WDR87

Summary

WDR87 (WD repeat domain 87, HGNC:29934) is a protein-coding gene on chromosome 19q13.13, encoding WD repeat-containing protein 87 (Q6ZQQ6).

At a glance

• Gene–disease (curated): cataract (Limited, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 606 total
• MANE Select transcript: NM_001291088

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29934
Approved symbol	WDR87
Name	WD repeat domain 87
Location	19q13.13
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP11
Ensembl gene	ENSG00000171804
Ensembl biotype	protein_coding
OMIM	620274
Entrez	83889

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000303868, ENST00000447313, ENST00000473328

RefSeq mRNA: 2 — MANE Select: NM_001291088 NM_001291088, NM_031951

CCDS: CCDS46063, CCDS74356

Canonical transcript exons

ENST00000447313 — 6 exons

Exon	Start	End
ENSE00001145121	37892578	37895456
ENSE00001478614	37891552	37891820
ENSE00001728565	37896138	37896308
ENSE00001825907	37906499	37906594
ENSE00001916169	37884823	37890276
ENSE00003641767	37898165	37898285

Expression profiles

Bgee: expression breadth broad, 27 present calls, max score 79.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1981 / max 98.7876, expressed in 73 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180739	0.1067	18
180738	0.0681	34
180740	0.0233	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	79.64	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.17	gold quality
left testis	UBERON:0004533	75.95	gold quality
pancreatic ductal cell	CL:0002079	74.96	silver quality
right testis	UBERON:0004534	74.54	gold quality
testis	UBERON:0000473	74.52	gold quality
buccal mucosa cell	CL:0002336	69.45	silver quality
left ventricle myocardium	UBERON:0006566	66.13	gold quality
ileal mucosa	UBERON:0000331	66.01	silver quality
deltoid	UBERON:0001476	66.01	silver quality
cardiac muscle of right atrium	UBERON:0003379	65.72	gold quality
lateral globus pallidus	UBERON:0002476	59.97	gold quality
nasal cavity epithelium	UBERON:0005384	59.73	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	58.48	gold quality
epithelial cell of pancreas	CL:0000083	56.47	gold quality
skin of hip	UBERON:0001554	56.37	silver quality
myocardium	UBERON:0002349	56.36	gold quality
cartilage tissue	UBERON:0002418	55.96	gold quality
sperm	CL:0000019	55.70	gold quality
upper leg skin	UBERON:0004262	55.63	gold quality
quadriceps femoris	UBERON:0001377	54.74	gold quality
parotid gland	UBERON:0001831	54.71	gold quality
heart right ventricle	UBERON:0002080	54.17	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
Brodmann (1909) area 46	UBERON:0006483	53.80	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
globus pallidus	UBERON:0001875	52.75	gold quality
medial globus pallidus	UBERON:0002477	52.61	gold quality
Brodmann (1909) area 23	UBERON:0013554	52.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting WDR87, 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-3925-3P	100.00	69.95	1237
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-6088	99.29	68.45	1284
HSA-MIR-4715-5P	97.62	67.47	506
HSA-MIR-493-3P	97.50	66.44	731
HSA-MIR-601	95.98	67.59	421

Literature-anchored findings (GeneRIF, showing 1)

• WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly. (PMID:36571501)

Cross-species orthologs

0 orthologs

Paralogs (2): CDC40 (ENSG00000168438), WDR25 (ENSG00000176473)

Protein

Protein identifiers

WD repeat-containing protein 87 — Q6ZQQ6 (reviewed: Q6ZQQ6)

Alternative names: Testis development protein NYD-SP11

All UniProt accessions (2): Q6ZQQ6, A0AA75ISB7

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZQQ6-1	1	yes
Q6ZQQ6-2	2

RefSeq proteins (2): NP_001278017, NP_114157 (=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

Pfam: PF00400

UniProt features (35 total): compositionally biased region 9, sequence conflict 8, repeat 7, region of interest 5, sequence variant 4, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q6ZQQ6 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, NFE2L2.V2, ARID5B_TARGET_GENES, FEV_TARGET_GENES, FOXD2_TARGET_GENES, ID1_TARGET_GENES, KAT5_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF197_TARGET_GENES, ZNF766_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR493_3P

