WDR64

Summary

WDR64 (WD repeat domain 64, HGNC:26570) is a protein-coding gene on chromosome 1q43, encoding WD repeat-containing protein 64 (B1ANS9).

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 159 total
• MANE Select transcript: NM_001367482

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26570
Approved symbol	WDR64
Name	WD repeat domain 64
Location	1q43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32978
Ensembl gene	ENSG00000162843
Ensembl biotype	protein_coding
Entrez	128025

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000366552, ENST00000414635, ENST00000425826, ENST00000437684, ENST00000461971, ENST00000472717, ENST00000478331, ENST00000496914

RefSeq mRNA: 1 — MANE Select: NM_001367482 NM_001367482

CCDS: CCDS91185

Canonical transcript exons

ENST00000437684 — 28 exons

Exon	Start	End
ENSE00001325177	241749547	241749722
ENSE00001385900	241744393	241744516
ENSE00002214946	241683487	241683701
ENSE00002221859	241723297	241723436
ENSE00002255235	241738363	241738489
ENSE00002288145	241711802	241711881
ENSE00002303998	241741516	241741664
ENSE00002317845	241660530	241660660
ENSE00003472554	241783272	241783381
ENSE00003477561	241766218	241766351
ENSE00003478215	241770621	241770690
ENSE00003486083	241787849	241788034
ENSE00003499994	241790591	241790696
ENSE00003510917	241771661	241771697
ENSE00003518613	241795207	241795287
ENSE00003525224	241775105	241775210
ENSE00003537036	241801132	241802777
ENSE00003543402	241772792	241772931
ENSE00003571683	241671074	241671176
ENSE00003576379	241780004	241780062
ENSE00003591373	241757283	241757459
ENSE00003604493	241679485	241679595
ENSE00003640566	241796257	241796370
ENSE00003660318	241674644	241674747
ENSE00003674835	241769404	241769505
ENSE00003746297	241687461	241687595
ENSE00003918910	241652281	241652629
ENSE00003922237	241678187	241678216

Expression profiles

Bgee: expression breadth ubiquitous, 103 present calls, max score 91.80.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0138 / max 11.9184, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9387	0.0138	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	91.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.65	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.23	gold quality
left testis	UBERON:0004533	73.47	gold quality
right testis	UBERON:0004534	73.36	gold quality
testis	UBERON:0000473	71.94	gold quality
sperm	CL:0000019	69.37	silver quality
bone marrow cell	CL:0002092	61.47	gold quality
adrenal tissue	UBERON:0018303	57.66	gold quality
vermiform appendix	UBERON:0001154	53.26	gold quality
upper leg skin	UBERON:0004262	52.71	gold quality
caecum	UBERON:0001153	50.32	gold quality
lymph node	UBERON:0000029	48.24	gold quality
adrenal gland	UBERON:0002369	46.97	gold quality
gall bladder	UBERON:0002110	46.79	gold quality
prefrontal cortex	UBERON:0000451	46.74	gold quality
right adrenal gland	UBERON:0001233	46.17	gold quality
left adrenal gland	UBERON:0001234	46.01	gold quality
right adrenal gland cortex	UBERON:0035827	45.85	gold quality
left adrenal gland cortex	UBERON:0035825	45.72	gold quality
tonsil	UBERON:0002372	45.64	gold quality
placenta	UBERON:0001987	45.38	gold quality
adrenal cortex	UBERON:0001235	45.34	gold quality
bone marrow	UBERON:0002371	45.08	silver quality
ganglionic eminence	UBERON:0004023	44.71	gold quality
muscle layer of sigmoid colon	UBERON:0035805	43.53	gold quality
minor salivary gland	UBERON:0001830	43.49	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
frontal cortex	UBERON:0001870	43.29	gold quality
saliva-secreting gland	UBERON:0001044	43.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-75367	yes	9.73
E-ANND-3	yes	6.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting WDR64, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-93-5P	99.88	73.98	2606

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-154o6.3	ENSDARG00000099846
mus_musculus	Wdr64	ENSMUSG00000026523
rattus_norvegicus	Wdr64	ENSRNOG00000038083
drosophila_melanogaster	WDY	FBGN0267449
caenorhabditis_elegans		WBGENE00004767

