RPAP3

Summary

RPAP3 (RNA polymerase II associated protein 3, HGNC:26151) is a protein-coding gene on chromosome 12q13.11, encoding RNA polymerase II-associated protein 3 (Q9H6T3). Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation. It is a selective cancer dependency (DepMap: 80.1% of cell lines).

This gene encodes an RNA polymerase II-associated protein. The encoded protein may function in transcriptional regulation and may also regulate apoptosis. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 79657 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 104 total
• Cancer dependency (DepMap): dependent in 80.1% of screened cell lines
• MANE Select transcript: NM_024604

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26151
Approved symbol	RPAP3
Name	RNA polymerase II associated protein 3
Location	12q13.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21908, spag, hSpagh, Tah1
Ensembl gene	ENSG00000005175
Ensembl biotype	protein_coding
OMIM	611477
Entrez	79657

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000005386, ENST00000380650, ENST00000432584, ENST00000547706, ENST00000548211, ENST00000548296, ENST00000551293, ENST00000888602, ENST00000888603, ENST00000939083, ENST00000968412, ENST00000968413, ENST00000968414

RefSeq mRNA: 3 — MANE Select: NM_024604 NM_001146075, NM_001146076, NM_024604

CCDS: CCDS53782, CCDS53783, CCDS8753

Canonical transcript exons

ENST00000005386 — 17 exons

Exon	Start	End
ENSE00000413227	47687876	47688001
ENSE00000737775	47690518	47690639
ENSE00000737797	47689125	47689195
ENSE00000737798	47686780	47686907
ENSE00000737800	47681696	47681817
ENSE00000737801	47679704	47679774
ENSE00000737802	47670107	47670345
ENSE00000737803	47668916	47669102
ENSE00000888016	47666980	47667080
ENSE00000888017	47667754	47667851
ENSE00000888018	47679493	47679594
ENSE00001290934	47705952	47706030
ENSE00002417823	47661249	47663590
ENSE00003483376	47696276	47696403
ENSE00003508340	47701464	47701604
ENSE00003518425	47697597	47697719
ENSE00003528691	47702688	47702846

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 93.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.4733 / max 531.8351, expressed in 1786 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130678	25.6464	1784
130677	0.8269	461

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	93.32	gold quality
mononuclear cell	CL:0000842	93.16	gold quality
leukocyte	CL:0000738	92.76	gold quality
calcaneal tendon	UBERON:0003701	92.31	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.74	gold quality
tendon	UBERON:0000043	89.22	gold quality
right ovary	UBERON:0002118	89.18	gold quality
epithelium of nasopharynx	UBERON:0001951	89.15	gold quality
gastrocnemius	UBERON:0001388	88.95	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.90	gold quality
adrenal tissue	UBERON:0018303	88.87	gold quality
left ovary	UBERON:0002119	88.74	gold quality
muscle of leg	UBERON:0001383	88.70	gold quality
vermiform appendix	UBERON:0001154	88.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.06	gold quality
islet of Langerhans	UBERON:0000006	88.05	gold quality
ventricular zone	UBERON:0003053	87.91	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.82	gold quality
rectum	UBERON:0001052	87.72	gold quality
stromal cell of endometrium	CL:0002255	87.62	gold quality
gall bladder	UBERON:0002110	87.26	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.69	gold quality
ovary	UBERON:0000992	86.59	gold quality
skeletal muscle organ	UBERON:0014892	86.50	gold quality
muscle organ	UBERON:0001630	86.47	gold quality
lymph node	UBERON:0000029	86.25	gold quality
bronchial epithelial cell	CL:0002328	86.16	gold quality
granulocyte	CL:0000094	85.66	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.34	gold quality
left adrenal gland	UBERON:0001234	85.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting RPAP3, 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-3924	100.00	72.09	2394
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-8084	99.73	69.57	1760

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 80.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 8)