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

818 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR87	AKR1E2	Q96JD6	596
WDR87	MFSD6L	Q8IWD5	519
WDR87	TAPT1	Q6NXT6	515
WDR87	RNLS	Q5VYX0	487
WDR87	SIPA1L3	O60292	476
WDR87	CARD14	Q9BXL6	443
WDR87	BFSP2	Q13515	429
WDR87	PIK3C2B	O00750	412
WDR87	RIC1	Q4ADV7	412
WDR87	CRYBB1	P53674	408
WDR87	DNMBP	Q6XZF7	405
WDR87	TTF2	Q9UNY4	404
WDR87	CRYBB3	P26998	400
WDR87	GCNT2	Q8N0V5	398
WDR87	DENND6A	Q8IWF6	391
WDR87	TAF1A	Q15573	391

IntAct

8 interactions, top by confidence:

A	B	Type	Score
GPS2	HDAC3	psi-mi:“MI:0914”(association)	0.900
WDR87	H1-4	psi-mi:“MI:0915”(physical association)	0.400
WDR87	HSPA8	psi-mi:“MI:0915”(physical association)	0.400
WDR87	NCL	psi-mi:“MI:0915”(physical association)	0.400
MAPT	LANCL1	psi-mi:“MI:0914”(association)	0.350
MAPT	NCAN	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350

BioGRID (22): WDR87 (Affinity Capture-MS), WDR87 (Affinity Capture-MS), WDR87 (Affinity Capture-MS), WDR87 (Proximity Label-MS), WDR87 (Proximity Label-MS), WDR87 (Proximity Label-MS), WDR87 (Proximity Label-MS), WDR87 (Affinity Capture-MS), WDR87 (Affinity Capture-MS), WDR87 (Affinity Capture-MS), WDR87 (Affinity Capture-MS), WDR87 (Affinity Capture-MS), WDR87 (Cross-Linking-MS (XL-MS)), WDR87 (Cross-Linking-MS (XL-MS)), WDR87 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1L8GXY4, A4D1P6, A8XSV3, B0JZ65, B0R160, B0WYR6, E9Q7R9, F1REV3, F6S215, O00443, O65418, P50748, Q09178, Q12769, Q17I16, Q19317, Q2TAW0, Q3MHH2, Q402B2, Q4V9P9, Q5R6T6, Q5RAY1, Q5RB52, Q5RE88, Q5ZJY3, Q5ZL79, Q5ZLL7, Q6DTM3, Q6GM71, Q6INI5, Q6P996, Q6X9E4, Q6ZQQ6, Q7TMQ7, Q86XI2, Q8BJW5, Q8BMQ2, Q8C3Y4, Q8K3E5, Q8N157

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	425
Likely benign	91
Benign	55

Top pathogenic / likely-pathogenic (0)

SpliceAI

1215 predictions. Top by Δscore:

Variant	Effect	Δscore
19:37891550:A:AC	donor_gain	1.0000
19:37891551:C:CC	donor_gain	1.0000
19:37891551:CTATG:C	donor_gain	1.0000
19:37891558:TTTTG:T	donor_gain	1.0000
19:37892576:A:AC	donor_gain	1.0000
19:37892577:C:CC	donor_gain	1.0000
19:37890277:C:CC	acceptor_gain	0.9900
19:37890278:T:G	acceptor_loss	0.9900
19:37891547:CATA:C	donor_gain	0.9900
19:37892577:CTG:C	donor_gain	0.9900
19:37892709:C:CT	acceptor_gain	0.9900
19:37895453:CAGC:C	acceptor_gain	0.9900
19:37895457:CTAGA:C	acceptor_loss	0.9900
19:37890273:TGGC:T	acceptor_gain	0.9800
19:37890281:A:T	acceptor_gain	0.9800
19:37892573:CTTA:C	donor_gain	0.9800
19:37892577:CT:C	donor_gain	0.9800
19:37892577:CTGCA:C	donor_gain	0.9800
19:37895457:C:CC	acceptor_gain	0.9800
19:37895458:T:C	acceptor_loss	0.9800
19:37898164:CCTTG:C	donor_gain	0.9800
19:37906650:T:TA	donor_gain	0.9800
19:37906651:C:A	donor_gain	0.9800
19:37890272:TTGGC:T	acceptor_gain	0.9700
19:37890274:GGC:G	acceptor_gain	0.9700
19:37890282:G:GC	acceptor_gain	0.9700
19:37891539:ACCC:A	donor_gain	0.9700
19:37891540:CCCC:C	donor_gain	0.9700
19:37892574:TTAC:T	donor_loss	0.9700
19:37892575:TACTG:T	donor_loss	0.9700