Paralogs (14): WDR54 (ENSG00000005448), FBXW11 (ENSG00000072803), FBXW7 (ENSG00000109670), TRAF7 (ENSG00000131653), FBXW9 (ENSG00000132004), FBXO36 (ENSG00000153832), FBXW12 (ENSG00000164049), BTRC (ENSG00000166167), WDR49 (ENSG00000174776), FBXW8 (ENSG00000174989), PAAF1 (ENSG00000175575), WDR86 (ENSG00000187260), FBXO16 (ENSG00000214050), EFCAB8 (ENSG00000215529)

Protein

Protein identifiers

WD repeat-containing protein 64 — B1ANS9 (reviewed: B1ANS9)

All UniProt accessions (5): A0A0A0MSY1, A0A0A0MTD4, A0A0C4DG52, B1ANS9, H0Y6L4

Isoforms (2)

UniProt ID	Names	Canonical?
B1ANS9-1	1	yes
B1ANS9-2	2

RefSeq proteins (1): NP_001354411* (*=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
IPR051242	WD-EF-hand_domain	Family

Pfam: PF00400

UniProt features (25 total): repeat 14, compositionally biased region 3, region of interest 2, sequence variant 2, sequence conflict 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B1ANS9-F1	70.20	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, TGACATY_UNKNOWN, chr1q43, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, ZNF184_TARGET_GENES, GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_DN, MIR4795_3P, MIR340_5P, MIR30B_5P_MIR30C_5P, MIR30D_5P, MIR30E_5P, MIR30A_5P, MIR5582_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

316 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR64	CCDC30	Q5VVM6	617
WDR64	OPN3	Q9H1Y3	582
WDR64	NAGPA	Q9UK23	574
WDR64	RGS7	P49802	520
WDR64	UXS1	Q8NBZ7	517
WDR64	CA10	Q9NS85	508
WDR64	PLD5	Q8N7P1	499
WDR64	ST6GAL2	Q96JF0	481
WDR64	RERE	Q9P2R6	476
WDR64	HMGXB4	Q9UGU5	458
WDR64	TTLL7	Q6ZT98	433
WDR64	CHST6	Q9GZX3	433
WDR64	TMEM108	Q6UXF1	430
WDR64	APEX2	Q9UBZ4	426
WDR64	ZNF488	Q96MN9	418

IntAct

2 interactions, top by confidence:

A	B	Type	Score
MST1R	SHTN1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (17): WDR64 (Proximity Label-MS), WDR64 (Affinity Capture-MS), WDR64 (Proximity Label-MS), SNX8 (Cross-Linking-MS (XL-MS)), STK11 (Cross-Linking-MS (XL-MS)), POLD3 (Cross-Linking-MS (XL-MS)), PDE4B (Cross-Linking-MS (XL-MS)), CENPF (Cross-Linking-MS (XL-MS)), TCEA1 (Cross-Linking-MS (XL-MS)), F8 (Cross-Linking-MS (XL-MS)), NDC80 (Cross-Linking-MS (XL-MS)), ENO1 (Cross-Linking-MS (XL-MS)), COL11A2 (Cross-Linking-MS (XL-MS)), CIAPIN1 (Cross-Linking-MS (XL-MS)), DNAH5 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0G2JEB6, A0JM56, B0DOB4, B0FXQ5, B1ANS9, B4F7L9, B4GQJ7, B5DHW4, B7FF06, B7FF07, B7FF08, B7FF09, B7FF12, C5IAW9, F1LW30, F1P4W9, O08747, O95185, P0DM40, Q008S8, Q18264, Q32NR9, Q3V0B4, Q402B2, Q4G0P3, Q5R4M2, Q5T0N1, Q5XI14, Q6AXU1, Q6DCF6, Q6NRS1, Q6P2C0, Q6P5D8, Q6UXZ4, Q6ZTR5, Q6ZU64, Q761X5, Q7T2Z5, Q80W93, Q86YR7

Diamond homologs: B1ANS9, Q9D565, Q8IV35

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	148
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4400 predictions. Top by Δscore:

