WDR89

Summary

WDR89 (WD repeat domain 89, HGNC:20489) is a protein-coding gene on chromosome 14q23.2, encoding WD repeat-containing protein 89 (Q96FK6).

Predicted to act upstream of or within corpus callosum development and ventricular system development.

Source: NCBI Gene 112840 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_080666

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20489
Approved symbol	WDR89
Name	WD repeat domain 89
Location	14q23.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC9907
Ensembl gene	ENSG00000140006
Ensembl biotype	protein_coding
Entrez	112840

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000267522, ENST00000394942, ENST00000554717, ENST00000620954, ENST00000854766, ENST00000854767, ENST00000854768, ENST00000932310, ENST00000932311, ENST00000932312, ENST00000941461

RefSeq mRNA: 10 — MANE Select: NM_080666 NM_001008726, NM_001258272, NM_001382423, NM_001382424, NM_001382425, NM_001382426, NM_001382427, NM_001382428, NM_001382429, NM_080666

CCDS: CCDS9759

Canonical transcript exons

ENST00000620954 — 3 exons

Exon	Start	End
ENSE00001520068	63597039	63599973
ENSE00001520070	63624928	63625033
ENSE00003915203	63641804	63641871

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 92.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1549 / max 214.7140, expressed in 1689 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143602	9.8718	1678
143600	0.2174	96
143601	0.0657	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	92.37	gold quality
kidney epithelium	UBERON:0004819	92.12	silver quality
buccal mucosa cell	CL:0002336	91.22	gold quality
tibialis anterior	UBERON:0001385	90.13	silver quality
calcaneal tendon	UBERON:0003701	88.31	gold quality
epithelial cell of pancreas	CL:0000083	87.95	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.21	gold quality
ileal mucosa	UBERON:0000331	87.07	gold quality
islet of Langerhans	UBERON:0000006	86.46	gold quality
ventricular zone	UBERON:0003053	85.95	gold quality
tendon	UBERON:0000043	85.82	gold quality
deltoid	UBERON:0001476	85.53	silver quality
cortical plate	UBERON:0005343	85.47	gold quality
pancreatic ductal cell	CL:0002079	85.43	silver quality
corpus callosum	UBERON:0002336	85.10	gold quality
superficial temporal artery	UBERON:0001614	84.77	silver quality
tendon of biceps brachii	UBERON:0008188	83.88	silver quality
ganglionic eminence	UBERON:0004023	83.61	gold quality
sperm	CL:0000019	83.60	gold quality
lymph node	UBERON:0000029	83.49	gold quality
vastus lateralis	UBERON:0001379	83.09	silver quality
quadriceps femoris	UBERON:0001377	82.64	silver quality
body of tongue	UBERON:0011876	82.39	silver quality
subthalamic nucleus	UBERON:0001906	82.35	silver quality
adrenal tissue	UBERON:0018303	82.21	gold quality
vena cava	UBERON:0004087	81.87	silver quality
dorsal plus ventral thalamus	UBERON:0001897	81.75	silver quality
globus pallidus	UBERON:0001875	81.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.69	gold quality
cardia of stomach	UBERON:0001162	81.67	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	232.05
E-ANND-3	yes	3.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

77 targeting WDR89, 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-340-5P	100.00	72.50	4437
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-548A-3P	99.76	70.58	3524

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr89	ENSDARG00000077265
mus_musculus	Wdr89	ENSMUSG00000045690
rattus_norvegicus	Wdr89	ENSRNOG00000021628
drosophila_melanogaster	CG12134	FBGN0033471

Protein

Protein identifiers

WD repeat-containing protein 89 — Q96FK6 (reviewed: Q96FK6)

All UniProt accessions (2): Q96FK6, G3V4B8

RefSeq proteins (10): NP_001008726, NP_001245201, NP_001369352, NP_001369353, NP_001369354, NP_001369355, NP_001369356, NP_001369357, NP_001369358, NP_542397* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR039328	WDR89	Family

Pfam: PF00400

UniProt features (7 total): repeat 6, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96FK6-F1	87.37	0.73

