DEPDC4

Summary

DEPDC4 (DEP domain containing 4, HGNC:22952) is a protein-coding gene on chromosome 12q23.1, encoding DEP domain-containing protein 4 (Q8N2C3).

Predicted to be involved in intracellular signal transduction.

Source: NCBI Gene 120863 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_001364818

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22952
Approved symbol	DEPDC4
Name	DEP domain containing 4
Location	12q23.1
Locus type	gene with protein product
Status	Approved
Aliases	DEP.4, FLJ33505
Ensembl gene	ENSG00000166153
Ensembl biotype	protein_coding
Entrez	120863

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000299185, ENST00000378244, ENST00000416321, ENST00000547823, ENST00000548313, ENST00000549100, ENST00000549249, ENST00000549341, ENST00000550587, ENST00000551642, ENST00000873178, ENST00000920380

RefSeq mRNA: 14 — MANE Select: NM_001364818 NM_001319310, NM_001319311, NM_001364818, NM_001387201, NM_001387205, NM_001387206, NM_001387207, NM_001387208, NM_001387209, NM_001387210, NM_001387211, NM_001387212, NM_001387213, NM_152317

CCDS: CCDS9075, CCDS91741

Canonical transcript exons

ENST00000550587 — 10 exons

Exon	Start	End
ENSE00001100266	100263497	100263893
ENSE00001476842	100266920	100267079
ENSE00003579811	100256049	100256226
ENSE00003637327	100262264	100262409
ENSE00003642827	100253489	100253715
ENSE00003917378	100248900	100248978
ENSE00003918155	100252394	100252536
ENSE00003919037	100252176	100252301
ENSE00003920082	100242486	100242569
ENSE00003921825	100240062	100241845

Expression profiles

Bgee: expression breadth ubiquitous, 155 present calls, max score 85.46.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.46	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.58	gold quality
ventricular zone	UBERON:0003053	74.86	gold quality
ganglionic eminence	UBERON:0004023	69.66	gold quality
right testis	UBERON:0004534	68.59	gold quality
left testis	UBERON:0004533	68.58	gold quality
testis	UBERON:0000473	68.06	gold quality
islet of Langerhans	UBERON:0000006	66.91	gold quality
body of pancreas	UBERON:0001150	66.26	gold quality
rectum	UBERON:0001052	65.85	gold quality
right lobe of liver	UBERON:0001114	65.18	gold quality
mucosa of transverse colon	UBERON:0004991	65.18	gold quality
pancreas	UBERON:0001264	65.01	gold quality
gall bladder	UBERON:0002110	64.27	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	63.19	gold quality
adrenal tissue	UBERON:0018303	63.06	gold quality
adult mammalian kidney	UBERON:0000082	62.81	gold quality
bone marrow cell	CL:0002092	62.70	gold quality
metanephros cortex	UBERON:0010533	62.12	gold quality
prefrontal cortex	UBERON:0000451	61.81	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	61.76	gold quality
lower esophagus mucosa	UBERON:0035834	61.57	gold quality
right uterine tube	UBERON:0001302	61.45	gold quality
right adrenal gland	UBERON:0001233	61.30	gold quality
body of stomach	UBERON:0001161	61.16	gold quality
spinal cord	UBERON:0002240	61.10	gold quality
right adrenal gland cortex	UBERON:0035827	60.52	gold quality
right ovary	UBERON:0002118	60.06	gold quality
anterior cingulate cortex	UBERON:0009835	59.97	gold quality
adenohypophysis	UBERON:0002196	59.93	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting DEPDC4, 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-4776-3P	100.00	68.73	1340
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-224-3P	98.91	68.42	1815
HSA-MIR-5590-5P	98.81	68.78	969
HSA-MIR-31-5P	98.58	68.35	1239
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-4659A-5P	98.03	66.42	819
HSA-MIR-4659B-5P	98.03	66.84	979
HSA-MIR-10400-3P	97.29	64.66	597

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	DEPDC4	ENSDARG00000089908
caenorhabditis_elegans		WBGENE00002368

Paralogs (3): DEPDC1 (ENSG00000024526), DEPDC1B (ENSG00000035499), DEPDC7 (ENSG00000121690)

Protein

Protein identifiers

DEP domain-containing protein 4 — Q8N2C3 (reviewed: Q8N2C3)

All UniProt accessions (5): E9PGM3, Q8N2C3, H0YI71, H0YIL0, Q3ZCN8

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N2C3-1	1	yes
Q8N2C3-2	2

RefSeq proteins (14): NP_001306239, NP_001306240, NP_001351747, NP_001374130, NP_001374134, NP_001374135, NP_001374136, NP_001374137, NP_001374138, NP_001374139, NP_001374140, NP_001374141, NP_001374142, NP_689530 (=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 (6 total): splice variant 2, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N2C3-F1	62.58	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 73 (showing top): ATF_B, CREBP1_Q2, GGGTGGRR_PAX4_03, CREB_Q2_01, CREB_Q3, CREBP1CJUN_01, CREB_01, SPZ1_01, MGGAAGTG_GABP_B, TGACGTCA_ATF3_Q6, chr12q23, ARNT2_TARGET_GENES, BARX1_TARGET_GENES, CREB3L4_TARGET_GENES, FEV_TARGET_GENES

GO Biological Process (1): intracellular signal transduction (GO:0035556)

GO Molecular Function (0):

GO Cellular Component (0):

