PCDH9

Summary

PCDH9 (protocadherin 9, HGNC:8661) is a protein-coding gene on chromosome 13q21.32, encoding Protocadherin-9 (Q9HC56). Potential calcium-dependent cell-adhesion protein.

This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.

Source: NCBI Gene 5101 — RefSeq curated summary.

At a glance

• GWAS associations: 32
• Clinical variants (ClinVar): 165 total
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_203487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8661
Approved symbol	PCDH9
Name	protocadherin 9
Location	13q21.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184226
Ensembl biotype	protein_coding
OMIM	603581
Entrez	5101

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000377861, ENST00000377865, ENST00000456367, ENST00000544246, ENST00000614931, ENST00000617020

RefSeq mRNA: 5 — MANE Select: NM_203487 NM_001318372, NM_001318373, NM_001318374, NM_020403, NM_203487

CCDS: CCDS81769, CCDS81770, CCDS9443, CCDS9444

Canonical transcript exons

ENST00000377865 — 5 exons

Exon	Start	End
ENSE00001296308	66631210	66631411
ENSE00001402879	66903504	66903605
ENSE00001475358	67225405	67228575
ENSE00002251932	66302834	66305028
ENSE00003850209	67229780	67230336

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 99.88.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1108 / max 244.0114, expressed in 409 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
137517	1.4584	288
137518	0.3071	98
137515	0.1034	37
137519	0.0988	43
137516	0.0965	41
137513	0.0357	10
137514	0.0109	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
inferior vagus X ganglion	UBERON:0005363	99.88	gold quality
superior vestibular nucleus	UBERON:0007227	99.76	gold quality
subthalamic nucleus	UBERON:0001906	99.75	gold quality
substantia nigra pars reticulata	UBERON:0001966	99.74	gold quality
ventral tegmental area	UBERON:0002691	99.74	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.73	gold quality
endothelial cell	CL:0000115	99.71	gold quality
lateral globus pallidus	UBERON:0002476	99.71	gold quality
medulla oblongata	UBERON:0001896	99.70	gold quality
substantia nigra pars compacta	UBERON:0001965	99.65	gold quality
pons	UBERON:0000988	99.62	gold quality
parietal lobe	UBERON:0001872	99.61	gold quality
inferior olivary complex	UBERON:0002127	99.57	gold quality
postcentral gyrus	UBERON:0002581	99.57	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.52	gold quality
entorhinal cortex	UBERON:0002728	99.51	gold quality
middle temporal gyrus	UBERON:0002771	99.44	gold quality
corpus callosum	UBERON:0002336	99.42	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	99.24	gold quality
cranial nerve II	UBERON:0000941	99.19	gold quality
globus pallidus	UBERON:0001875	99.15	gold quality
medial globus pallidus	UBERON:0002477	98.99	gold quality
frontal pole	UBERON:0002795	98.79	gold quality
middle frontal gyrus	UBERON:0002702	98.78	gold quality
superior frontal gyrus	UBERON:0002661	98.62	gold quality
dorsal plus ventral thalamus	UBERON:0001897	98.59	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.47	gold quality
orbitofrontal cortex	UBERON:0004167	98.30	gold quality
dorsal root ganglion	UBERON:0000044	98.26	gold quality
Brodmann (1909) area 10	UBERON:0013541	97.96	gold quality

Single-cell (SCXA)

Detected in 27 experiment(s), a significant marker in 23.

Experiment	Marker?	Max mean expression
E-HCAD-30	yes	19372.12
E-HCAD-35	yes	18042.36
E-HCAD-25	yes	12931.90
E-GEOD-70580	yes	2179.21
E-MTAB-7316	yes	1398.91
E-MTAB-9154	yes	1393.81
E-GEOD-76312	yes	1251.43
E-CURD-6	yes	977.80
E-MTAB-8884	yes	373.83
E-MTAB-6386	yes	304.63
E-HCAD-4	yes	79.28
E-CURD-119	yes	63.97
E-HCAD-10	yes	47.33
E-CURD-112	yes	44.28
E-GEOD-84465	yes	24.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

185 targeting PCDH9, 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-3134	100.00	66.43	777
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-589-3P	99.91	69.62	2088

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 9)

