DEPDC1

Summary

DEPDC1 (DEP domain containing 1, HGNC:22949) is a protein-coding gene on chromosome 1p31.3, encoding DEP domain-containing protein 1A (Q5TB30). May be involved in transcriptional regulation as a transcriptional corepressor. It is a selective cancer dependency (DepMap: 12.4% of cell lines).

Predicted to enable GTPase activator activity. Involved in negative regulation of DNA-templated transcription. Located in nucleus. Part of transcription repressor complex.

Source: NCBI Gene 55635 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 115 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 12.4% of screened cell lines
• MANE Select transcript: NM_001114120

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22949
Approved symbol	DEPDC1
Name	DEP domain containing 1
Location	1p31.3
Locus type	gene with protein product
Status	Approved
Aliases	DEP.8, FLJ20354, SDP35, DEPDC1A
Ensembl gene	ENSG00000024526
Ensembl biotype	protein_coding
OMIM	612002
Entrez	55635

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000370966, ENST00000456315, ENST00000488146, ENST00000489862, ENST00000525124, ENST00000932348, ENST00000932349, ENST00000932350

RefSeq mRNA: 2 — MANE Select: NM_001114120 NM_001114120, NM_017779

CCDS: CCDS44159, CCDS644

Canonical transcript exons

ENST00000456315 — 12 exons

Exon	Start	End
ENSE00000774472	68486937	68486984
ENSE00000774474	68482046	68482897
ENSE00000798431	68483950	68484090
ENSE00001713412	68494430	68494695
ENSE00001815174	68474152	68477069
ENSE00002179186	68496952	68497082
ENSE00003477831	68479144	68479320
ENSE00003492799	68481440	68481612
ENSE00003527546	68477787	68477972
ENSE00003577088	68488916	68489034
ENSE00003668457	68488374	68488504
ENSE00003682873	68489452	68489608

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 88.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.6252 / max 265.9175, expressed in 1303 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12793	7.6157	1158
12792	4.4388	939
12794	2.2584	829
12795	0.3123	166

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	88.50	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.99	gold quality
trabecular bone tissue	UBERON:0002483	84.43	gold quality
sperm	CL:0000019	82.08	gold quality
ganglionic eminence	UBERON:0004023	81.38	gold quality
male germ cell	CL:0000015	79.39	gold quality
stromal cell of endometrium	CL:0002255	78.00	gold quality
bone marrow	UBERON:0002371	76.64	gold quality
rectum	UBERON:0001052	74.19	gold quality
esophagus squamous epithelium	UBERON:0006920	73.93	gold quality
ileal mucosa	UBERON:0000331	73.84	gold quality
adrenal tissue	UBERON:0018303	73.51	gold quality
lower esophagus mucosa	UBERON:0035834	72.52	gold quality
testis	UBERON:0000473	72.42	gold quality
placenta	UBERON:0001987	71.93	gold quality
mucosa of transverse colon	UBERON:0004991	71.90	gold quality
right testis	UBERON:0004534	71.39	gold quality
left testis	UBERON:0004533	70.93	gold quality
epithelium of esophagus	UBERON:0001976	70.31	gold quality
esophagus mucosa	UBERON:0002469	70.19	gold quality
oral cavity	UBERON:0000167	69.97	gold quality
embryo	UBERON:0000922	69.39	gold quality
squamous epithelium	UBERON:0006914	68.19	silver quality
vermiform appendix	UBERON:0001154	67.72	gold quality
tibia	UBERON:0000979	67.64	silver quality
cartilage tissue	UBERON:0002418	67.61	silver quality
duodenum	UBERON:0002114	67.23	gold quality
lymph node	UBERON:0000029	67.06	gold quality
gingival epithelium	UBERON:0001949	66.74	silver quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	377.44
E-MTAB-10596	yes	292.11
E-GEOD-110499	yes	127.38
E-ANND-3	yes	3.94
E-MTAB-6142	no	254.52
E-MTAB-9689	no	180.32
E-MTAB-6524	no	136.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting DEPDC1, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 31)

