PDZD2

Summary

PDZD2 (PDZ domain containing 2, HGNC:18486) is a protein-coding gene on chromosome 5p13.3, encoding PDZ domain-containing protein 2 (O15018).

The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis.

Source: NCBI Gene 23037 — RefSeq curated summary.

At a glance

• GWAS associations: 22
• Clinical variants (ClinVar): 576 total
• Phenotypes (HPO): 1
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
• MANE Select transcript: NM_178140

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18486
Approved symbol	PDZD2
Name	PDZ domain containing 2
Location	5p13.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0300
Ensembl gene	ENSG00000133401
Ensembl biotype	protein_coding
OMIM	610697
Entrez	23037

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding_CDS_not_defined, 3 protein_coding, 2 retained_intron

ENST00000397559, ENST00000438447, ENST00000502489, ENST00000502824, ENST00000503961, ENST00000509256, ENST00000510285, ENST00000513184, ENST00000513490, ENST00000513852, ENST00000513910, ENST00000515115, ENST00000942338

RefSeq mRNA: 1 — MANE Select: NM_178140 NM_178140

CCDS: CCDS34137

Canonical transcript exons

ENST00000438447 — 25 exons

Exon	Start	End
ENSE00000804497	32092907	32093024
ENSE00000804498	32097279	32097380
ENSE00000804499	32098364	32098634
ENSE00001226408	32087131	32091175
ENSE00001226415	32077462	32077606
ENSE00001226679	32107969	32110932
ENSE00001783572	31639131	31639437
ENSE00003458388	31983155	31983656
ENSE00003476977	32059239	32059356
ENSE00003479309	32073832	32074643
ENSE00003493907	31995576	31995718
ENSE00003501826	32048539	32048684
ENSE00003504520	32053769	32053883
ENSE00003513482	32057655	32057728
ENSE00003536497	32000139	32000271
ENSE00003542228	32061002	32061134
ENSE00003550471	31798889	31799724
ENSE00003587389	32037231	32037342
ENSE00003602602	32072161	32072317
ENSE00003608571	32010330	32010482
ENSE00003621521	32101105	32101239
ENSE00003623452	32069569	32069650
ENSE00003648047	32052611	32052730
ENSE00003675571	32057878	32058103
ENSE00003686218	32071384	32071418

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 97.87.

FANTOM5 (CAGE): breadth broad, TPM avg 5.1832 / max 172.0409, expressed in 776 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
55968	2.0844	421
55975	1.0172	388
55982	0.9820	218
55973	0.3109	142
55974	0.2892	142
55976	0.2605	96
55967	0.0963	37
55966	0.0903	45
55984	0.0276	8
55991	0.0139	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
trigeminal ganglion	UBERON:0001675	97.87	gold quality
dorsal root ganglion	UBERON:0000044	96.60	gold quality
upper leg skin	UBERON:0004262	96.48	gold quality
postcentral gyrus	UBERON:0002581	96.26	gold quality
lateral globus pallidus	UBERON:0002476	96.23	gold quality
choroid plexus epithelium	UBERON:0003911	95.53	gold quality
parietal lobe	UBERON:0001872	95.52	gold quality
skin of hip	UBERON:0001554	94.55	gold quality
buccal mucosa cell	CL:0002336	94.49	gold quality
placenta	UBERON:0001987	94.32	gold quality
sural nerve	UBERON:0015488	94.31	gold quality
orbitofrontal cortex	UBERON:0004167	94.29	gold quality
heart right ventricle	UBERON:0002080	94.23	gold quality
pigmented layer of retina	UBERON:0001782	93.79	gold quality
lower lobe of lung	UBERON:0008949	93.77	gold quality
superior frontal gyrus	UBERON:0002661	93.68	gold quality
olfactory bulb	UBERON:0002264	93.58	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.52	gold quality
Brodmann (1909) area 46	UBERON:0006483	93.29	gold quality
germinal epithelium of ovary	UBERON:0001304	93.09	gold quality
substantia nigra pars compacta	UBERON:0001965	92.94	gold quality
entorhinal cortex	UBERON:0002728	92.52	gold quality
caudate nucleus	UBERON:0001873	92.32	gold quality
nucleus accumbens	UBERON:0001882	92.29	gold quality
putamen	UBERON:0001874	92.27	gold quality
tibia	UBERON:0000979	92.18	gold quality
subthalamic nucleus	UBERON:0001906	91.72	gold quality
inferior vagus X ganglion	UBERON:0005363	91.48	gold quality
CA1 field of hippocampus	UBERON:0003881	91.42	gold quality
tibial nerve	UBERON:0001323	91.21	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-131882	yes	2235.06
E-CURD-119	yes	2203.06
E-HCAD-35	yes	93.17
E-GEOD-84465	yes	26.85
E-HCAD-25	yes	23.83
E-ANND-3	yes	17.51

