WDR17

Summary

WDR17 (WD repeat domain 17, HGNC:16661) is a protein-coding gene on chromosome 4q34.2, encoding WD repeat-containing protein 17 (Q8IZU2).

This gene encodes a WD repeat-containing protein. It is abundantly expressed in retina and testis, and is thought to be a candidate gene for retinal disease. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 116966 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 203 total
• MANE Select transcript: NM_181265

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16661
Approved symbol	WDR17
Name	WD repeat domain 17
Location	4q34.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000150627
Ensembl biotype	protein_coding
OMIM	609005
Entrez	116966

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000280190, ENST00000443118, ENST00000505894, ENST00000507824, ENST00000508596, ENST00000508773, ENST00000509792, ENST00000513261, ENST00000939746, ENST00000939747, ENST00000950580, ENST00000950581, ENST00000950582

RefSeq mRNA: 7 — MANE Select: NM_181265 NM_001350727, NM_001378103, NM_001378104, NM_001378105, NM_001378106, NM_170710, NM_181265

CCDS: CCDS3825, CCDS43284

Canonical transcript exons

ENST00000508596 — 29 exons

Exon	Start	End
ENSE00000995653	176177471	176177654
ENSE00000995655	176172375	176172516
ENSE00001081653	176162075	176162174
ENSE00001081655	176163154	176163293
ENSE00001081656	176159994	176160126
ENSE00001081658	176160911	176161002
ENSE00001081659	176177058	176177156
ENSE00001081660	176156079	176156143
ENSE00001295768	176150043	176150173
ENSE00001297189	176151812	176151967
ENSE00001297541	176135108	176135276
ENSE00001299377	176148133	176148335
ENSE00001301879	176131554	176131738
ENSE00001302738	176141983	176142069
ENSE00001311319	176150468	176150593
ENSE00001315352	176149807	176149956
ENSE00001315701	176125104	176125355
ENSE00001319330	176145995	176146159
ENSE00001322207	176128738	176128860
ENSE00001322907	176139892	176139974
ENSE00001384170	176115796	176115979
ENSE00002061446	176168672	176168783
ENSE00002066996	176065841	176066079
ENSE00003499661	176173267	176173369
ENSE00003571152	176174617	176174718
ENSE00003617792	176119867	176120097
ENSE00003636241	176111575	176111703
ENSE00003791338	176137520	176137611
ENSE00003908611	176179460	176182815

Expression profiles

Bgee: expression breadth ubiquitous, 203 present calls, max score 93.09.

FANTOM5 (CAGE): breadth broad, TPM avg 4.0689 / max 150.6209, expressed in 748 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
50697	2.8114	704
50698	0.7148	233
50699	0.5427	183

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	93.09	gold quality
cortical plate	UBERON:0005343	87.32	gold quality
prefrontal cortex	UBERON:0000451	84.66	gold quality
Brodmann (1909) area 46	UBERON:0006483	83.58	gold quality
Brodmann (1909) area 23	UBERON:0013554	83.43	gold quality
ventricular zone	UBERON:0003053	82.94	gold quality
frontal cortex	UBERON:0001870	82.68	gold quality
neocortex	UBERON:0001950	81.90	gold quality
superior frontal gyrus	UBERON:0002661	81.85	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.47	gold quality
primary visual cortex	UBERON:0002436	81.46	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.34	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.84	gold quality
pituitary gland	UBERON:0000007	80.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.66	gold quality
cerebral cortex	UBERON:0000956	80.50	gold quality
cerebellar cortex	UBERON:0002129	80.36	gold quality
cerebellar hemisphere	UBERON:0002245	80.33	gold quality
right frontal lobe	UBERON:0002810	80.09	gold quality
cerebellum	UBERON:0002037	79.98	gold quality
occipital lobe	UBERON:0002021	79.91	gold quality
caudate nucleus	UBERON:0001873	79.70	gold quality
telencephalon	UBERON:0001893	79.70	gold quality
nucleus accumbens	UBERON:0001882	79.60	gold quality
adenohypophysis	UBERON:0002196	79.53	gold quality
ganglionic eminence	UBERON:0004023	79.49	gold quality
forebrain	UBERON:0001890	79.37	gold quality
entorhinal cortex	UBERON:0002728	79.34	gold quality
brain	UBERON:0000955	79.01	gold quality
anterior cingulate cortex	UBERON:0009835	78.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.03