• Overexpression of RPAP3 in HEK 293 cells potentiated caspase-3 activation and apoptosis. (PMID:18538670)
• RPAP3 interacts with Reptin to modulate UV-induced DNA damage by regulating H2AX phosphorylation (PMID:19180575)
• Is part of an RNA polymerase II-associated complex with possible chaperone activity. (PMID:19450687)
• Data indicate that RNA polymerase II is built in the cytoplasm and reveal quality-control mechanisms that link HSP90 and its cochaperone hSpagh (RPAP3) to the nuclear import of fully assembled enzymes. (PMID:20864038)
• These results indicate that RPAP3 may be a novel modulator of NF-kappaB pathway in apoptosis induced by anti-cancer chemotherapeutic agents. (PMID:21184742)
• this study investigated the interaction between RPAP3 and PIH1D1. (PMID:23159623)
• RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co-chaperone complex. (PMID:29662061)
• Results show the TPR2 domain in RPAP3 is responsible for the recruitment of HSP90, its N-terminal domain participates to the positive regulation of HSP90. (PMID:30033218)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rpap3	ENSDARG00000087962
mus_musculus	Rpap3	ENSMUSG00000022466
rattus_norvegicus	Rpap3	ENSRNOG00000053405
drosophila_melanogaster	spag	FBGN0015544

Paralogs (18): TOMM34 (ENSG00000025772), ST13 (ENSG00000100380), STUB1 (ENSG00000103266), SPAG1 (ENSG00000104450), SGTA (ENSG00000104969), TTC1 (ENSG00000113312), TTC31 (ENSG00000115282), UNC45A (ENSG00000140553), UNC45B (ENSG00000141161), SPATA16 (ENSG00000144962), TTC12 (ENSG00000149292), TOMM70 (ENSG00000154174), SUGT1 (ENSG00000165416), STIP1 (ENSG00000168439), TTC32 (ENSG00000183891), SGTB (ENSG00000197860), TTC4 (ENSG00000243725), DNAAF4 (ENSG00000256061)

Protein

Protein identifiers

RNA polymerase II-associated protein 3 — Q9H6T3 (reviewed: Q9H6T3)

All UniProt accessions (1): Q9H6T3

UniProt curated annotations — full annotation on UniProt →

Function. Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation.

Subunit / interactions. Tightly associated with the RNA polymerase II complex. Component of the R2TP complex composed at least of RUVBL1, RUVBL2, RPAP3 and PIHD1. Component of the PAQosome complex which is responsible for the biogenesis of several protein complexes and which consists of R2TP complex members RUVBL1, RUVBL2, RPAP3 and PIH1D1, URI complex members PFDN2, PFDN6, PDRG1, UXT and URI1 as well as ASDURF, POLR2E and DNAAF10/WDR92. Interacts with PIH1D1. Interacts with TSC1 and TSC2. Interacts with PRPF8 and EFTUD2 in a ZNHIT2-dependent manner.

Similarity. Belongs to the RPAP3 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9H6T3-1	1	yes
Q9H6T3-2	2
Q9H6T3-3	3

RefSeq proteins (3): NP_001139547, NP_001139548, NP_078880* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat
IPR025986	RPAP3-like_C	Domain
IPR051966	RPAP3	Family

Pfam: PF00515, PF13181, PF13432, PF13877

UniProt features (52 total): helix 25, repeat 7, modified residue 6, strand 3, region of interest 2, splice variant 2, initiator methionine 1, chain 1, compositionally biased region 1, cross-link 1, sequence variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
6ZBK	X-RAY DIFFRACTION	1.49
6FM8	X-RAY DIFFRACTION	1.78
4CGV	X-RAY DIFFRACTION	2.54
6GXZ	X-RAY DIFFRACTION	2.96
4CGW	X-RAY DIFFRACTION	3
6FO1	ELECTRON MICROSCOPY	3.57
6EZ4	SOLUTION NMR
6FD7	SOLUTION NMR
6FDP	SOLUTION NMR
6FDT	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6T3-F1	74.97	0.40

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (7): 2, 87, 116, 119, 121, 481, 498