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HSF1

miRNA regulators (miRDB)

160 targeting PDZD2, 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-4425	100.00	67.59	1049
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4803	99.98	71.99	3117
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-607	99.97	73.62	5593
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AJ-3P	99.96	73.38	5345

Literature-anchored findings (GeneRIF, showing 9)

• the first reported multi-PDZ protein that is processed by proteolytic cleavage to generate a secreted peptide containing two PDZ domains (PMID:12671685)
• The mitogenic effect of secreted PDZD2 was concentration-dependent, and was associated with a slight inhibition of the insulin promoter activity at high sPDZD2 concentrations. (PMID:16413998)
• Results show that a novel pancreatic developmental factor, PDZD2, is sufficient to promote the proliferation of human fetal PPCs while limiting differentiation of ICCs into islet/endocrine cells. (PMID:18037333)
• sPDZD2 sensitized mutant p53-positive DU145 cells and wild-type p53-positive MCF-7 cells to apoptosis induction through genotoxic stress imposed by sub-lethal concentration of hydrogen peroxide (PMID:18639375)
• PDZ-domain containing-2 (PDZD2) drives the maturity of human fetal pancreatic progenitor-derived islet-like cell clusters with functional responsiveness against membrane depolarization. (PMID:19046020)
• This study does not support the association of PDZD2, GOLPH3, and MTMR12 genes with schizophrenia. (PMID:21451436)
• The DNA copy number variations disrupt PDZD2 and GOLPH3 genes predominantly expressed in placenta, and it may represent a novel risk factor for recurrent miscarriage. (PMID:24827138)
• we systematically evaluating RCC risk-associated SNPs indentified from previous GWAS in a Chinese population, finding that one SNP located in PDZD2 and two SNPs located in ITPR2 were ccRCC-risk associated in Chinese population. (PMID:26918600)
• Study results revealed that MG-63 osteosarcoma cells contained low levels of miR-363, and that overexpression of miR-363 in MG-63 cells significantly inhibited the vitality, proliferation, and colony formation ability of the cells. Bioinformatics analysis and luciferase reporter assay indicated that PDZD2 was a direct target of miR-363. In vivo xenograft model further confirmed that miR-363 functioned as tumor suppressor. (PMID:30896877)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdzd2	ENSDARG00000059801
mus_musculus	Pdzd2	ENSMUSG00000022197
rattus_norvegicus	Pdzd2	ENSRNOG00000013140

Paralogs (1): IL16 (ENSG00000172349)

Protein

Protein identifiers

PDZ domain-containing protein 2 — O15018 (reviewed: O15018)

Alternative names: Activated in prostate cancer protein, PDZ domain-containing protein 3

All UniProt accessions (2): D6RF66, O15018

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with SCN10A, CTNND2 and PKP4.

Subcellular location. Nucleus. Cytoplasm. Endoplasmic reticulum Secreted.

Tissue specificity. Isoform 2 is expressed (at protein level) in prostate and many prostate tumors.

Post-translational modifications. A secreted form is produced by caspase-mediated proteolytic cleavage.

Miscellaneous. May be due to aberrant splicing.

Isoforms (2)

UniProt ID	Names	Canonical?
O15018-1	1	yes
O15018-2	2

RefSeq proteins (1): NP_835260* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR036034	PDZ_sf	Homologous_superfamily

Pfam: PF00595

UniProt features (72 total): compositionally biased region 24, region of interest 20, sequence variant 7, domain 6, splice variant 5, modified residue 4, sequence conflict 3, chain 2, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for O15018 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Functional residue map

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

Catalytic / active sites (1): 2492–2493 (cleavage; by caspases)

Post-translational modifications (4): 568, 944, 948, 1850

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 191 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GCACCTT_MIR18A_MIR18B, GCM_MAP4K4, BENPORATH_ES_WITH_H3K27ME3, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, RACCACAR_AML_Q6, COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, MCLACHLAN_DENTAL_CARIES_DN, AML_Q6, GATA6_01, TCF11_01, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, HP1SITEFACTOR_Q6, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5