• Coimmunoprecipitation and immunocytochemistry revealed that DEPDC1 interacted and colocalized with zinc finger transcription factor ZNF224, a known transcriptional repressor. (PMID:20587513)
• Inhibition of DEPDC1A, a bad prognostic marker in multiple myeloma, delays growth and induces mature plasma cell markers in malignant plasma cells. (PMID:23646139)
• DEPDC1 regulates vincristine-induced cell death by promoting JNK-dependent degradation of the BCL-2 family protein MCL1. (PMID:25064737)
• High DEPDC1 mRNA expression is associated with hepatocellular carcinoma/ (PMID:25605201)
• DEPDC1, plays a pivotal role in the regulation of proper mitotic progression. (PMID:25902835)
• Results suggest that protocadherin 10 (PCDH10)-Dishevelled, EGL-10 and Pleckstrin domain containing 1 (DEPDC1)-caspase signaling may be a novel regulatory axis in endometrial endometrioid carcinoma (EEC) development. (PMID:26970279)
• miR-130a is an epigenetically regulated miRNA involved in regulation of key molecular and phenotypic features of prostate carcinogenesis, acting as a tumour suppressor miRNA by targeting SEC23B and DEPDC1. (PMID:27984115)
• The results of this study suggest that DEPDC1 represents a target molecule for the treatment of glioma. (PMID:28555424)
• DEPDC1a, but not DEPDC1b, was required for the integrity of centrosome and organization of the bipolar spindle (PMID:28602627)
• DEPDC1 mRNA and protein expression levels were dramatically increased in prostate cancer tissues and cell lines. Overexpression of DEPDC1 promoted, but depletion of DEPDC1 inhibited cell proliferation by regulating the G1-S phase cell cycle transition. (PMID:28634077)
• Our results demonstrated that increased expression of SDP35/DEPDC1A and XPT1/DEPDC1B correlates with metastatic progression of metastatic soft tissue sarcoma (PMID:29297565)
• Differential DEP domain containing 1 (DEPDC1) expression level shows diagnostic and prognostic significance in liver hepatocellular carcinoma (LIHC) samples. (PMID:30417471)
• DEPDC1, negatively regulated by miR-26b, promotes cell proliferation and tumor growth via up-regulating FOXM1 expression, implying an important underlying mechanism of regulating the progression of triple negative breast cancer. (PMID:30419349)
• MicroRNA-374c-5p inhibits the development of breast cancer through TATA-box binding protein associated factor 7-mediated transcriptional regulation of DEP domain containing 1. (PMID:31162714)
• High DEPDC1 expression is associated with hepatocellular carcinoma cell proliferation, invasion and angiogenesis. (PMID:31322256)
• High expression of DEPDC1 in tumor tissue appears to be associated with tumor progression and poor prognosis (PMID:31366540)
• DEP Domain Containing 1 Promotes Proliferation, Invasion, and Epithelial-Mesenchymal Transition in Colorectal Cancer by Enhancing Expression of Suppressor of Zest 12. (PMID:32343606)
• DEPDC1 up-regulates RAS expression to inhibit autophagy in lung adenocarcinoma cells. (PMID:33021072)
• Overexpression of gene DEP domain containing 1 and its clinical prognostic significance in colorectal cancer. (PMID:33140894)
• DEPDC1 upregulation promotes cell proliferation and predicts poor prognosis in patients with gastric cancer. (PMID:33361586)
• Long noncoding RNA KTN1 antisense RNA 1exerts an oncogenic function in lung adenocarcinoma by regulating DEP domain containing 1 expression via activating epithelial-mesenchymal transition. (PMID:33491970)
• [DEPDC1 is Highly Expressed in Lung Adenocarcinoma and Promotes Tumor Cell Proliferation]. (PMID:34134185)
• ALPK2 acts as tumor promotor in development of bladder cancer through targeting DEPDC1A. (PMID:34210956)
• Long non-coding RNA DEPDC1-AS1 promotes proliferation and migration of human gastric cancer cells HGC-27 via the human antigen R-F11R pathway. (PMID:35466755)
• FOXO3amodulated DEPDC1 promotes malignant progression of nephroblastoma via the Wnt/betacatenin signaling pathway. (PMID:35795985)
• Silencing eL31 suppresses the progression of colorectal cancer via targeting DEPDC1. (PMID:36309731)
• DEPDC1 as a crucial factor in the progression of human osteosarcoma. (PMID:36479633)
• Glycolysis-Related Gene Analyses Indicate That DEPDC1 Promotes the Malignant Progression of Oral Squamous Cell Carcinoma via the WNT/beta-Catenin Signaling Pathway. (PMID:36768316)
• DEPDC1 and KIF4A synergistically inhibit the malignant biological behavior of osteosarcoma cells through Hippo signaling pathway. (PMID:36849972)
• Comprehensive analysis and validation reveal DEPDC1 as a potential diagnostic biomarker associated with tumor immunity in non-small-cell lung cancer. (PMID:38564630)
• DEPDC1 as a metabolic target regulates glycolysis in renal cell carcinoma through AKT/mTOR/HIF1alpha pathway. (PMID:39068164)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	depdc1a	ENSDARG00000018165
mus_musculus	Depdc1a	ENSMUSG00000028175
rattus_norvegicus	Depdc1	ENSRNOG00000009503
caenorhabditis_elegans		WBGENE00002368