• Our results suggest that PCDH9 might function as a tumor suppressor during cancer development and progression (PMID:22300792)
• Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3beta in hepatocellular carcinoma. (PMID:25172662)
• Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis in gastric cancer (PMID:25869928)
• miR-215-5p up-regulation and PCDH9 down-regulation occurs in glioma samples. miR-215-5p could inhibit the mRNA and protein levels of PCDH9 in glioma cell lines by targeting its promoter and 3’ UTR at the same time. (PMID:28055966)
• PCDH9 acts as a potential tumor suppressor gene, and that the loss of PCDH9 expression appears be a driver in a significant fraction of hepatocarcinogenesis cases. (PMID:28791409)
• convergent lines of evidence suggest that PCDH9 is likely a novel risk gene for MDD. (PMID:28990594)
• This review discusses the role and potential use as biomarkers of semaphorin 3A (SEMA3A), protocadherin 9 (PCDH9), and S100 calcium binding protein A3 (S100A3) in carcinogenesis and chemoresistance of various tumors, including ovarian cancer. (PMID:31059116)
• COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma. (PMID:35084653)
• Expression of Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) Candidate Genes EDA2R, PCDH9, and TRAF7 in Normal Human Kidney Development and CAKUT. (PMID:38927638)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pcdh9	ENSDARG00000063264
danio_rerio	pcdh11	ENSDARG00000105441
mus_musculus	Pcdh9	ENSMUSG00000055421
rattus_norvegicus	Pcdh9	ENSRNOG00000038068

Paralogs (33): CDH1 (ENSG00000039068), CDH10 (ENSG00000040731), CDH3 (ENSG00000062038), CDH19 (ENSG00000071991), CDHR2 (ENSG00000074276), CDH17 (ENSG00000079112), CDH7 (ENSG00000081138), PCDH11Y (ENSG00000099715), CDHR5 (ENSG00000099834), CDH20 (ENSG00000101542), PCDH11X (ENSG00000102290), CDH23 (ENSG00000107736), CDH9 (ENSG00000113100), CDH6 (ENSG00000113361), CDH26 (ENSG00000124215), CDHR3 (ENSG00000128536), CDH15 (ENSG00000129910), CDH24 (ENSG00000139880), CDH11 (ENSG00000140937), CDH13 (ENSG00000140945), CDH18 (ENSG00000145526), CDHR1 (ENSG00000148600), CDH22 (ENSG00000149654), CDH8 (ENSG00000150394), CDH12 (ENSG00000154162), PCDH1 (ENSG00000156453), DCHS1 (ENSG00000166341), PCDH7 (ENSG00000169851), CDH2 (ENSG00000170558), CDH4 (ENSG00000179242), CDH5 (ENSG00000179776), DCHS2 (ENSG00000197410), PCDH20 (ENSG00000280165)

Protein

Protein identifiers

Protocadherin-9 — Q9HC56 (reviewed: Q9HC56)

All UniProt accessions (5): A0A087WZW0, B7ZM79, Q9HC56, Q5VT82, X5D7N0

UniProt curated annotations — full annotation on UniProt →

Function. Potential calcium-dependent cell-adhesion protein.

Subcellular location. Cell membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9HC56-1	1	yes
Q9HC56-2	2

RefSeq proteins (5): NP_001305301, NP_001305302, NP_001305303, NP_065136, NP_982354* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002126	Cadherin-like_dom	Domain
IPR013164	Cadherin_N	Domain
IPR013585	Protocadherin	Domain
IPR015919	Cadherin-like_sf	Homologous_superfamily
IPR020894	Cadherin_CS	Conserved_site
IPR050174	Protocadherin/Cadherin-CA	Family

Pfam: PF00028, PF08266, PF08374

UniProt features (49 total): glycosylation site 14, domain 7, strand 7, region of interest 5, compositionally biased region 5, topological domain 2, sequence conflict 2, turn 2, signal peptide 1, chain 1, transmembrane region 1, splice variant 1, helix 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2EE0	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HC56-F1	67.83	0.38

Functional residue map

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

Glycosylation sites (14): 48, 148, 306, 307, 347, 368, 450, 511, 630, 681, 734, 754, 775, 780