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 133 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, MODULE_255, MODULE_317, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, GOBP_PROTEIN_STABILIZATION, MODULE_301, GOBP_REGULATION_OF_PROTEIN_STABILITY, SENESE_HDAC1_TARGETS_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, SENESE_HDAC1_AND_HDAC2_TARGETS_UP, HAMAI_APOPTOSIS_VIA_TRAIL_UP, WEST_ADRENOCORTICAL_TUMOR_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B

GO Biological Process (1): protein stabilization (GO:0050821)

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

GO Cellular Component (8): acrosomal vesicle (GO:0001669), cytosol (GO:0005829), cilium (GO:0005929), ciliary basal body (GO:0036064), R2TP complex (GO:0097255), ciliary tip (GO:0097542), protein folding chaperone complex (GO:0101031), RPAP3/R2TP/prefoldin-like complex (GO:1990062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cilium	2
protein-containing complex	2
regulation of protein stability	1
binding	1
secretory granule	1
cytoplasm	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
microtubule organizing center	1
intracellular protein-containing complex	1

Protein interactions and networks

STRING

2924 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RPAP3	RUVBL1	P82276	999
RPAP3	RUVBL2	Q9Y230	999
RPAP3	PIH1D1	Q9NWS0	998
RPAP3	PFDN6	O15212	962
RPAP3	HSP90AA1	P07900	945
RPAP3	HSP90AB1	P08238	944
RPAP3	DNAAF10	Q96MX6	933
RPAP3	RPAP1	Q9BWH6	930
RPAP3	GPN1	Q9HCN4	921
RPAP3	RPAP2	Q8IXW5	913
RPAP3	PDRG1	Q9NUG6	857
RPAP3	UXT	Q9UBK9	855
RPAP3	PFDN2	Q9UHV9	833
RPAP3	POLR2E	P19388	829
RPAP3	POLR2J	P52435	818

IntAct

186 interactions, top by confidence:

A	B	Type	Score
PARD6A	PRKCI	psi-mi:“MI:0914”(association)	0.950
NPHP1	NPHP4	psi-mi:“MI:2364”(proximity)	0.930
PIK3CA	PIK3R2	psi-mi:“MI:0914”(association)	0.900
POLR2E	POLR3A	psi-mi:“MI:0914”(association)	0.870
RUVBL1	ZNHIT1	psi-mi:“MI:0914”(association)	0.860
RPAP3	HSP90AA1	psi-mi:“MI:0407”(direct interaction)	0.850
HSP90AA1	RPAP3	psi-mi:“MI:0915”(physical association)	0.850
POLR2E	POLR1C	psi-mi:“MI:0914”(association)	0.770
TELO2	TTI1	psi-mi:“MI:0914”(association)	0.760
RPAP3	DNAAF10	psi-mi:“MI:0915”(physical association)	0.760
DNAAF10	RPAP3	psi-mi:“MI:0915”(physical association)	0.760
PPP1CB	CCDC85C	psi-mi:“MI:0914”(association)	0.750
PIH1D1	ECD	psi-mi:“MI:0914”(association)	0.740
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
PPP1CC	CCDC85C	psi-mi:“MI:2364”(proximity)	0.740
STK11	HSP90AA1	psi-mi:“MI:0914”(association)	0.740
POLR2E	MED19	psi-mi:“MI:0914”(association)	0.730
POLR3E	POLR3A	psi-mi:“MI:0914”(association)	0.730
POLR2J	POLR2D	psi-mi:“MI:0914”(association)	0.730
RPRD1B	POLR2D	psi-mi:“MI:0914”(association)	0.730
POLR2G	RECQL5	psi-mi:“MI:0914”(association)	0.730

BioGRID (420): RPAP3 (Affinity Capture-MS), RPAP3 (Affinity Capture-MS), RPAP3 (Affinity Capture-MS), PIH1D1 (Affinity Capture-Western), RPAP3 (Affinity Capture-MS), RPAP3 (Two-hybrid), RPAP3 (Affinity Capture-MS), PIH1D1 (Co-fractionation), RPAP3 (Co-fractionation), URI1 (Co-fractionation), WDR92 (Co-fractionation), RPAP3 (Affinity Capture-MS), RPAP3 (Proximity Label-MS), RPAP3 (Proximity Label-MS), RPAP3 (Proximity Label-MS)

