DEPDC7

Summary

DEPDC7 (DEP domain containing 7, HGNC:29899) is a protein-coding gene on chromosome 11p13, encoding DEP domain-containing protein 7 (Q96QD5).

Predicted to be involved in intracellular signal transduction.

Source: NCBI Gene 91614 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_001077242

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29899
Approved symbol	DEPDC7
Name	DEP domain containing 7
Location	11p13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000121690
Ensembl biotype	protein_coding
OMIM	612294
Entrez	91614

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 retained_intron

ENST00000241051, ENST00000311388, ENST00000427755, ENST00000532078, ENST00000865044

RefSeq mRNA: 2 — MANE Select: NM_001077242 NM_001077242, NM_139160

CCDS: CCDS41632, CCDS41633

Canonical transcript exons

ENST00000241051 — 9 exons

Exon	Start	End
ENSE00000824360	33027686	33027813
ENSE00001136826	33015878	33016028
ENSE00001166044	33031378	33031589
ENSE00001290373	33032668	33032793
ENSE00001311292	33032336	33032478
ENSE00001311760	33028603	33028792
ENSE00001315245	33032889	33032967
ENSE00002182522	33033262	33033582
ENSE00003535705	33025659	33026049

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 99.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0847 / max 142.3760, expressed in 1324 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113647	5.7812	1307
113646	0.2727	126
113648	0.0308	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	99.50	gold quality
secondary oocyte	CL:0000655	99.08	gold quality
jejunal mucosa	UBERON:0000399	97.22	gold quality
right lobe of liver	UBERON:0001114	95.32	gold quality
liver	UBERON:0002107	92.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.69	gold quality
ileal mucosa	UBERON:0000331	90.11	gold quality
duodenum	UBERON:0002114	89.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.67	gold quality
left testis	UBERON:0004533	86.13	gold quality
right testis	UBERON:0004534	85.92	gold quality
testis	UBERON:0000473	85.38	gold quality
sperm	CL:0000019	85.29	gold quality
jejunum	UBERON:0002115	83.76	gold quality
kidney epithelium	UBERON:0004819	83.37	gold quality
tibial nerve	UBERON:0001323	82.17	gold quality
small intestine	UBERON:0002108	81.76	gold quality
adult organism	UBERON:0007023	81.33	gold quality
small intestine Peyer’s patch	UBERON:0003454	81.27	gold quality
stromal cell of endometrium	CL:0002255	80.18	gold quality
mucosa of transverse colon	UBERON:0004991	79.18	gold quality
rectum	UBERON:0001052	78.97	gold quality
adult mammalian kidney	UBERON:0000082	77.47	gold quality
body of pancreas	UBERON:0001150	77.33	gold quality
gastrocnemius	UBERON:0001388	77.01	gold quality
intestine	UBERON:0000160	76.99	gold quality
gall bladder	UBERON:0002110	76.74	gold quality
muscle of leg	UBERON:0001383	76.55	gold quality
transverse colon	UBERON:0001157	76.23	gold quality
muscle layer of sigmoid colon	UBERON:0035805	75.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting DEPDC7, 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-190A-3P	100.00	80.35	5520
HSA-MIR-4282	99.99	75.36	6408
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-8066	99.05	68.66	1532
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-1261	98.62	68.10	896
HSA-MIR-3201	97.16	65.42	1044

Literature-anchored findings (GeneRIF, showing 3)

• The study identified the DEP domain-containing protein DEPDC7 as cellular binding partner of CARMA2 and CARMA3 proteins. (PMID:25541973)
• DEPDC7 hypomethylation in peripheral blood DNA may be associated with recent depressive symptomatology. (PMID:25952135)
• RNA interference (RNAi) recombinant lentiviral vector particle targeting DEPDC7 was constructed in order to knockdown its gene expression in human hepatocellular carcinoma cell line HepG2. (PMID:27016254)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	depdc7b	ENSDARG00000053246
danio_rerio	depdc7a	ENSDARG00000055043
mus_musculus	Depdc7	ENSMUSG00000027173
rattus_norvegicus	Depdc7	ENSRNOG00000012262
caenorhabditis_elegans		WBGENE00002368

Paralogs (3): DEPDC1 (ENSG00000024526), DEPDC1B (ENSG00000035499), DEPDC4 (ENSG00000166153)

Protein

Protein identifiers

DEP domain-containing protein 7 — Q96QD5 (reviewed: Q96QD5)

Alternative names: Protein TR2/D15

All UniProt accessions (1): Q96QD5

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in liver.