Variant	Effect	Δscore
1:241723432:CAAAG:C	donor_loss	1.0000
1:241723433:AAAGG:A	donor_loss	1.0000
1:241723435:AG:A	donor_loss	1.0000
1:241723436:GGTA:G	donor_loss	1.0000
1:241723437:G:T	donor_loss	1.0000
1:241723438:T:A	donor_loss	1.0000
1:241738357:TTCCA:T	acceptor_loss	1.0000
1:241738358:TCCA:T	acceptor_loss	1.0000
1:241738359:CCA:C	acceptor_loss	1.0000
1:241738360:CAGGT:C	acceptor_loss	1.0000
1:241738361:AGGT:A	acceptor_loss	1.0000
1:241738362:G:GC	acceptor_loss	1.0000
1:241738487:CGGG:C	donor_loss	1.0000
1:241738488:GG:G	donor_gain	1.0000
1:241738488:GGGTA:G	donor_loss	1.0000
1:241738489:GG:G	donor_gain	1.0000
1:241738489:GGTAA:G	donor_loss	1.0000
1:241738490:G:C	donor_loss	1.0000
1:241738490:G:GG	donor_gain	1.0000
1:241738491:T:G	donor_loss	1.0000
1:241741663:GG:G	donor_gain	1.0000
1:241741664:GG:G	donor_gain	1.0000
1:241741665:G:GG	donor_gain	1.0000
1:241744481:A:T	donor_gain	1.0000
1:241744506:A:T	donor_gain	1.0000
1:241757457:GAT:G	donor_gain	1.0000
1:241766212:CTTCA:C	acceptor_loss	1.0000
1:241766213:TTCA:T	acceptor_loss	1.0000
1:241766214:TCA:T	acceptor_loss	1.0000
1:241766215:CA:C	acceptor_loss	1.0000

AlphaMissense

7268 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:241723419:A:C	S383R	1.000
1:241723421:C:A	S383R	1.000
1:241723421:C:G	S383R	1.000
1:241683583:G:T	G231W	0.999
1:241723320:T:A	W350R	0.999
1:241723320:T:C	W350R	0.999
1:241738375:T:A	W393R	0.999
1:241738375:T:C	W393R	0.999
1:241679540:C:A	A180D	0.998
1:241683578:T:C	L229P	0.998
1:241683583:G:A	G231R	0.998
1:241683583:G:C	G231R	0.998
1:241683584:G:A	G231E	0.998
1:241683596:G:A	G235D	0.998
1:241687490:T:A	V280D	0.998
1:241723315:G:C	R348P	0.998
1:241674710:C:A	A149D	0.997
1:241679494:T:A	W165R	0.997
1:241679494:T:C	W165R	0.997
1:241679531:G:C	R177P	0.997
1:241687531:T:C	S294P	0.997
1:241711873:T:A	V339D	0.997
1:241738370:G:C	R391P	0.997
1:241738377:G:C	W393C	0.997
1:241738377:G:T	W393C	0.997
1:241787853:T:A	W894R	0.997
1:241787853:T:C	W894R	0.997
1:241679539:G:C	A180P	0.996
1:241679566:T:A	W189R	0.996
1:241679566:T:C	W189R	0.996

dbSNP variants (sampled 300 via entrez): RS1000009151 (1:241770030 G>A), RS1000014180 (1:241727587 T>G), RS1000035176 (1:241681142 T>C), RS1000066395 (1:241727310 T>C), RS1000093510 (1:241693085 C>T), RS1000133265 (1:241774767 A>C), RS1000188043 (1:241704300 A>G), RS1000188555 (1:241762572 A>T), RS1000212155 (1:241674724 T>A,C), RS1000218609 (1:241715890 T>C), RS1000265230 (1:241722113 T>G), RS1000284205 (1:241692882 A>G), RS1000293949 (1:241768534 G>A), RS1000348785 (1:241714706 G>T), RS1000374073 (1:241756486 G>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

8 associations (top):

Study	Trait	p-value
GCST000823_5	Radiation response	2.000000e-06
GCST002133_8	Illicit drug use	3.000000e-06
GCST007666_2	Depressive symptom improvement	4.000000e-07
GCST007667_6	Treatment resistant depression	9.000000e-07
GCST009391_1065	Metabolite levels	4.000000e-06
GCST010249_4	Chronic obstructive pulmonary disease	6.000000e-06
GCST010396_74	Gut microbiota (bacterial taxa, hurdle binary method)	9.000000e-06
GCST012490_334	Femur bone mineral density x serum urate levels interaction	2.000000e-09

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0005431	illegal drug consumption
EFO:0007006	depressive symptom measurement
EFO:0009854	treatment resistant depression
EFO:0010364	lysophosphatidylcholine 20:5 measurement
EFO:0007874	gut microbiome measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tungsten carbide	decreases expression, affects binding	1
cobaltous chloride	increases expression	1
CGP 52608	affects binding, increases reaction	1
Cobalt	affects binding, decreases expression	1
Methotrexate	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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