Paralogs (3): DEPDC1B (ENSG00000035499), DEPDC7 (ENSG00000121690), DEPDC4 (ENSG00000166153)

Protein

Protein identifiers

DEP domain-containing protein 1A — Q5TB30 (reviewed: Q5TB30)

All UniProt accessions (3): Q5TB30, E9PL61, H0YES2

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation as a transcriptional corepressor. The DEPDC1A-ZNF224 complex may play a critical role in bladder carcinogenesis by repressing the transcription of the A20 gene, leading to transport of NF-KB protein into the nucleus, resulting in suppression of apoptosis of bladder cancer cells.

Subunit / interactions. Isoform 2 and isoform 5 can form homodimers and heterodimers. Interacts with ZNF224.

Subcellular location. Nucleus.

Tissue specificity. Expressed in testis. Up-regulated in bladder cancer cells (at protein level).

Isoforms (2)

UniProt ID	Names	Canonical?
Q5TB30-5	1, DEPDC1-V1	yes
Q5TB30-2	2, DEPDC1-V2

RefSeq proteins (2): NP_001107592, NP_060249 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000591	DEP_dom	Domain
IPR008936	Rho_GTPase_activation_prot	Homologous_superfamily
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily

Pfam: PF00610

UniProt features (18 total): strand 5, helix 3, domain 2, splice variant 2, chain 1, turn 1, region of interest 1, modified residue 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2YSR	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TB30-F1	60.89	0.18

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 (1): 512

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 202 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, HORIUCHI_WTAP_TARGETS_DN, MODULE_308, KONG_E2F3_TARGETS, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, WEI_MYCN_TARGETS_WITH_E_BOX, FISCHER_G2_M_CELL_CYCLE, RIGGI_EWING_SARCOMA_PROGENITOR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOZGIT_ESR1_TARGETS_UP, FUJII_YBX1_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS, BASAKI_YBX1_TARGETS_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP

GO Biological Process (3): intracellular signal transduction (GO:0035556), negative regulation of DNA-templated transcription (GO:0045892), signal transduction (GO:0007165)

GO Molecular Function (2): GTPase activator activity (GO:0005096), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), transcription repressor complex (GO:0017053)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
signal transduction	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
binding	1
intracellular membrane-bounded organelle	1
transcription regulator complex	1