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• cloning and characterization of gene which represents a new member of the WD repeat family abundant in retina and testis (PMID:12401215)
• Strong candidate gene for retinitis pigmentosa, RP29 (human 4q32-q34). Conclusion is based on a massive expression data set for mouse (103 strains) and joint analysis of RetNet database. (PMID:19727342)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr17	ENSDARG00000075098
mus_musculus	Wdr17	ENSMUSG00000039375
rattus_norvegicus	Wdr17	ENSRNOG00000048847

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), WDR43 (ENSG00000163811), POC1A (ENSG00000164087), WDR88 (ENSG00000166359), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363), WDR5B (ENSG00000196981)

Protein

Protein identifiers

WD repeat-containing protein 17 — Q8IZU2 (reviewed: Q8IZU2)

All UniProt accessions (5): Q8IZU2, E7ESC9, E9PFA2, H0YAE4, H0YAG1

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IZU2-1	1	yes
Q8IZU2-2	2

RefSeq proteins (7): NP_001337656, NP_001365032, NP_001365033, NP_001365034, NP_001365035, NP_733828, NP_851782* (*=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
IPR019775	WD40_repeat_CS	Conserved_site
IPR020472	WD40_PAC1	Repeat
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily

Pfam: PF00400

UniProt features (25 total): repeat 12, sequence variant 6, splice variant 2, sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZU2-F1	85.42	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, chr4q34, WTGAAAT_UNKNOWN, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, RFX1_01, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, PAX3_TARGET_GENES, MYCMAX_02, MIR607, MIR1277_5P, MIR335_3P, MIR3671

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1642 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR17	LRIT2	A6NDA9	575
WDR17	FMN2	Q9NZ56	564
WDR17	CCDC126	Q96EE4	542
WDR17	ZNF582	Q96NG8	542
WDR17	ASB5	Q8WWX0	538
WDR17	SPCS3	P12280	537
WDR17	ZNF583	Q96ND8	507
WDR17	TLDC2	A0PJX2	501
WDR17	GRIFIN	A4D1Z8	492
WDR17	SPATA4	Q8NEY3	489
WDR17	FAM169A	Q9Y6X4	470
WDR17	KCNJ14	Q9UNX9	459
WDR17	GRAMD1C	Q8IYS0	454
WDR17	TMEM205	Q6UW68	441
WDR17	LRIT1	Q9P2V4	434

IntAct

9 interactions, top by confidence:

A	B	Type	Score
MET	NDUFA4	psi-mi:“MI:0914”(association)	0.420
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
ARL2	PTPDC1	psi-mi:“MI:0914”(association)	0.350
WHAMMP3	EXOC5	psi-mi:“MI:0914”(association)	0.350
ETS1	WDR17	psi-mi:“MI:0915”(physical association)	0.000
RSPH1	WDR17	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): WDR17 (Proximity Label-MS), WDR17 (Affinity Capture-MS), WDR17 (Affinity Capture-MS), WDR17 (Affinity Capture-MS), WDR17 (Affinity Capture-MS), WDR17 (Affinity Capture-MS), WDR17 (Two-hybrid), HSPA9 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JP70, A2CEI4, A5D8Q8, A8Q2R5, A9X1C6, B3MET8, B3NSK1, B4GIJ0, B4HND9, B4J8H6, B4KRQ4, B4MFM2, B4P7H8, B4QB64, O65555, Q13216, Q16MY0, Q1LZ08, Q28YY2, Q3SXM0, Q3U821, Q4KLQ5, Q4QR85, Q566T0, Q567G2, Q58DC2, Q5BIM8, Q5FVP5, Q6DFC6, Q6NPN9, Q6NUD0, Q6P4I2, Q6TEN6, Q6ZJW8, Q6ZJX0, Q7ZVR1, Q8BX17, Q8CFJ9, Q8IZU2, Q8L4M1

Diamond homologs: A1CH75, A1CXL0, A2QI22, A3LQ86, A4R2Q6, A5DL92, A5DST9, A6R3K5, A6S0T8, A6ZPA9, A7ECP3, A7TMF9, A8IR43, B0Y5V6, B2B5V0, B2VZH2, B3RQN1, G0SFB5, O74184, P41318, P61480, Q0CLJ4, Q0UXP3, Q12024, Q1DJF7, Q1JQD2, Q2GXT0, Q2T9T9, Q2UGK1, Q4WP10, Q5APF0, Q5B4R1, Q5BJ90, Q5XI13, Q5XUX1, Q5ZJW8, Q6BLS5, Q6CEW7, Q6CU59, Q6FKK3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	177
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