GO Biological Process (1): cell adhesion (GO:0007155)

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

GO Cellular Component (8): extracellular region (GO:0005576), nucleus (GO:0005634), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), plasma membrane (GO:0005886), cell-cell junction (GO:0005911), centriolar satellite (GO:0034451)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
intracellular membrane-bounded organelle	2
cytoplasm	2
cellular process	1
binding	1
intracellular anatomical structure	1
endomembrane system	1
membrane	1
cell periphery	1
anchoring junction	1
centrosome	1

Protein interactions and networks

STRING

776 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDZD2	PKP4	Q99569	915
PDZD2	CTNND2	Q9UQB3	895
PDZD2	SCN10A	Q9Y5Y9	524
PDZD2	FRMPD4	Q14CM0	492
PDZD2	NPR3	P17342	449
PDZD2	UBAP2L	Q14157	446
PDZD2	ABCA12	Q86UK0	444
PDZD2	ADRA2C	P18825	433
PDZD2	DLG4	P78352	428
PDZD2	KLHL18	O94889	424
PDZD2	CST3	P01034	415
PDZD2	ZBTB22	O15209	413
PDZD2	EXTL3	O43909	407
PDZD2	SORBS1	Q9BX66	407
PDZD2	SORBS3	O60504	404

IntAct

497 interactions, top by confidence:

A	B	Type	Score
E	PDZD2	psi-mi:“MI:0915”(physical association)	0.710
PDZD2	E	psi-mi:“MI:0915”(physical association)	0.710
E	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.710
E	PDZD2	psi-mi:“MI:0915”(physical association)	0.590
NRXN1	PDZD2	psi-mi:“MI:0915”(physical association)	0.590
Tax	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.540
PDZD2	E6	psi-mi:“MI:0407”(direct interaction)	0.440
NRXN3	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD2	PTEN	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD2	RPS6KA1	psi-mi:“MI:0407”(direct interaction)	0.440
GAS2L2	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
PKP4	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD2	HTR2A	psi-mi:“MI:0407”(direct interaction)	0.440
CTNND2	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
ARVCF	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
WWTR1	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD2	YAP1	psi-mi:“MI:0407”(direct interaction)	0.440
GJD4	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
PLEKHA2	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
RAPGEF2	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
ABCA1	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
MMP24	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
GJC1	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
HTR2C	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
SDK2	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
PKN2	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
RAPGEF6	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (30): PDZD2 (Proximity Label-MS), PTOV1 (Affinity Capture-Western), DDX24 (Affinity Capture-Western), PRPF40A (Affinity Capture-Western), PDZD2 (Affinity Capture-RNA), PDZD2 (Affinity Capture-RNA), RAB11FIP5 (Co-fractionation), CTNND2 (Reconstituted Complex), PDZD2 (Affinity Capture-Western), PKP4 (Reconstituted Complex), PDZD2 (Affinity Capture-MS), PDZD2 (Affinity Capture-MS), PDZD2 (Affinity Capture-MS), PDZD2 (Affinity Capture-MS), PKP4 (Affinity Capture-Western)

ESM2 similar proteins: A1A5G4, D3YZU1, E9Q9R9, F1MAD2, O15018, O35346, O35867, O60759, P34152, P97306, P97879, Q00944, Q4L1J4, Q5F488, Q5I0L6, Q5JV73, Q5RD32, Q5SGD7, Q5TCQ9, Q68DX3, Q69Z98, Q6DD51, Q6P9H4, Q6RHR9, Q6ZWJ1, Q812E4, Q8BH60, Q8BMA3, Q8IWQ3, Q8TDM6, Q8TDW5, Q8TEW0, Q8TEW8, Q91VY6, Q925T6, Q96QZ7, Q99469, Q99NH2, Q9CSB4, Q9EQJ9

Diamond homologs: A0A140LI67, A5PKA5, A7UA95, E1JIT7, O14910, O15018, O19132, O35274, O35867, O35889, O62666, O62674, O62675, O62676, O62677, O62678, O88951, O88952, P11434, P29475, P29476, P31016, P51140, P55196, P57105, P78352, Q07436, Q0P5F3, Q12923, Q14005, Q29498, Q2KIB6, Q32LM6, Q3T0C9, Q3UHD6, Q4KL35, Q5F425, Q5RAA5, Q62108, Q64512