Protein interactions and networks

STRING

1272 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DEPDC1	ZNF224	P17033	821
DEPDC1	LY6K	Q17RY6	702
DEPDC1	TTK	P33981	660
DEPDC1	FOXM1	Q08050	643
DEPDC1	KIF20B	Q96Q89	593
DEPDC1	HMMR	O75330	592
DEPDC1	PLEK2	Q9NYT0	590
DEPDC1	PLEK	P08567	587
DEPDC1	CENPN	Q96H22	579
DEPDC1	TPX2	Q9ULW0	573
DEPDC1	RACGAP1	Q9H0H5	540
DEPDC1	MCM10	Q7L590	527
DEPDC1	KIF20A	O95235	526
DEPDC1	SHCBP1	Q8NEM2	510
DEPDC1	NUF2	Q9BZD4	506

IntAct

33 interactions, top by confidence:

A	B	Type	Score
FAM234B	ABCD4	psi-mi:“MI:0914”(association)	0.620
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
LRFN4	RIMOC1	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
VSIG1	TNPO2	psi-mi:“MI:0914”(association)	0.530
IL27RA	B4GALT5	psi-mi:“MI:0914”(association)	0.530
FOXM1	PES1	psi-mi:“MI:0914”(association)	0.500
MORC3	RDH10	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
FKBP5	IFT56	psi-mi:“MI:0914”(association)	0.350
PTGES3	KIFBP	psi-mi:“MI:0914”(association)	0.350
BSCL2	TMEM223	psi-mi:“MI:0914”(association)	0.350
CTLA4	TMEM120B	psi-mi:“MI:0914”(association)	0.350
HIDE1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
CD6	CIBAR1	psi-mi:“MI:0914”(association)	0.350
GYPA	HYKK	psi-mi:“MI:0914”(association)	0.350
LRRC25	POTEF	psi-mi:“MI:0914”(association)	0.350
EFNB1	KRBA1	psi-mi:“MI:0914”(association)	0.350
TACSTD2	RIMOC1	psi-mi:“MI:0914”(association)	0.350
SIGLECL1	RBFOX3	psi-mi:“MI:0914”(association)	0.350
DGCR2	CCDC85C	psi-mi:“MI:0914”(association)	0.350
GLMP	RTL8C	psi-mi:“MI:0914”(association)	0.350
BACE2	FAM171A2	psi-mi:“MI:0914”(association)	0.350
CUL9	NVL	psi-mi:“MI:0914”(association)	0.350

BioGRID (49): DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), DEPDC1 (Affinity Capture-MS), ICK (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVS7, A2CE83, A2VDU1, A5D992, A8KBE0, O43597, O43609, O43610, P28290, Q02223, Q08AD1, Q08E39, Q14CH0, Q1L0X2, Q2PFN5, Q2TBG9, Q3UUD2, Q4R815, Q5R959, Q5RGQ8, Q5TB30, Q66H35, Q6AYK4, Q6DD45, Q6GPM0, Q6NRB7, Q6P995, Q6PEM6, Q6ZUJ8, Q7ZX27, Q866R9, Q86VY9, Q8BGN6, Q8C3K5, Q8C817, Q8IYD9, Q8N957, Q96HH4, Q9BZD6, Q9C004

Diamond homologs: Q4R623, Q5TB30, Q5ZLD2, Q6ING4, Q803Q4, Q8BH88, Q8CIG0, Q8WUY9, Q8N2C3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	94
Likely benign	3
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
830561	NC_000001.11:g.(?68438187)(68484090_?)del	Pathogenic

SpliceAI

1918 predictions. Top by Δscore:

Variant	Effect	Δscore
1:68477781:TCTTA:T	donor_loss	1.0000
1:68477782:CTTA:C	donor_loss	1.0000
1:68477783:TTA:T	donor_loss	1.0000
1:68477784:TAC:T	donor_loss	1.0000
1:68477785:A:AT	donor_loss	1.0000
1:68479134:CAATA:C	donor_gain	1.0000
1:68479138:ACTT:A	donor_loss	1.0000
1:68479139:CTT:C	donor_loss	1.0000
1:68479140:T:TA	donor_loss	1.0000
1:68479141:TA:T	donor_loss	1.0000
1:68479142:A:AC	donor_gain	1.0000
1:68479142:ACA:A	donor_loss	1.0000
1:68479143:C:CC	donor_gain	1.0000
1:68479143:CATG:C	donor_gain	1.0000
1:68479143:CATGT:C	donor_gain	1.0000
1:68479317:TCAT:T	acceptor_gain	1.0000
1:68479318:CAT:C	acceptor_gain	1.0000
1:68479318:CATC:C	acceptor_gain	1.0000
1:68479321:C:CA	acceptor_loss	1.0000
1:68479321:C:CC	acceptor_gain	1.0000
1:68482709:T:C	donor_gain	1.0000
1:68484246:T:TA	donor_gain	1.0000
1:68486930:AACT:A	donor_loss	1.0000
1:68486931:ACTT:A	donor_loss	1.0000
1:68486932:CT:C	donor_loss	1.0000
1:68486933:TT:T	donor_loss	1.0000
1:68486934:TA:T	donor_loss	1.0000
1:68486935:A:AC	donor_gain	1.0000
1:68486935:ACAA:A	donor_loss	1.0000
1:68486936:C:CA	donor_gain	1.0000

AlphaMissense

5390 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:68486970:A:G	W246R	0.999
1:68486970:A:T	W246R	0.999
1:68494613:A:G	F44S	0.999
1:68494695:A:G	W17R	0.999
1:68494695:A:T	W17R	0.999
1:68494520:A:G	L75P	0.998
1:68494612:G:C	F44L	0.998
1:68494612:G:T	F44L	0.998
1:68494614:A:G	F44L	0.998
1:68494693:C:A	W17C	0.998
1:68494693:C:G	W17C	0.998
1:68481534:C:G	R614P	0.997
1:68486968:C:A	W246C	0.997
1:68486968:C:G	W246C	0.997
1:68494508:A:G	F79S	0.997
1:68494574:A:G	L57S	0.997
1:68494599:C:G	A49P	0.997
1:68484047:A:C	F271L	0.996
1:68484047:A:T	F271L	0.996
1:68484049:A:G	F271L	0.996
1:68486957:G:T	A250D	0.996
1:68494586:A:G	L53P	0.996
1:68494661:A:G	M28T	0.996
1:68477068:A:G	F767S	0.995
1:68481519:A:G	L619P	0.995
1:68481525:A:G	L617P	0.995
1:68481535:G:T	R614S	0.995
1:68486937:A:G	W257R	0.995
1:68486937:A:T	W257R	0.995
1:68494490:A:T	I85N	0.995

dbSNP variants (sampled 300 via entrez): RS1000064177 (1:68489749 C>A,T), RS1000218537 (1:68496997 C>T), RS1000353839 (1:68475366 C>A), RS1000631480 (1:68481362 G>A), RS1000681997 (1:68496637 G>A,C), RS1000689498 (1:68476955 GTT>G), RS1000724934 (1:68494389 T>C), RS1001336911 (1:68496452 A>G), RS1001501707 (1:68495785 C>A,T), RS1001587664 (1:68475884 TA>T,TAA), RS1001954403 (1:68488701 A>C,G), RS1002170784 (1:68489781 T>C), RS1002184578 (1:68496139 G>A,T), RS1002625537 (1:68491623 C>A), RS1002690263 (1:68490297 T>C,G)