ESM2 similar proteins: A0JMA8, A1A5P5, A2A6Q5, A6QNM3, A7Z061, E7F187, E9Q6P5, F7BJB9, O13046, O76094, P09798, P10505, P17885, P30260, P33731, P38042, P41889, Q05B30, Q06AN9, Q07617, Q13099, Q13416, Q32NR4, Q32NU8, Q3UMY5, Q4R6M4, Q4V8A2, Q5R629, Q5RE52, Q5TYV4, Q5U245, Q5ZKQ3, Q61371, Q6NU95, Q6PA97, Q6XV80, Q7Z3E5, Q7ZUV2, Q86TV6, Q8BGB2

Diamond homologs: A2ZLU6, A4K2V0, A5PKG6, A6HD62, D3ZSP7, D7REX8, E4NKF8, E9Q735, F1RBN2, F8RP11, O13754, O13797, O14217, O16259, O35814, O54981, O80742, O81902, O88196, P0C6E7, P0CT30, P15705, P25638, P31948, P53041, P53042, P53804, Q07617, Q0IMG9, Q0JL44, Q14139, Q15785, Q32PZ3, Q388N2, Q3KRD5, Q3ZBR5, Q3ZBZ8, Q43468, Q496Y0, Q4R8N7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
RPAP3	“form complex”	“R2TP core co-chaperone”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 162 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
RNA Polymerase III Chain Elongation	11	65.2×	7e-16
FGFR2 mutant receptor activation	8	56.9×	2e-11
RNA Polymerase III Transcription Termination	11	51.0×	6e-15
RNA Polymerase III Transcription Initiation From Type 2 Promoter	12	47.4×	1e-15
RNA Polymerase III Transcription Initiation From Type 1 Promoter	12	45.7×	1e-15
RNA Polymerase III Transcription Initiation From Type 3 Promoter	12	45.7×	1e-15
Signaling by FGFR2 IIIa TM	8	44.9×	1e-10
Abortive elongation of HIV-1 transcript in the absence of Tat	9	41.8×	2e-11

GO biological processes:

GO term	Partners	Fold	FDR
protein dephosphorylation	7	10.8×	7e-04
protein folding	14	10.1×	5e-08
protein stabilization	21	9.8×	3e-12
obsolete positive regulation of NF-kappaB transcription factor activity	6	8.6×	5e-03
transcription by RNA polymerase II	10	4.9×	4e-03
intracellular signal transduction	14	3.7×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	86
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2568 predictions. Top by Δscore:

Variant	Effect	Δscore
12:47663591:C:CC	acceptor_gain	1.0000
12:47666978:A:AC	donor_gain	1.0000
12:47666978:ACT:A	donor_gain	1.0000
12:47666979:C:CC	donor_gain	1.0000
12:47666979:CT:C	donor_gain	1.0000
12:47666979:CTC:C	donor_gain	1.0000
12:47666979:CTCT:C	donor_gain	1.0000
12:47667092:C:T	acceptor_gain	1.0000
12:47667092:CAAA:C	acceptor_gain	1.0000
12:47667752:A:AC	donor_gain	1.0000
12:47667753:C:CA	donor_gain	1.0000
12:47667753:CT:C	donor_gain	1.0000
12:47667753:CTCA:C	donor_gain	1.0000
12:47667753:CTCAA:C	donor_gain	1.0000
12:47667756:A:AC	donor_gain	1.0000
12:47667826:T:C	acceptor_gain	1.0000
12:47667848:TTTG:T	acceptor_gain	1.0000
12:47667849:T:C	acceptor_gain	1.0000
12:47667849:T:TC	acceptor_gain	1.0000
12:47667853:T:C	acceptor_gain	1.0000
12:47667853:T:TC	acceptor_gain	1.0000
12:47668938:T:C	donor_gain	1.0000
12:47669103:C:CC	acceptor_gain	1.0000
12:47669110:A:C	acceptor_gain	1.0000
12:47669111:T:C	acceptor_gain	1.0000
12:47669111:T:TC	acceptor_gain	1.0000
12:47669114:C:CT	acceptor_gain	1.0000
12:47669115:A:T	acceptor_gain	1.0000
12:47669119:G:C	acceptor_gain	1.0000
12:47669119:G:GC	acceptor_gain	1.0000