AlphaMissense

19269 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:37894775:A:G	W271R	0.997
19:37894775:A:T	W271R	0.997
19:37894773:C:A	W271C	0.995
19:37894773:C:G	W271C	0.995
19:37894810:A:G	L259P	0.993
19:37894804:G:T	T261K	0.991
19:37895180:A:G	W136R	0.991
19:37895180:A:T	W136R	0.991
19:37892762:A:G	W942R	0.990
19:37892762:A:T	W942R	0.990
19:37894774:C:G	W271S	0.990
19:37894801:G:T	A262D	0.989
19:37894802:C:G	A262P	0.989
19:37894804:G:C	T261R	0.989
19:37893806:A:G	W594R	0.988
19:37893806:A:T	W594R	0.988
19:37894432:A:G	L385P	0.988
19:37894493:A:G	W365R	0.987
19:37894493:A:T	W365R	0.987
19:37894807:A:G	L260P	0.987
19:37894934:A:C	Y218D	0.987
19:37893721:A:G	L622P	0.985
19:37893257:A:G	W777R	0.984
19:37893257:A:T	W777R	0.984
19:37893718:A:G	L623P	0.984
19:37893989:C:G	A533P	0.984
19:37894513:C:A	G358V	0.984
19:37894514:C:A	G358W	0.984
19:37894747:C:G	R280P	0.984
19:37893215:G:T	R791S	0.983

dbSNP variants (sampled 300 via entrez): RS1000023629 (19:37905867 G>C,T), RS1000351543 (19:37899244 C>A), RS1000545913 (19:37906728 A>AAG), RS1000571172 (19:37899730 G>A), RS1000948697 (19:37901139 A>G,T), RS1000979593 (19:37886348 C>A), RS1000997976 (19:37893311 C>T), RS1001083480 (19:37907397 G>A), RS1001303930 (19:37900820 C>T), RS1001403399 (19:37901120 C>T), RS1001507431 (19:37900231 G>A,C), RS1001702170 (19:37894184 G>A,C,T), RS1001771165 (19:37896101 G>A), RS1001898982 (19:37906290 C>G,T), RS1001945560 (19:37889755 C>G,T)

Disease associations

OMIM: gene MIM:620274 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
cataract	Limited	Autosomal recessive

Mondo (1): cataract (MONDO:0005129)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008747_173	Estimated glomerular filtration rate	2.000000e-14

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D002386	Cataract	C11.510.245