Disease associations

OMIM: gene MIM:612002 | disease phenotypes: MIM:142623, MIM:204100, MIM:613794

GenCC curated gene-disease

Mondo (3): Hirschsprung disease (MONDO:0018309), Leber congenital amaurosis 2 (MONDO:0008765), retinitis pigmentosa 20 (MONDO:0013425)

Orphanet (3): Hirschsprung disease (Orphanet:388), Leber congenital amaurosis (Orphanet:65), Retinitis pigmentosa (Orphanet:791)

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST002783_567	Body mass index	7.000000e-07
GCST003075_80	Cognitive decline rate in late mild cognitive impairment	7.000000e-08
GCST003075_97	Cognitive decline rate in late mild cognitive impairment	6.000000e-06
GCST003817_1	Mortality in sepsis	3.000000e-06
GCST009464_11	Facial morphology	8.000000e-09
GCST009464_37	Facial morphology	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007710	cognitive decline measurement
EFO:0004352	mortality

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D006627	Hirschsprung Disease	C06.198.439; C06.405.469.158.701.439; C16.131.314.439
C536601	Amaurosis congenita of Leber, type 2 (supp.)
C566718	Retinitis Pigmentosa 20 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	decreases methylation, affects expression, decreases expression	4
trichostatin A	decreases expression, affects expression, affects cotreatment	3
sodium arsenite	decreases expression, increases expression	3
Cyclosporine	decreases expression	3
bisphenol A	affects cotreatment, decreases expression	2
Arsenic Trioxide	decreases expression, increases expression	2
Acetaminophen	decreases expression, affects expression	2
Benzo(a)pyrene	decreases expression	2
Coumestrol	affects cotreatment, increases expression, affects reaction	2
Doxorubicin	decreases expression	2
Tetrachlorodibenzodioxin	affects expression, decreases expression	2
Valproic Acid	affects expression, decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
propionaldehyde	decreases expression	1
nobiletin	decreases expression	1
sulforaphane	increases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects cotreatment	1
diallyl trisulfide	decreases expression	1
pentanal	decreases expression	1
brequinar	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
azoxystrobin	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D8JX	Ubigene HCT 116 DEPDC1 KO	Cancer cell line	Male
CVCL_D9D5	Ubigene HEK293 DEPDC1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02343562	PHASE4	UNKNOWN	Probiotics for Prophylaxis of Postoperative Hirschsprungs Associated Enterocolitis
NCT07186647	PHASE4	COMPLETED	Laparoscopic-Assisted Transanal Pull-Through for Hirschsprung Disease in Pediatric:Short and Intermediate Outcomes of Two Different Techniques
NCT03660176	PHASE3	UNKNOWN	Effects of Butyrate Enemas on Postoperative Intestinal Mobility Disorders in Hirschsprung’s Disease
NCT04904081	PHASE3	UNKNOWN	Feasibility of Use of Indocyanine Green in Pediatric Colorectal Surgery
NCT00630838	PHASE2	COMPLETED	Probiotic Prophylaxis of Hirschprung’s Disease Associated Enterocolitis (HAEC)
NCT00671684	PHASE1/PHASE2	UNKNOWN	Endoscopic Mucosal Resection (EMR) for Diagnosis of Hirschsprung’s Disease
NCT01985646	EARLY_PHASE1	COMPLETED	A Trial on Conservative Treatment for Infants’ Hirschsprung Disease
NCT00478712	Not specified	RECRUITING	Hirschsprung Disease Genetic Study
NCT01515501	Not specified	COMPLETED	Endoscopic Mucosal Resection for the Diagnosis of a-Ganglionosis, a Controlled Prospective Trial (EDGE Trial)
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT01927809	Not specified	UNKNOWN	Genetic Mosaicism in Hirschsprung’s Disease