AlphaMissense

4401 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:47681705:C:G	A369P	0.999
12:47681735:C:G	A359P	0.999
12:47681740:C:T	G357E	0.999
12:47681745:T:A	R355S	0.999
12:47681745:T:G	R355S	0.999
12:47681746:C:G	R355T	0.999
12:47681757:T:A	K351N	0.999
12:47681757:T:G	K351N	0.999
12:47681793:G:C	C339W	0.999
12:47681795:A:G	C339R	0.999
12:47681807:C:G	A335P	0.999
12:47686792:A:G	L327P	0.999
12:47686906:C:T	G289E	0.999
12:47686907:C:A	G289W	0.999
12:47690565:C:G	R207P	0.999
12:47696302:T:A	R173S	0.999
12:47696302:T:G	R173S	0.999
12:47696403:C:G	G140R	0.999
12:47701481:A:G	W93R	0.999
12:47701481:A:T	W93R	0.999
12:47681734:G:T	A359E	0.998
12:47681741:C:G	G357R	0.998
12:47681741:C:T	G357R	0.998
12:47681758:T:A	K351I	0.998
12:47681759:T:C	K351E	0.998
12:47681786:C:G	A342P	0.998
12:47686798:G:T	A325D	0.998
12:47686799:C:G	A325P	0.998
12:47686805:C:G	A323P	0.998
12:47686806:T:A	R322S	0.998

dbSNP variants (sampled 300 via entrez): RS1000047953 (12:47700335 G>A), RS1000186126 (12:47669606 A>G), RS1000190090 (12:47688044 A>G), RS1000262604 (12:47676268 C>A,T), RS1000284848 (12:47687698 G>C), RS1000356820 (12:47674387 C>G,T), RS1000442854 (12:47674365 C>T), RS1000557116 (12:47674594 G>A), RS1000697873 (12:47705038 G>C), RS1000720124 (12:47661556 T>A), RS1000775903 (12:47673948 T>A,G), RS1000784966 (12:47667992 C>T), RS1000809288 (12:47698705 G>A), RS1000887668 (12:47678913 G>A), RS1000928813 (12:47705060 A>G)

Disease associations

OMIM: gene MIM:611477 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST002626_10	Vertical cup-disc ratio	3.000000e-08
GCST004047_4	Optic nerve measurement (cup-to-disc ratio)	5.000000e-06
GCST005790_25	Rosacea symptom severity	3.000000e-07
GCST007611_20	Chronic obstructive pulmonary disease or high blood pressure (pleiotropy)	7.000000e-11
GCST008891_13	Cognitive performance (processing speed)	1.000000e-06
GCST009724_95	Vertical cup-disc ratio (multi-trait analysis)	2.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006939	cup-to-disc ratio measurement
EFO:0009180	rosacea severity measurement
EFO:0004363	information processing speed

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects expression, affects cotreatment, decreases expression	4
Valproic Acid	decreases expression, decreases methylation	3
bisphenol A	decreases expression, decreases methylation	2
Particulate Matter	increases methylation, decreases expression, increases abundance	2
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
sodium arsenate	decreases expression	1
sodium arsenite	decreases expression	1
manganese chloride	increases abundance, increases expression	1
beta-methylcholine	affects expression	1
azoxystrobin	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
pyrachlostrobin	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
jinfukang	decreases expression	1
picoxystrobin	decreases expression	1
Bortezomib	increases expression	1
Temozolomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Antimycin A	decreases expression	1
Caffeine	increases phosphorylation	1
Dactinomycin	affects cotreatment, increases secretion	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Manganese	increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1

Clinical trials (associated diseases)

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