	57.15	gold quality
cerebellar cortex	UBERON:0002129	57.05	gold quality
cerebellar hemisphere	UBERON:0002245	57.04	gold quality
rectum	UBERON:0001052	57.03	gold quality
Brodmann (1909) area 9	UBERON:0013540	57.02	gold quality
right hemisphere of cerebellum	UBERON:0014890	56.53	gold quality
ventricular zone	UBERON:0003053	56.24	gold quality
cerebellum	UBERON:0002037	55.97	gold quality
adenohypophysis	UBERON:0002196	55.87	gold quality
right coronary artery	UBERON:0001625	55.62	gold quality
gall bladder	UBERON:0002110	55.41	gold quality
caecum	UBERON:0001153	55.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting WDR88, 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-4760-5P	99.80	69.88	1619
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-8061	99.63	69.44	1411
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-376A-5P	97.70	65.61	863
HSA-MIR-191-5P	95.88	67.82	171

Literature-anchored findings (GeneRIF, showing 1)

• Genome-wide significant support for contributing to schizophrenia has been found for the WDR88 (WD repeat-containing protein 88), a gene of unknown function. (PMID:26740555)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Wdr88	ENSMUSG00000118454
rattus_norvegicus	Wdr88	ENSRNOG00000037393

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), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363), WDR5B (ENSG00000196981)

Protein

Protein identifiers

WD repeat-containing protein 88 — Q6ZMY6 (reviewed: Q6ZMY6)

Alternative names: PQQ repeat and WD repeat-containing protein

All UniProt accessions (2): Q6ZMY6, K7EPH1

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZMY6-1	1	yes
Q6ZMY6-2	2

RefSeq proteins (1): NP_775750* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR011047	Quinoprotein_ADH-like_sf	Homologous_superfamily
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR018391	PQQ_b-propeller_rpt	Repeat
IPR019775	WD40_repeat_CS	Conserved_site
IPR020472	WD40_PAC1	Repeat

Pfam: PF00400

UniProt features (14 total): repeat 7, sequence variant 2, region of interest 2, chain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZMY6-F1	77.33	0.55

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): GSE8685_IL15_ACT_IL2_STARVED_VS_IL21_ACT_IL2_STARVED_CD4_TCELL_DN, MYOCD_TARGET_GENES, GSE26928_NAIVE_VS_CXCR5_POS_CD4_TCELL_UP, GSE26928_CENTR_MEMORY_VS_CXCR5_POS_CD4_TCELL_UP, GSE29614_DAY3_VS_DAY7_TIV_FLU_VACCINE_PBMC_UP, chr19q13, GSE36888_UNTREATED_VS_IL2_TREATED_STAT5_AB_KNOCKIN_TCELL_17H_UP, GSE32034_UNTREATED_VS_ROSIGLIZATONE_TREATED_LY6C_LOW_MONOCYTE_UP

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

518 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR88	ASB12	Q8WXK4	454
WDR88	LCE2D	Q5TA82	440
WDR88	STK32A	Q8WU08	406
WDR88	ZZEF1	O43149	398
WDR88	MAST3	O60307	383
WDR88	IGFL2	Q6UWQ7	377
WDR88	ADAM18	Q9Y3Q7	351
WDR88	TROAP	Q12815	324
WDR88	HIBCH	Q6NVY1	319
WDR88	CRTAC1	Q9NQ79	314
WDR88	TMEM45A	Q9NWC5	312
WDR88	DNAH7	Q8WXX0	311
WDR88	CNN3	Q15417	289
WDR88	AATK	Q6ZMQ8	271
WDR88	ST3GAL5	Q9UNP4	270

IntAct

16 interactions, top by confidence:

A	B	Type	Score
WDR88	MTA2	psi-mi:“MI:0915”(physical association)	0.400
NUDC	WDR88	psi-mi:“MI:0915”(physical association)	0.400
	WDR88	psi-mi:“MI:0915”(physical association)	0.000
WDR88	metE	psi-mi:“MI:0915”(physical association)	0.000
sph	WDR88	psi-mi:“MI:0915”(physical association)	0.000
WDR88		psi-mi:“MI:0915”(physical association)	0.000
cpfC1	WDR88	psi-mi:“MI:0915”(physical association)	0.000
argG	WDR88	psi-mi:“MI:0915”(physical association)	0.000
WDR88	yopM	psi-mi:“MI:0915”(physical association)	0.000
WDR88	appA	psi-mi:“MI:0915”(physical association)	0.000
pntA	WDR88	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): WDR88 (Affinity Capture-RNA), WDR88 (Proximity Label-MS), WDR88 (Cross-Linking-MS (XL-MS)), WDR88 (Cross-Linking-MS (XL-MS)), WDR88 (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A0JM23, A0JP70, B2RZ17, E1BVR9, O14727, O54927, O88879, O94952, P0CI65, Q08BB3, Q08DV6, Q13309, Q32KQ2, Q3U3W5, Q3U821, Q3UDP0, Q3UMR0, Q3UR70, Q58D00, Q5R5S1, Q5REW9, Q5XJS5, Q60584, Q68EI0, Q6AX81, Q6AZT7, Q6DFC6, Q6P1V3, Q6P2P2, Q6P2S7, Q6ZMY6, Q7T2F6, Q7TNH6, Q7Z494, Q8BHD1, Q8C5V5, Q8IWA0, Q8NA23, Q8VDH1, Q96NW4