NCT02193685	Not specified	UNKNOWN	Identification Genetic, Immunologic and Microbial Markers of Hirschsprung Associated Enterocolitis in Children With Hirschsprung Disease
NCT02216994	Not specified	UNKNOWN	A New Scoring System Improves Diagnostic Accuracy of Intestinal Dysganglionosis –a Prospective Study
NCT02296008	Not specified	COMPLETED	3D High Resolution Anorectal Manometry in Children After Surgery for Anorectal Disorders
NCT02776176	Not specified	UNKNOWN	Enhanced Recovery After Surgery In Hirschsprung Disease
NCT02857205	Not specified	COMPLETED	MICROPRUNG : Intestinal Microbiota Analysis in Patients With or Without Hirschsprung’s Associated EnteroColitis
NCT03269812	Not specified	UNKNOWN	Laparoscopic Assisted Pull-through Versus Other Surgical Procedures for Treatment of Hirschsprung Disease
NCT03406741	Not specified	COMPLETED	Neuropsychological Development and Functional Outcome Sin Children With Hirschsprung Disease at School Age
NCT03626350	Not specified	ACTIVE_NOT_RECRUITING	Prospective Evaluation of the Efficacy and Safety of Submucosal Endoscopy
NCT03666767	Not specified	COMPLETED	Management and Outcomes of Congenital Anomalies in Low-, Middle- and High-Income Countries
NCT04020939	Not specified	COMPLETED	The Role of Indocyanine Green Angiography Fluorescence on Intestinal Resections in Pediatric Surgery.
NCT04106947	Not specified	UNKNOWN	Transition of Care for Patients With Hirschsprung Disease and Anorectal Malformations
NCT04149093	Not specified	UNKNOWN	The Association Between Calretinin and the Function of Ganglion Cells in Hirschsprung Disease
NCT04150120	Not specified	COMPLETED	eHealth as an Aid for Facilitating and Supporting Self-management in Families With Long-term Childhood Illness
NCT04213976	Not specified	UNKNOWN	Ostomy in Continuity or Conventional Ileostomy: a Retrospective Multicentric Analysis
NCT04476225	Not specified	COMPLETED	Induced Pluripotent Stem Cells for Disease Research
NCT04598841	Not specified	COMPLETED	Nutrition Support for Hirschsprung Disease
NCT04622410	Not specified	RECRUITING	Registry for Hirschsprung Disease of the BELAPS
NCT04624334	Not specified	TERMINATED	Non-invasive Assessment of Colonic Motility
NCT04713085	Not specified	COMPLETED	Sacral Neuromodulation in Children and Adolescents
NCT04730128	Not specified	COMPLETED	Translation and Validation of a Disease-specific Questionnaire for Hirschsprung’s Disease in Danish Patients
NCT04837963	Not specified	COMPLETED	Does Hirschsprung Disease Increase the Risk of Febrile Urinary Tract Infection in Children
NCT04957667	Not specified	COMPLETED	Scintigraphic Defecography for Evaluation of Functional Outcome in an Adult Hirschsprung Population
NCT05038345	Not specified	TERMINATED	Hirschsprung Disease Trends in the United States: Analysis of the National Inpatient Sample
NCT05044741	Not specified	COMPLETED	Risk Factors of Perforated HSCR in Neonates
NCT05293353	Not specified	UNKNOWN	Neokare Safety and Tolerability Assessment in Neonates With GI Problems
NCT05307419	Not specified	UNKNOWN	Full Thickness vs. Rectal Suction Biopsy in the Diagnosis of Hirschsprungs Disease
NCT05450991	Not specified	RECRUITING	Long-term Qualitative and Quantitative Outcomes of Children With Hirschsprung’s Disease and Anorectal Malformations
NCT05655845	Not specified	UNKNOWN	Risk Factors for Bowel Dysfunction at Preschool and Early Childhood Age in Children With Hirschsprung Disease
NCT06072976	Not specified	RECRUITING	The Influence of Feeding Source on the Gut Microbiome and Time to Full Feeds in Neonates With Congenital Gastrointestinal Pathologies