Similarity. Belongs to the DEPDC7 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96QD5-1	1	yes
Q96QD5-2	2

RefSeq proteins (2): NP_001070710, NP_631899 (=MANE)

Domains & families (InterPro)

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

Pfam: PF00610

UniProt features (7 total): sequence variant 2, sequence conflict 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96QD5-F1	73.96	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, HNF3ALPHA_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, TGACCTY_ERR1_Q2, IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM, FOXD3_01, USF_01, RIGGI_EWING_SARCOMA_PROGENITOR_DN, AACTTT_UNKNOWN, USF_02, ISRE_01, TGGAAA_NFAT_Q4_01, CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN, USF2_Q6

GO Biological Process (2): intracellular signal transduction (GO:0035556), biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (1): cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
signal transduction	1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DEPDC7	CSTF3	Q12996	928
DEPDC7	EIF3M	Q7L2H7	926
DEPDC7	KIAA1549L	Q6ZVL6	873
DEPDC7	CARD14	Q9BXL6	631
DEPDC7	TCP11L1	Q9NUJ3	609
DEPDC7	CCDC73	Q6ZRK6	556
DEPDC7	WT1	P19544	542
DEPDC7	QSER1	Q2KHR3	541
DEPDC7	ABTB2	Q8N961	532
DEPDC7	CSTF1	Q05048	496
DEPDC7	PRRG4	Q9BZD6	476
DEPDC7	ATP8B4	Q8TF62	466
DEPDC7	RASL10B	Q96S79	428
DEPDC7	FLRT3	Q9NZU0	427
DEPDC7	FAM177A1	Q8N128	426

IntAct

13 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
S	EZR	psi-mi:“MI:2364”(proximity)	0.480
DEPDC7	APOD	psi-mi:“MI:0915”(physical association)	0.400
GTF2B	DEPDC7	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
SLX4	SMAP	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
SNW1		psi-mi:“MI:0914”(association)	0.350
CDC5L		psi-mi:“MI:0914”(association)	0.350
KCNK3	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (57): DEPDC7 (Affinity Capture-RNA), DEPDC7 (Two-hybrid), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Affinity Capture-RNA), DEPDC7 (Proximity Label-MS), DEPDC7 (Proximity Label-MS), APOD (Affinity Capture-MS), DEPDC7 (Affinity Capture-MS), DEPDC7 (Proximity Label-MS)

ESM2 similar proteins: A1A5K6, A6H8I2, F1M386, F1PBJ0, F1QRX7, F1QWA8, F6UMY3, O02697, O14830, O97790, P26675, P48736, Q08CX5, Q21029, Q29RJ2, Q2KI13, Q3UUG6, Q3UYK3, Q3V3E1, Q5E9C4, Q5R8B7, Q5SVR0, Q5ZJX5, Q66K14, Q6DDI6, Q6DDZ9, Q6DEY8, Q6P6R7, Q6ZT07, Q7T2D0, Q8BGG7, Q8CHG7, Q8R5A6, Q8TC07, Q8TEU7, Q8TF42, Q8VCZ6, Q8WZA2, Q91WS7, Q95LL3

Diamond homologs: Q0VGW0, Q1JQ19, Q4QR86, Q5R8B7, Q6AZT6, Q8N2C3, Q91WS7, Q95JW3, Q96QD5, Q8CIG0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1188 predictions. Top by Δscore:

Variant	Effect	Δscore
11:33016027:GG:G	donor_gain	1.0000
11:33016028:GG:G	donor_gain	1.0000
11:33026015:T:G	donor_gain	1.0000
11:33028589:T:G	acceptor_gain	1.0000
11:33028596:T:A	acceptor_gain	1.0000
11:33028598:T:TA	acceptor_gain	1.0000
11:33028601:A:AG	acceptor_gain	1.0000
11:33028602:G:GC	acceptor_gain	1.0000
11:33028602:GT:G	acceptor_gain	1.0000
11:33028602:GTT:G	acceptor_gain	1.0000
11:33028602:GTTA:G	acceptor_gain	1.0000
11:33028602:GTTAT:G	acceptor_gain	1.0000
11:33028724:G:GT	donor_gain	1.0000
11:33028744:GCA:G	donor_gain	1.0000
11:33028747:G:GG	donor_gain	1.0000
11:33028776:GCT:G	donor_gain	1.0000
11:33028789:CTCA:C	donor_gain	1.0000
11:33028790:TCA:T	donor_gain	1.0000
11:33028791:CA:C	donor_gain	1.0000
11:33028792:AG:A	donor_loss	1.0000
11:33028793:G:GG	donor_gain	1.0000
11:33028793:GT:G	donor_loss	1.0000
11:33028794:T:G	donor_loss	1.0000
11:33028800:G:GT	donor_gain	1.0000
11:33031373:TATA:T	acceptor_loss	1.0000
11:33031374:ATAG:A	acceptor_gain	1.0000
11:33031374:ATAGG:A	acceptor_gain	1.0000
11:33031375:T:G	acceptor_gain	1.0000
11:33031375:TAG:T	acceptor_loss	1.0000
11:33031376:A:AG	acceptor_gain	1.0000

AlphaMissense

3384 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:33025782:T:C	F66S	0.999
11:33025700:T:A	W39R	0.998
11:33025700:T:C	W39R	0.998
11:33025781:T:C	F66L	0.998
11:33025783:T:A	F66L	0.998
11:33025783:T:G	F66L	0.998
11:33025880:T:C	C99R	0.998
11:33025882:T:G	C99W	0.998
11:33025979:T:G	Y132D	0.998
11:33031388:T:A	W265R	0.998
11:33031388:T:C	W265R	0.998
11:33025722:T:C	L46P	0.997
11:33025787:G:C	G68R	0.997
11:33025890:T:C	L102P	0.997
11:33025908:T:C	F108S	0.997
11:33025702:G:C	W39C	0.996
11:33025702:G:T	W39C	0.996
11:33025782:T:G	F66C	0.996
11:33025788:G:A	G68D	0.996
11:33025881:G:A	C99Y	0.996
11:33025955:T:C	F124L	0.996
11:33025956:T:C	F124S	0.996
11:33025957:T:A	F124L	0.996
11:33025957:T:G	F124L	0.996
11:33025961:G:C	D126H	0.996
11:33032375:T:C	L345P	0.996
11:33025722:T:A	L46H	0.995
11:33025797:C:A	A71D	0.995
11:33025821:T:C	L79P	0.995
11:33025890:T:A	L102H	0.995

dbSNP variants (sampled 300 via entrez): RS1000093722 (11:33017494 G>A), RS1000329550 (11:33020795 G>C), RS1000439372 (11:33027708 T>A), RS1000513915 (11:33029134 T>C), RS1000668074 (11:33022253 A>G), RS1000721422 (11:33022713 T>C,G), RS1000829323 (11:33029512 T>A), RS1000879926 (11:33015714 C>G,T), RS1000894857 (11:33028095 T>C), RS1001032866 (11:33031113 C>T), RS1001273868 (11:33016914 T>C), RS1001348633 (11:33024428 A>G,T), RS1001404726 (11:33023767 C>T), RS1001454282 (11:33024352 A>G), RS1001510021 (11:33021446 A>G)

Disease associations

OMIM: gene MIM:612294 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004749_31	Lung cancer in ever smokers	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	7
trichostatin A	affects cotreatment, increases expression	3
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression	3
Tretinoin	decreases expression, increases expression	3
bisphenol A	decreases expression, affects cotreatment, increases methylation	2
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
entinostat	increases expression, affects cotreatment	2
belinostat	affects cotreatment, increases expression	2
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	2
Cyclosporine	decreases expression	2
Cadmium Chloride	decreases expression	2
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
2,4,5,2’,4’,5’-hexachlorobiphenyl	decreases expression	1
zinc chromate	increases abundance, increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
hydroquinone	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
incobotulinumtoxinA	decreases expression	1

Clinical trials (associated diseases)

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