Diamond homologs: A1CJY4, A1D7I5, A4RDD7, B0XYC8, O00423, O80990, O95834, Q05BC3, Q05BV3, Q0CXH9, Q1DPU4, Q1JQD2, Q26613, Q29RH4, Q2TAF3, Q2UQ34, Q32P44, Q3UMY5, Q4V8C3, Q4WX90, Q5B8Y3, Q5SQM0, Q6DIP5, Q6ED65, Q6P6T4, Q6ZMW3, Q6ZMY6, Q7RXH4, Q7TNG5, Q8BQM8, Q8VC03, Q8VE80, Q96J01, Q9HC35, Q9XW12, Q9Y1C1, A3LX18, B0XAF3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2196 predictions. Top by Δscore:

Variant	Effect	Δscore
19:33137784:GTGG:G	donor_gain	1.0000
19:33144832:C:A	acceptor_gain	1.0000
19:33144835:T:A	acceptor_gain	1.0000
19:33148809:A:G	acceptor_gain	1.0000
19:33137781:GCT:G	donor_gain	0.9900
19:33137788:G:GG	donor_gain	0.9900
19:33137799:GCTGT:G	donor_gain	0.9900
19:33148759:T:A	acceptor_gain	0.9900
19:33148770:A:AG	acceptor_gain	0.9900
19:33148771:G:GG	acceptor_gain	0.9900
19:33148906:CAAAG:C	donor_loss	0.9900
19:33148907:AAAGG:A	donor_loss	0.9900
19:33148909:AGGT:A	donor_loss	0.9900
19:33148910:GGTG:G	donor_loss	0.9900
19:33148911:G:C	donor_loss	0.9900
19:33148912:T:A	donor_loss	0.9900
19:33151311:G:GG	donor_gain	0.9900
19:33175379:A:AG	acceptor_gain	0.9900
19:33175380:A:G	acceptor_gain	0.9900
19:33132402:TGCCG:T	donor_gain	0.9800
19:33132403:GCCGG:G	donor_gain	0.9800
19:33132443:AAGG:A	donor_loss	0.9800
19:33132444:AG:A	donor_loss	0.9800
19:33132445:GGTC:G	donor_loss	0.9800
19:33132446:GTCA:G	donor_loss	0.9800
19:33137671:TTTCA:T	acceptor_loss	0.9800
19:33137672:TTCA:T	acceptor_loss	0.9800
19:33137673:TCAG:T	acceptor_loss	0.9800
19:33137674:CA:C	acceptor_loss	0.9800
19:33137675:A:T	acceptor_loss	0.9800

AlphaMissense

3130 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:33137755:A:C	S119R	0.998
19:33137757:T:A	S119R	0.998
19:33137757:T:G	S119R	0.998
19:33156410:T:C	C289R	0.997
19:33164261:C:T	S382F	0.997
19:33156416:A:C	S291R	0.996
19:33156418:C:A	S291R	0.996
19:33156418:C:G	S291R	0.996
19:33156443:T:A	W300R	0.996
19:33156443:T:C	W300R	0.996
19:33160458:T:A	W348R	0.996
19:33160458:T:C	W348R	0.996
19:33164261:C:A	S382Y	0.996
19:33172366:T:A	W390R	0.996
19:33172366:T:C	W390R	0.996
19:33156412:T:G	C289W	0.995
19:33156414:C:A	T290K	0.995
19:33156516:T:A	V324D	0.995
19:33156518:A:C	S325R	0.995
19:33156520:T:A	S325R	0.995
19:33156520:T:G	S325R	0.995
19:33164260:T:C	S382P	0.995
19:33160428:T:C	S338P	0.994
19:33160432:G:A	G339E	0.994
19:33156414:C:G	T290R	0.993
19:33156445:G:C	W300C	0.993
19:33156445:G:T	W300C	0.993
19:33164254:T:C	S380P	0.993
19:33172348:G:C	D384H	0.993
19:33156419:T:C	S292P	0.992

dbSNP variants (sampled 300 via entrez): RS1000145500 (19:33173461 C>T), RS1000199153 (19:33174662 T>G), RS1000264937 (19:33148178 C>T), RS1000303596 (19:33135449 C>A,G,T), RS1000311865 (19:33160058 A>G), RS1000379501 (19:33165439 A>G), RS1000577607 (19:33171806 C>T), RS1000585925 (19:33136555 T>C), RS1000654049 (19:33135135 C>A), RS1000724849 (19:33165862 T>C), RS1000731997 (19:33130528 G>A,C,T), RS1000735875 (19:33136533 T>C), RS1000741761 (19:33130746 A>C), RS1000749110 (19:33171959 G>C,T), RS1000944110 (19:33166210 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009798_7	Asthma	1.000000e-23
GCST010703_314	Brain morphology (MOSTest)	4.000000e-23

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects methylation, increases methylation	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	affects methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases expression	1

Clinical trials (associated diseases)

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