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 185 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
Tight junction interactions	10	29.2×	3e-10
Long-term potentiation	5	18.9×	9e-04
Neurexins and neuroligins	7	10.9×	8e-04
Assembly and cell surface presentation of NMDA receptors	5	10.1×	6e-03
Potassium Channels	7	7.5×	4e-03
RHO GTPase cycle	9	4.3×	1e-02
Neuronal System	11	3.9×	6e-03

GO biological processes:

GO term	Partners	Fold	FDR
calcium-independent cell-cell adhesion	10	46.9×	4e-12
positive regulation of synaptic transmission, glutamatergic	6	21.9×	6e-05
bicellular tight junction assembly	11	21.3×	2e-09
positive regulation of excitatory postsynaptic potential	6	18.5×	1e-04
excitatory postsynaptic potential	5	13.0×	3e-03
synaptic transmission, glutamatergic	5	10.5×	5e-03
regulation of synaptic plasticity	6	9.1×	3e-03
calcium ion transmembrane transport	7	8.6×	2e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — PLMESO.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	407
Likely benign	82
Benign	50

Top pathogenic / likely-pathogenic (0)

SpliceAI

8646 predictions. Top by Δscore:

Variant	Effect	Δscore
5:31693149:C:G	donor_gain	1.0000
5:31983153:A:AG	acceptor_gain	1.0000
5:31983154:G:GT	acceptor_gain	1.0000
5:31983154:GTT:G	acceptor_gain	1.0000
5:31993090:G:GT	donor_gain	1.0000
5:32010325:CATA:C	acceptor_loss	1.0000
5:32010327:TA:T	acceptor_loss	1.0000
5:32010328:A:AG	acceptor_gain	1.0000
5:32010328:AG:A	acceptor_gain	1.0000
5:32010328:AGG:A	acceptor_loss	1.0000
5:32010329:G:GG	acceptor_gain	1.0000
5:32010329:GG:G	acceptor_gain	1.0000
5:32010329:GGA:G	acceptor_gain	1.0000
5:32010329:GGAA:G	acceptor_gain	1.0000
5:32010329:GGAAA:G	acceptor_gain	1.0000
5:32010478:GAGCA:G	donor_gain	1.0000
5:32010479:AGCA:A	donor_gain	1.0000
5:32010480:GCA:G	donor_gain	1.0000
5:32010480:GCAG:G	donor_gain	1.0000
5:32010481:CA:C	donor_gain	1.0000
5:32010481:CAG:C	donor_loss	1.0000
5:32010482:AG:A	donor_loss	1.0000
5:32010483:G:GG	donor_gain	1.0000
5:32010484:TAAGT:T	donor_loss	1.0000
5:32010485:AAGTG:A	donor_loss	1.0000
5:32048527:T:A	acceptor_gain	1.0000
5:32048534:TCAAG:T	acceptor_loss	1.0000
5:32048535:CAA:C	acceptor_loss	1.0000
5:32048536:A:AG	acceptor_gain	1.0000
5:32048536:AAG:A	acceptor_gain	1.0000

AlphaMissense

18437 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:31995685:T:A	V363D	1.000
5:32000168:T:C	L384P	1.000
5:32000228:T:C	L404P	1.000
5:32000255:T:C	L413P	1.000
5:32052711:T:C	L589S	1.000
5:32053775:G:C	G598R	1.000
5:32053776:G:A	G598D	1.000
5:32053778:T:C	F599L	1.000
5:32053779:T:C	F599S	1.000
5:32053780:T:A	F599L	1.000
5:32053780:T:G	F599L	1.000
5:32053785:T:A	I601N	1.000
5:32053830:T:A	V616D	1.000
5:32053875:T:A	L631H	1.000
5:32053875:T:C	L631P	1.000
5:32057664:T:G	I637S	1.000
5:32057667:T:C	L638P	1.000
5:32057711:G:C	A653P	1.000
5:32057724:T:C	F657S	1.000
5:32061006:G:A	G775R	1.000
5:32061006:G:C	G775R	1.000
5:32061007:G:A	G775E	1.000
5:32061010:A:T	D776V	1.000
5:31995607:T:C	L337P	0.999
5:31995640:T:A	V348D	0.999
5:32000150:T:C	L378P	0.999
5:32000168:T:A	L384Q	0.999
5:32000171:T:C	L385P	0.999
5:32000180:A:T	N388I	0.999
5:32000192:T:C	L392P	0.999