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 376 (showing top): chr13q21, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, NKX25_02, CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY, GCANCTGNY_MYOD_Q6, HASLINGER_B_CLL_WITH_MUTATED_VH_GENES, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, MODULE_128, GTTAAAG_MIR302B, SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN, CHX10_01, GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN, CAGCTG_AP4_Q5, BONCI_TARGETS_OF_MIR15A_AND_MIR16_1, GOBP_FOREBRAIN_DEVELOPMENT

GO Biological Process (3): cell adhesion (GO:0007155), homophilic cell-cell adhesion (GO:0007156), forebrain development (GO:0030900)

GO Molecular Function (2): calcium ion binding (GO:0005509), cell adhesion molecule binding (GO:0050839)

GO Cellular Component (6): plasma membrane (GO:0005886), growth cone (GO:0030426), cell-cell contact zone (GO:0044291), synaptic membrane (GO:0097060), glutamatergic synapse (GO:0098978), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
synapse	2
cellular process	1
cell-cell adhesion	1
brain development	1
anatomical structure development	1
metal ion binding	1
protein binding	1
membrane	1
cell periphery	1
site of polarized growth	1
distal axon	1
cell-cell junction	1
plasma membrane region	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1210 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCDH9	ATP7B	P35670	654
PCDH9	DPP6	P42658	505
PCDH9	DPP10	Q8N608	478
PCDH9	UNC5D	Q6UXZ4	444
PCDH9	CDH10	Q9Y6N8	419
PCDH9	CLDN11	O75508	418
PCDH9	MTDH	Q86UE4	414
PCDH9	COL11A1	P12107	409
PCDH9	SLC37A3	Q8NCC5	404
PCDH9	RUNX1	Q01196	398
PCDH9	ITGA4	P13612	397
PCDH9	SLC5A7	Q9GZV3	394
PCDH9	RIOK2	Q9BVS4	393
PCDH9	ATRN	O75882	392
PCDH9	MSRA	Q9UJ68	387
PCDH9	SETD4	Q9NVD3	387

IntAct

25 interactions, top by confidence:

A	B	Type	Score
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
PCDHGB1	FAM171A2	psi-mi:“MI:0914”(association)	0.530
TPCN2	AP3B1	psi-mi:“MI:0914”(association)	0.530
LGALS1	PODXL	psi-mi:“MI:0914”(association)	0.530
RYK	PCDH7	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
PCDH9	CYSLTR2	psi-mi:“MI:0915”(physical association)	0.370
PCDH9	MEOX2	psi-mi:“MI:0915”(physical association)	0.370
APBB1	SSPOP	psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350
	TNFRSF10A	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
TMEM74	KLRG2	psi-mi:“MI:0914”(association)	0.350
MAGEA8	METTL15	psi-mi:“MI:0914”(association)	0.350
SPSB4	CCDC85C	psi-mi:“MI:0914”(association)	0.350
KCNE3	PIK3R2	psi-mi:“MI:0914”(association)	0.350
RYK	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
UPK2	NRP2	psi-mi:“MI:0914”(association)	0.350
PCDH9	TNKS	psi-mi:“MI:0914”(association)	0.350
BCL6	CACNA1A	psi-mi:“MI:0914”(association)	0.350
KRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
HRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
PCDH9	IKBIP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (63): PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), PCDH9 (Affinity Capture-MS), IKBIP (Affinity Capture-MS), PCDH9 (Proximity Label-MS), PCDH9 (Proximity Label-MS), PCDH9 (Proximity Label-MS), PCDH9 (Affinity Capture-MS)

ESM2 similar proteins: A7MB46, F8W3X3, O14917, O35902, O54800, O97799, P05622, P16234, P20786, P26618, P26619, P32926, P35546, P55286, P55289, P79749, P97291, Q05030, Q08DJ5, Q13634, Q14126, Q28889, Q5RJH3, Q68SP4, Q6KEQ9, Q6W3B0, Q6WXV7, Q6WYY1, Q6X862, Q71M42, Q7TMD7, Q7TSF0, Q7YRU7, Q80TF3, Q86SJ6, Q8AXC6, Q8AXC7, Q8BIZ0, Q8N6Y1, Q8TAB3

Diamond homologs: B8V7Q1, G5EDK5, O18926, O55075, O93319, P08641, P09803, P20310, P33146, P33147, P55289, P55291, P70407, Q00174, Q08DJ5, Q13634, Q5DRA4, Q5DRA5, Q5DRA7, Q5DRA9, Q5DWV1, Q5DWV2, Q5RJH3, Q63149, Q63315, Q6KEQ9, Q6PFX6, Q6WXV7, Q6WYY1, Q6X862, Q71M42, Q86UP0, Q8BM92, Q8QGH3, Q90762, Q90763, Q90Z37, Q91838, Q9BZA8, Q9HBT6