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	2
sodium arsenite	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases expression	1
Catechin	decreases expression, affects cotreatment	1
Copper	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00273221	PHASE4	UNKNOWN	Combined Phacotube vs Phacotrabeculectomy:A Randomized Controlled Trial
NCT00312299	PHASE4	COMPLETED	Posterior Capsule Opacification Study
NCT00345046	PHASE4	COMPLETED	A Comparison of Three Different Formulations of Prednisolone Acetate 1%
NCT00347243	PHASE4	COMPLETED	Wavefront Analisys and Contrast Sensitivity of Spherical and Aspherical Intraocular Lenses
NCT00347503	PHASE4	COMPLETED	Aqueous Concentrations and PGE2 Inhibition of Ketorolac 0.4% vs. Bromfenac 0.09% in Cataract Patients
NCT00348244	PHASE4	COMPLETED	Ketorolac vs. Steroid in the Prevention of CME
NCT00348270	PHASE4	COMPLETED	Comparison of the Quality of Vision Provided by AMO Tecnis Z9000 and Alcon Laboratories MA60 Acrysof Posterior Chamber Intraocular Lenses
NCT00348582	PHASE4	COMPLETED	Acular LS vs. Nevanac in Post op Inflammation Following Cataract Surgery
NCT00348621	PHASE4	COMPLETED	A Study of Interventions to Reduce Disability From Visual Loss in Nursing Home Residents
NCT00349583	PHASE4	COMPLETED	Efficacy of Topical Cyclosporine Versus Tears for Improving Visual Outcomes Following Multifocal IOL Implantation
NCT00355446	PHASE4	COMPLETED	Bioavailability of Bimatoprost Ophthalmic Solution in Human Aqueous.
NCT00386438	PHASE4	COMPLETED	Efficacy of Honan Balloon in Intraocular Pressure Reduction Before Phacoemulsification
NCT00392275	PHASE4	COMPLETED	Penetrance of Third Generation Fluoroquinolones in Eyes With Functioning Filtering Blebs
NCT00428363	PHASE4	COMPLETED	Effect of Optic Edge Design in a Silicone Intraocular Lens on Posterior Capsule Opacification
NCT00449267	PHASE4	COMPLETED	Aurolab Hydrophobic Foldable Intraocular Lens Study
NCT00459303	PHASE4	COMPLETED	Comparison of Functional Vision Provided by AMO Tecnis Z9000 and Alcon SA60AT Acrysof
NCT00469690	PHASE4	COMPLETED	Aqueous Concentrations and PGE2 Inhibition of Ketorolac 0.4% vs. Bromfenac 0.09% in Cataract Patients: Trough Drug Effects
NCT00576485	PHASE4	COMPLETED	Spherical Aberration and Contrast Sensitivity in IOLs
NCT00612729	PHASE4	COMPLETED	Light Filters in Intraocular Lenses (IOLs) and Its Influence on Colour and Contrast Vision.
NCT00612781	PHASE4	COMPLETED	Yellow Versus White Study
NCT00630019	PHASE4	COMPLETED	Ocular Tissue Levels of 1.5% Levofloxacin Ophthalmic Solution Compared to an Active Comparator
NCT00673803	PHASE4	COMPLETED	Influence of Two Different Preloaded Intraocular Lens (IOLs) on Posterior Capsule Opacification
NCT00684138	PHASE4	COMPLETED	ACRYSOF® ReSTOR® Aspheric +3.0 D Add Power Intraocular Lens (IOL)
NCT00698724	PHASE4	COMPLETED	Comparing Optical Coherence Tomography (OCT) and Visual Acuity Outcomes in Subjects Undergoing Cataract Surgery, Who Receive Xibrom Ophthalmic Solution and Standard Presurgical Care vs. Xibrom Ophthalmic Solution Plus Prednisolone Acetate 1% and Standard Presurgical Care
NCT00710905	PHASE4	TERMINATED	Visual Function With Contralateral AcrySof® ReSTOR® Aspheric SN6AD1 and SN6AD3
NCT00710931	PHASE4	COMPLETED	Visual Function With Bilateral AcrySof® ReSTOR® Aspheric SN6AD1
NCT00711347	PHASE4	COMPLETED	Intraoperative Floppy Iris Syndrome
NCT00712244	PHASE4	COMPLETED	DisCoVisc Versus DuoVisc, Healon5 and AmVisc Plus
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00719732	PHASE4	COMPLETED	Visual Function After Implantation of Bilateral AcrySof ReSTOR Aspheric +3
NCT00721253	PHASE4	COMPLETED	Visual Outcomes of Subjects Bilaterally Implanted With ReSTOR Aspheric +4 vs. Tecnis or Acri.LISA
NCT00731640	PHASE4	COMPLETED	Contralateral ReSTOR / Monofocal or Phakic Eye
NCT00732030	PHASE4	COMPLETED	Low Cylinder Toric
NCT00758199	PHASE4	COMPLETED	Determination of Optimum Duration of Treatment With Bromfenac (Xibrom) Eyedrops Following Cataract Surgery
NCT00760058	PHASE4	WITHDRAWN	Visual Outcome and Visual Quality After Bilateral Implantation of the AcrySof® IQ IOL Compared to MI60® and Tecnis® IOL
NCT00760487	PHASE4	COMPLETED	Visual Function After Implantation of Bilateral AcrySof® Toric Natural Intraocular Lens
NCT00761488	PHASE4	WITHDRAWN	Recommendations for Monitoring Clinical Experience Following Implantation of the AcrySof® Toric
NCT00763360	PHASE4	COMPLETED	To Compare the Ability of DiscoVisc® OVD to Protect the Corneal Endothelium and Maintain Anterior Chamber Space With Healon® and Amvisc® PLUS During Cataract Surgery.
NCT00786370	PHASE4	COMPLETED	Dexmedetomidine vs. Propofol for Cataract Surgery
NCT00786565	PHASE4	COMPLETED	Clinical Evaluation of a New Aspheric Intraocular Lens.