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): GOBP_VENTRICULAR_SYSTEM_DEVELOPMENT, GOBP_FOREBRAIN_DEVELOPMENT, MODULE_205, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_HEAD_DEVELOPMENT, chr14q23, GOBP_TELENCEPHALON_DEVELOPMENT, GOBP_CORPUS_CALLOSUM_DEVELOPMENT, WANG_TUMOR_INVASIVENESS_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, ZWANG_DOWN_BY_2ND_EGF_PULSE, ARNT2_TARGET_GENES, ASH1L_TARGET_GENES, BANP_TARGET_GENES

GO Biological Process (2): ventricular system development (GO:0021591), corpus callosum development (GO:0022038)

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
brain development	1
system development	1
telencephalon development	1
anatomical structure development	1
binding	1

Protein interactions and networks

STRING

892 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR89	CCDC24	Q8N4L8	499
WDR89	TMEM247	A6NEH6	478
WDR89	WDR13	Q9H1Z4	461
WDR89	BEAN1	Q3B7T3	438
WDR89	CEP170B	Q9Y4F5	437
WDR89	ARL5C	A6NH57	430
WDR89	DDX56	Q9NY93	400
WDR89	WDR47	O94967	383
WDR89	PIANP	Q8IYJ0	383
WDR89	GOLGA6L2	Q8N9W4	380
WDR89	DCAF4L2	Q8NA75	370
WDR89	SLC9D1	Q6UWJ1	365
WDR89	DHX40	Q8IX18	361
WDR89	WDR75	Q8IWA0	355
WDR89	WDR33	Q9C0J8	355

IntAct

38 interactions, top by confidence:

A	B	Type	Score
CCT2	TXNDC9	psi-mi:“MI:0914”(association)	0.730
RPL10A	RRP8	psi-mi:“MI:0914”(association)	0.640
CCT3	TXNDC9	psi-mi:“MI:0914”(association)	0.640
IGHMBP2	THAP12	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
HMGA1	MACROH2A1	psi-mi:“MI:0914”(association)	0.530
SIGLEC7	WDR89	psi-mi:“MI:0915”(physical association)	0.400
URB2	WDR89	psi-mi:“MI:0915”(physical association)	0.400
SOCS6	WDR89	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
NOL8	URB1	psi-mi:“MI:0914”(association)	0.350
SIGLEC7	LGALS1	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
rep	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
rl3_rl3l_human	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
ILF3	GTPBP10	psi-mi:“MI:0914”(association)	0.350
APOBEC3C	GTPBP10	psi-mi:“MI:0914”(association)	0.350
RPL13A	GTPBP10	psi-mi:“MI:0914”(association)	0.350
CCT2	WDR91	psi-mi:“MI:0914”(association)	0.350
FGFBP1	ZNF724	psi-mi:“MI:0914”(association)	0.350
TFPI2	AP3B1	psi-mi:“MI:0914”(association)	0.350
PIGF	SUPT5H	psi-mi:“MI:0914”(association)	0.350
DDX55	URB1	psi-mi:“MI:0914”(association)	0.350
RPL10A	RPL13	psi-mi:“MI:0914”(association)	0.350
ANKRD49	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (53): WDR89 (Affinity Capture-MS), WDR89 (Co-fractionation), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS), WDR89 (Two-hybrid), WDR89 (Two-hybrid), WDR89 (Two-hybrid), WDR89 (Affinity Capture-MS), WDR89 (Affinity Capture-MS)

ESM2 similar proteins: A5DL92, A7RHG8, A7TMF9, A8Q2R5, A8QB65, A8XL02, B0W517, B3MJV8, B3N534, B3RQN1, B4GT01, B4HWV6, B4JPT9, B4KKN1, B4LS78, B4MU54, B4P116, B4Q9T6, B5DG67, F1DLK1, O74865, O94533, P20053, P38328, P61480, P91343, Q0VC24, Q17BB0, Q20059, Q29KQ0, Q3ZBK1, Q5BJ90, Q5RBZ3, Q5REE6, Q6CU59, Q6FKK3, Q6NNP0, Q6NX08, Q6TNS2, Q756D0

Diamond homologs: P53962, Q3ZBK1, Q54QU5, Q5RBZ3, Q6FXI8, Q96FK6, Q9D0R9, Q5FVP5, A5E6M3, O14053

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

877 predictions. Top by Δscore:

Variant	Effect	Δscore
14:63599969:AAACT:A	acceptor_gain	1.0000
14:63599970:AACT:A	acceptor_gain	1.0000
14:63599972:CT:C	acceptor_gain	1.0000
14:63599974:C:CC	acceptor_gain	1.0000
14:63599973:TC:T	acceptor_loss	0.9900
14:63624974:ATGT:A	donor_gain	0.9900
14:63641807:AGTAG:A	donor_gain	0.9900
14:63599971:ACT:A	acceptor_gain	0.9800
14:63599972:CTC:C	acceptor_gain	0.9800
14:63599973:TCT:T	acceptor_gain	0.9800
14:63599976:G:C	acceptor_gain	0.9800
14:63629485:T:TA	donor_gain	0.9800
14:63641680:C:A	donor_gain	0.9800
14:63599974:C:G	acceptor_gain	0.9700
14:63624926:A:AC	donor_gain	0.9700
14:63624927:C:CC	donor_gain	0.9700
14:63641800:GTAC:G	donor_loss	0.9700
14:63641801:TA:T	donor_loss	0.9700
14:63641802:A:AT	donor_loss	0.9700
14:63641803:CCTT:C	donor_loss	0.9700
14:63641814:TCA:T	donor_gain	0.9700
14:63599983:A:AC	acceptor_gain	0.9600
14:63624922:ACT:A	donor_loss	0.9600
14:63624924:TTACC:T	donor_loss	0.9600
14:63624925:T:TA	donor_loss	0.9600
14:63624926:A:C	donor_loss	0.9600
14:63624926:AC:A	donor_gain	0.9600
14:63624927:C:CT	donor_loss	0.9600
14:63624927:CC:C	donor_gain	0.9600
14:63641816:A:AT	donor_gain	0.9600

AlphaMissense

2558 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:63599273:A:G	W224R	0.995
14:63599273:A:T	W224R	0.995
14:63599375:A:G	S190P	0.994
14:63599377:C:T	G189D	0.992
14:63599409:G:C	F178L	0.991
14:63599409:G:T	F178L	0.991
14:63599411:A:G	F178L	0.991
14:63599213:A:G	W244R	0.990
14:63599213:A:T	W244R	0.990
14:63599359:A:T	V195E	0.986
14:63599548:G:T	A132D	0.986
14:63598901:A:G	W348R	0.985
14:63598901:A:T	W348R	0.985
14:63598972:A:T	V324D	0.985
14:63599381:A:G	S188P	0.985
14:63599507:A:G	W146R	0.985
14:63599507:A:T	W146R	0.985
14:63599243:A:G	C234R	0.984
14:63599552:A:G	C131R	0.984
14:63599241:G:C	C234W	0.983
14:63599362:A:G	L194P	0.983
14:63599378:C:G	G189R	0.980
14:63599410:A:G	F178S	0.979
14:63599271:C:A	W224C	0.978
14:63599271:C:G	W224C	0.978
14:63599368:T:A	D192V	0.978
14:63599550:A:C	C131W	0.977
14:63599545:C:T	G133D	0.976
14:63598969:C:G	R325P	0.975
14:63599211:C:A	W244C	0.974

dbSNP variants (sampled 300 via entrez): RS1000007999 (14:63632699 A>T), RS1000015639 (14:63620333 T>C), RS1000046216 (14:63598330 A>G), RS1000047457 (14:63604871 A>T), RS1000068339 (14:63643705 T>C), RS1000139130 (14:63598731 G>A), RS1000232021 (14:63614009 C>A), RS1000317346 (14:63608049 T>A,C), RS1000370818 (14:63602086 G>C), RS1000402882 (14:63640340 G>C), RS1000465345 (14:63640515 G>A), RS1000537465 (14:63620874 G>C,T), RS1000588987 (14:63625191 G>A,C), RS1000658054 (14:63618648 C>G), RS1000733536 (14:63630189 C>A)

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

1 associations (top):

Study	Trait	p-value
GCST002949_17	Epilepsy and lamotrigine-induced maculopapular eruptions	1.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:1001253	maculopapular eruption

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, increases expression	2
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Formaldehyde	decreases expression	2
Nickel	increases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	decreases expression	1
Vorinostat	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Estradiol	affects expression	1
Ethyl Methanesulfonate	decreases expression	1
Lead	increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	decreases expression	1
Dronabinol	decreases expression	1
Tretinoin	decreases expression	1
Gold Compounds	decreases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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