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
PCDH9	“up-regulates activity”	ITGB1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	138
Likely benign	11
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

3726 predictions. Top by Δscore:

Variant	Effect	Δscore
13:66305024:CCCAT:C	acceptor_gain	1.0000
13:66305025:CCAT:C	acceptor_gain	1.0000
13:66305025:CCATC:C	acceptor_gain	1.0000
13:66305026:CAT:C	acceptor_gain	1.0000
13:66305026:CATC:C	acceptor_gain	1.0000
13:66305029:C:CC	acceptor_gain	1.0000
13:66305029:CTGCA:C	acceptor_loss	1.0000
13:66305030:T:C	acceptor_loss	1.0000
13:66305039:C:CT	acceptor_gain	1.0000
13:66305040:A:T	acceptor_gain	1.0000
13:66402769:G:C	acceptor_gain	1.0000
13:66402772:A:C	acceptor_gain	1.0000
13:66631203:GACTC:G	donor_loss	1.0000
13:66631204:ACTCA:A	donor_loss	1.0000
13:66631205:CTCA:C	donor_loss	1.0000
13:66631206:TCA:T	donor_loss	1.0000
13:66631207:CA:C	donor_loss	1.0000
13:66631208:A:AC	donor_gain	1.0000
13:66631208:AC:A	donor_gain	1.0000
13:66631209:C:CA	donor_gain	1.0000
13:66631209:C:T	donor_loss	1.0000
13:66631209:CC:C	donor_gain	1.0000
13:66631209:CCA:C	donor_gain	1.0000
13:66631209:CCAG:C	donor_gain	1.0000
13:66631209:CCAGA:C	donor_gain	1.0000
13:66305027:AT:A	acceptor_gain	0.9900
13:66305032:C:CT	acceptor_gain	0.9900
13:66359255:A:AC	donor_gain	0.9900
13:66359256:C:CC	donor_gain	0.9900
13:66402768:CGTAA:C	acceptor_gain	0.9900

AlphaMissense

8226 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:66304971:C:G	C1133S	1.000
13:66304972:A:G	C1133R	1.000
13:66304972:A:T	C1133S	1.000
13:67226166:C:A	G759W	1.000
13:67226183:A:T	V753D	1.000
13:67226243:C:A	G733V	1.000
13:67226243:C:T	G733D	1.000
13:67226264:A:G	F726S	1.000
13:67226336:G:T	A702E	1.000
13:67226432:T:G	D670A	1.000
13:67226447:A:T	V665D	1.000
13:67226507:A:T	V645D	1.000
13:67226561:A:T	I627K	1.000
13:67226666:C:T	G592E	1.000
13:67226667:C:A	G592W	1.000
13:67226667:C:G	G592R	1.000
13:67226667:C:T	G592R	1.000
13:67226726:A:G	F572S	1.000
13:67226732:G:T	P570H	1.000
13:67226756:A:T	V562D	1.000
13:67226762:A:T	V560D	1.000
13:67226799:C:A	G548W	1.000
13:67226805:C:G	D546H	1.000
13:67226810:G:T	A544D	1.000
13:67226870:A:G	L524S	1.000
13:67226876:C:A	G522V	1.000
13:67226876:C:T	G522E	1.000
13:67226925:A:C	Y506D	1.000
13:67226952:C:G	D497H	1.000
13:67226963:G:T	A493D	1.000

dbSNP variants (sampled 300 via entrez): RS1000003863 (13:66394675 T>G), RS1000004465 (13:66402041 A>G), RS1000008856 (13:66813818 T>C), RS1000010002 (13:66771623 C>A,G,T), RS1000012965 (13:66628068 G>A), RS1000017050 (13:66347245 C>A,T), RS1000017791 (13:66855880 G>A,C), RS1000017990 (13:67090043 T>A), RS1000020540 (13:67216850 A>T), RS1000021718 (13:67083250 T>A), RS1000022858 (13:66483929 T>C), RS1000032407 (13:66896992 G>C), RS1000036733 (13:67230790 C>T), RS1000037341 (13:66988448 T>C), RS1000037595 (13:67054460 T>C)