5409 predictions. Top by Δscore:

Variant	Effect	Δscore
4:176066076:CCAGG:C	donor_loss	1.0000
4:176066077:CAGG:C	donor_loss	1.0000
4:176066080:GTA:G	donor_loss	1.0000
4:176066081:T:G	donor_loss	1.0000
4:176096586:G:GG	donor_gain	1.0000
4:176111570:TCAA:T	acceptor_loss	1.0000
4:176111571:CAA:C	acceptor_loss	1.0000
4:176111572:A:AG	acceptor_gain	1.0000
4:176111572:AAG:A	acceptor_gain	1.0000
4:176111573:A:AG	acceptor_gain	1.0000
4:176111574:G:GG	acceptor_gain	1.0000
4:176111574:GGCA:G	acceptor_gain	1.0000
4:176111701:CAGGT:C	donor_loss	1.0000
4:176111702:AGGT:A	donor_loss	1.0000
4:176111703:GGTAA:G	donor_loss	1.0000
4:176111704:GTA:G	donor_loss	1.0000
4:176111705:T:A	donor_loss	1.0000
4:176115794:A:AG	acceptor_gain	1.0000
4:176115794:AGTT:A	acceptor_gain	1.0000
4:176115794:AGTTG:A	acceptor_gain	1.0000
4:176115795:G:GG	acceptor_gain	1.0000
4:176115795:GTTG:G	acceptor_gain	1.0000
4:176115795:GTTGG:G	acceptor_gain	1.0000
4:176128726:T:TA	acceptor_gain	1.0000
4:176128736:A:AG	acceptor_gain	1.0000
4:176128737:G:GG	acceptor_gain	1.0000
4:176128856:AAAGT:A	donor_gain	1.0000
4:176128857:AAGT:A	donor_gain	1.0000
4:176128858:AGTGT:A	donor_loss	1.0000
4:176128859:GT:G	donor_gain	1.0000

AlphaMissense

8403 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:176142053:T:A	W529R	1.000
4:176142053:T:C	W529R	1.000
4:176146006:C:A	A538D	1.000
4:176146113:T:A	W574R	1.000
4:176146113:T:C	W574R	1.000
4:176146143:A:C	S584R	1.000
4:176146145:T:A	S584R	1.000
4:176146145:T:G	S584R	1.000
4:176148146:T:A	W594R	1.000
4:176148146:T:C	W594R	1.000
4:176148215:T:A	W617R	1.000
4:176148215:T:C	W617R	1.000
4:176115901:A:C	S101R	0.999
4:176115903:T:A	S101R	0.999
4:176115903:T:G	S101R	0.999
4:176125184:T:A	W231R	0.999
4:176125184:T:C	W231R	0.999
4:176135126:T:C	F397L	0.999
4:176135128:T:A	F397L	0.999
4:176135128:T:G	F397L	0.999
4:176135198:T:A	W421R	0.999
4:176135198:T:C	W421R	0.999
4:176135267:T:A	W444R	0.999
4:176135267:T:C	W444R	0.999
4:176139922:T:A	W488R	0.999
4:176139922:T:C	W488R	0.999
4:176142055:G:C	W529C	0.999
4:176142055:G:T	W529C	0.999
4:176146030:T:A	V546D	0.999
4:176146033:G:C	R547P	0.999

dbSNP variants (sampled 300 via entrez): RS10000026 (4:176121709 A>G), RS1000004391 (4:176132987 G>T), RS10000614 (4:176118580 G>A), RS1000077836 (4:176070669 A>C), RS1000083200 (4:176065129 T>C), RS1000098143 (4:176171037 A>G,T), RS10001419 (4:176113462 G>A,T), RS1000144028 (4:176143158 CG>C), RS10001518 (4:176113624 G>T), RS1000165671 (4:176110135 T>C), RS1000172890 (4:176069069 A>G), RS1000217593 (4:176110324 G>A,C), RS1000262548 (4:176151386 G>A,T), RS10003404 (4:176122932 A>G), RS1000346537 (4:176164759 A>G,T)

Disease associations

OMIM: gene MIM:609005 | 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
GCST005566_27	Insomnia	7.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation, increases mutagenesis	4
sodium arsenite	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
trichostatin A	increases expression	1
potassium chromate(VI)	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	increases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	decreases expression, increases abundance	1
Clorgyline	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Vanadates	decreases expression	1
Vincristine	decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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