dbSNP variants (sampled 300 via entrez): RS1000001861 (5:31895552 G>C), RS1000008009 (5:31638645 C>T), RS1000013829 (5:32096543 T>C), RS1000016995 (5:31779427 T>C,G), RS1000018983 (5:32016079 A>G), RS1000021624 (5:32100037 T>C), RS1000029829 (5:31886436 T>C,G), RS1000033983 (5:31701401 C>T), RS1000040626 (5:31876485 G>C,T), RS1000058689 (5:32038269 A>G), RS1000061447 (5:31859096 G>C,T), RS1000075349 (5:31741958 C>G,T), RS1000082684 (5:31853880 A>T), RS1000085287 (5:32051950 G>C), RS1000086275 (5:31765822 G>A,C)

Disease associations

OMIM: gene MIM:610697 | disease phenotypes: MIM:607432

GenCC curated gene-disease

Mondo (1): lissencephaly spectrum disorders (MONDO:0018838)

Orphanet (1): Lissencephaly (Orphanet:48471)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0001339	Lissencephaly

GWAS associations

22 associations (top):

Study	Trait	p-value
GCST001750_2	Renal cell carcinoma	8.000000e-07
GCST001762_266	Obesity-related traits	4.000000e-06
GCST002549_4	Response to serotonin reuptake inhibitors in major depressive disorder (plasma drug and metabolite levels)	3.000000e-07
GCST003471_3	Myocardial infarction	3.000000e-10
GCST004075_40	Vertical cup-disc ratio	5.000000e-09
GCST004075_41	Vertical cup-disc ratio	7.000000e-09
GCST005417_1	Chronic obstructive pulmonary disease	2.000000e-08
GCST005576_25	Intracranial aneurysm	3.000000e-06
GCST006991_2	Cerebrospinal fluid t-tau levels in Alzheimer’s disease dementia	9.000000e-07
GCST007508_2	Self-reported childhood asthma in adult smokers	4.000000e-07
GCST008163_132	Height	8.000000e-06
GCST008892_6	Working memory	9.000000e-06
GCST009216_3	Corpus callosum central volume	1.000000e-06
GCST009412_10	Vertical cup-disc ratio	7.000000e-12
GCST009462_57	Optic disc size	8.000000e-19
GCST009723_37	Vertical cup-disc ratio (adjusted for vertical disc diameter)	1.000000e-14
GCST009724_41	Vertical cup-disc ratio (multi-trait analysis)	2.000000e-21
GCST012053_12	Weight	9.000000e-07
GCST012490_568	Femur bone mineral density x serum urate levels interaction	2.000000e-11
GCST90002385_267	High light scatter reticulocyte count	2.000000e-09
GCST90002386_14	High light scatter reticulocyte percentage of red cells	3.000000e-10
GCST90002406_157	Reticulocyte fraction of red cells	1.000000e-09

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0005000	leptin measurement
EFO:0005658	response to selective serotonin reuptake inhibitor
EFO:0006939	cup-to-disc ratio measurement
EFO:0004760	t-tau measurement
EFO:0004335	short-term memory
EFO:0004338	body weight
EFO:0004531	urate measurement
EFO:0007986	reticulocyte count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D054082	Lissencephaly	C10.500.507.450.499; C16.131.666.507.450.499

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Arsenic	increases abundance, affects methylation, decreases expression	3
Tobacco Smoke Pollution	affects expression, decreases expression, increases methylation	3
sodium arsenite	decreases expression, increases abundance	2
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, decreases expression	2
Benzo(a)pyrene	affects methylation	2
Estradiol	affects cotreatment, increases expression	2
Nickel	decreases expression	2
Progesterone	increases expression, affects cotreatment	2
Valproic Acid	increases expression	2
Cadmium Chloride	increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
bufotalin	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
sodium arsenate	decreases expression, increases abundance	1
arsenite	affects binding, decreases reaction	1
sulforaphane	decreases expression	1
nickel chloride	increases expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	decreases expression	1
aflatoxin B2	decreases methylation	1
nickel sulfate	decreases expression	1
epigallocatechin gallate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
quinocetone	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1

Clinical trials (associated diseases)

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