Disease associations

OMIM: gene MIM:603581 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

32 associations (top):

Study	Trait	p-value
GCST001057_14	Obesity	7.000000e-07
GCST001201_2	Response to platinum-based chemotherapy (cisplatin)	3.000000e-06
GCST001444_20	Pulmonary function decline	4.000000e-06
GCST001540_3	Male fertility	4.000000e-06
GCST001713_22	Dental caries	3.000000e-06
GCST002880_4	Recalcitrant atopic dermatitis	1.000000e-08
GCST002955_2	Forced expiratory volume in 1 second (occupational environmental exposures interaction)	1.000000e-06
GCST003174_14	Sense of smell	4.000000e-06
GCST003174_5	Sense of smell	3.000000e-06
GCST003992_26	Photic sneeze reflex	9.000000e-74
GCST004861_14	Itch intensity from mosquito bite	4.000000e-07
GCST004862_98	Itch intensity from mosquito bite adjusted by bite size	5.000000e-07
GCST004865_11	Itch intensity from mosquito bite adjusted by bite size	1.000000e-06
GCST005566_22	Insomnia	7.000000e-07
GCST005917_2	Current cigarettes per day in chronic obstructive pulmonary disease	8.000000e-08
GCST006041_31	Major depressive disorder	9.000000e-07
GCST006585_347	Blood protein levels	2.000000e-15
GCST006948_62	Feeling nervous	3.000000e-08
GCST007327_47	Smoking status (ever vs never smokers)	1.000000e-08
GCST007576_86	Chronotype	5.000000e-09
GCST007650_2	Postoperative survival time in hepatocellular carcinoma	5.000000e-20
GCST007709_117	General factor of neuroticism	1.000000e-09
GCST007731_2	Postoperative survival time in hepatocellular carcinoma	5.000000e-20
GCST007860_6	Latent naming speed	5.000000e-07
GCST009391_1170	Metabolite levels	8.000000e-07
GCST010002_188	Refractive error	7.000000e-13
GCST010988_471	Adult body size	2.000000e-08
GCST010989_59	Body size at age 10	5.000000e-17
GCST011703_17	Smoking initiation	4.000000e-09
GCST012277_21	Clostridioides difficle infection	4.000000e-06

EFO canonical traits (21, from GWAS)

EFO ID	Trait name
EFO:0004713	FEV/FVC ratio
EFO:0004802	family size
EFO:0004803	male fertility
EFO:1000651	recalcitrant atopic dermatitis
EFO:0004314	forced expiratory volume
EFO:0006992	response to biological dust exposure
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0008378	mosquito bite reaction size measurement
EFO:0006525	cigarettes per day measurement
EFO:0009597	feeling nervous measurement
EFO:0004318	smoking behavior
EFO:0008328	chronotype measurement
EFO:0000638	overall survival
EFO:0007660	neuroticism measurement
EFO:0005301	reading and spelling ability
EFO:0006524	L-arginine measurement
EFO:0009819	comparative body size at age 10, self-reported
EFO:0005670	smoking initiation
EFO:0009130	clostridium difficile infection
EFO:0009101	age at first birth measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression, decreases methylation	8
trichostatin A	affects cotreatment, increases expression	3
Estradiol	affects expression, affects cotreatment, increases expression	3
Aflatoxin B1	decreases expression, decreases methylation, increases methylation	3
methylmercuric chloride	increases expression	2
sodium arsenite	affects methylation, decreases expression	2
Air Pollutants	decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Silicon Dioxide	decreases expression	2
Tobacco Smoke Pollution	increases expression, increases methylation	2
Tretinoin	increases expression	2
Cyclosporine	decreases expression	2
Asbestos, Crocidolite	decreases expression, increases methylation	2
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	affects methylation	1
cupric chloride	decreases expression	1
cupric oxide	decreases expression	1
mercuric bromide	increases expression	1
pentanal	decreases expression	1
15-acetyldeoxynivalenol	increases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TC47	HAP1 PCDH9 (-) 1	Cancer cell line	Male
CVCL_TC48	HAP1 PCDH9 (-) 2	Cancer cell line	Male
CVCL_TC49	HAP1 PCDH9 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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