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

288 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DEPDC4	S4R3Q2	S4R3Q2	620
DEPDC4	OR6S1	Q8NH40	599
DEPDC4	KRTAP4-8	Q9BYQ9	581
DEPDC4	ZNF233	A6NK53	507
DEPDC4	NPIPB12	F8W0I5	505
DEPDC4	HEATR4	Q86WZ0	487
DEPDC4	ZNF227	Q86WZ6	476
DEPDC4	ACTR6	Q9GZN1	458
DEPDC4	NPIPB5	A8MRT5	448
DEPDC4	NPIPB4	C9JG80	448
DEPDC4	NPIPB13	A6NJU9	447
DEPDC4	KLHL18	O94889	438
DEPDC4	BLTP3B	A0JNW5	429
DEPDC4	ZNF461	Q8TAF7	418
DEPDC4	TMPRSS13	Q9BYE2	410

IntAct

0 interactions, top by confidence:

BioGRID (1): HDAC1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A494C086, A0A494C0Z2, A0A494C191, A0JPH4, A6NHP3, A6NIY4, A6NJR5, A6NLX3, A6NNV3, A6QLI5, B0BNE4, O08918, O60543, O70302, O75916, P0CI01, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, P24864, P39949, P49805, Q12967, Q495Y7, Q495Y8, Q4VXA5, Q4ZIN3, Q5IBH6, Q5IBH7, Q5MJ70, Q5SYB0, Q5XIQ2, Q5ZJR9, Q61457, Q6AYG1

Diamond homologs: Q0VGW0, Q1JQ19, Q4QR86, Q5R8B7, Q6AZT6, Q8N2C3, Q91WS7, Q95JW3, Q96QD5, Q8CIG0, Q4R623, Q5TB30, Q5ZLD2, Q6ING4, Q803Q4, Q8BH88, Q8WUY9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2636 predictions. Top by Δscore:

Variant	Effect	Δscore
12:100204931:T:TA	acceptor_gain	1.0000
12:100204937:TA:T	acceptor_loss	1.0000
12:100204938:A:AG	acceptor_gain	1.0000
12:100204938:AG:A	acceptor_gain	1.0000
12:100204938:AGG:A	acceptor_gain	1.0000
12:100204938:AGGGT:A	acceptor_loss	1.0000
12:100204939:G:GT	acceptor_gain	1.0000
12:100204939:GG:G	acceptor_gain	1.0000
12:100204939:GGG:G	acceptor_gain	1.0000
12:100204939:GGGT:G	acceptor_gain	1.0000
12:100204939:GGGTT:G	acceptor_gain	1.0000
12:100205053:AAAAG:A	donor_loss	1.0000
12:100205055:AAGGT:A	donor_loss	1.0000
12:100205056:AGG:A	donor_loss	1.0000
12:100205058:GTA:G	donor_loss	1.0000
12:100205059:T:A	donor_loss	1.0000
12:100207658:TATA:T	acceptor_loss	1.0000
12:100207661:A:AC	acceptor_loss	1.0000
12:100207661:AGGTT:A	acceptor_gain	1.0000
12:100207662:G:A	acceptor_loss	1.0000
12:100207662:GGTT:G	acceptor_gain	1.0000
12:100207662:GGTTG:G	acceptor_gain	1.0000
12:100207719:A:AG	acceptor_gain	1.0000
12:100207784:ATGGT:A	donor_loss	1.0000
12:100207785:TGGT:T	donor_loss	1.0000
12:100207786:GGTGA:G	donor_loss	1.0000
12:100207787:G:GG	donor_gain	1.0000
12:100207787:GTG:G	donor_loss	1.0000
12:100207788:TGA:T	donor_loss	1.0000
12:100207789:GAG:G	donor_loss	1.0000

AlphaMissense

3272 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:100263601:A:C	F150L	0.935
12:100263601:A:T	F150L	0.935
12:100263603:A:G	F150L	0.935
12:100263778:G:C	F91L	0.933
12:100263778:G:T	F91L	0.933
12:100263780:A:G	F91L	0.933
12:100263877:A:C	F58L	0.911
12:100263877:A:T	F58L	0.911
12:100263879:A:G	F58L	0.911
12:100263571:A:C	F160L	0.895
12:100263571:A:T	F160L	0.895
12:100263573:A:G	F160L	0.895
12:100263652:A:C	F133L	0.891
12:100263652:A:T	F133L	0.891
12:100263654:A:G	F133L	0.891
12:100267017:G:C	F20L	0.889
12:100267017:G:T	F20L	0.889
12:100267019:A:G	F20L	0.889
12:100263861:A:G	W64R	0.808
12:100263861:A:T	W64R	0.808
12:100263859:C:A	W64C	0.806
12:100263859:C:G	W64C	0.806
12:100263779:A:G	F91S	0.795
12:100263667:C:A	M128I	0.765
12:100263667:C:G	M128I	0.765
12:100263667:C:T	M128I	0.765
12:100263572:A:G	F160S	0.755
12:100263817:T:A	K78N	0.706
12:100263817:T:G	K78N	0.706
12:100263602:A:C	F150C	0.699

dbSNP variants (sampled 300 via entrez): RS1000044384 (12:100253109 G>C), RS1000061488 (12:100244852 T>G), RS1000064368 (12:100246674 T>C), RS1000070133 (12:100266201 C>T), RS1000250468 (12:100282881 A>G), RS1000267642 (12:100240241 A>G), RS1000292512 (12:100238505 G>A,T), RS1000351987 (12:100257802 T>C), RS1000448328 (12:100270297 A>G), RS1000468638 (12:100233500 G>A), RS1000473708 (12:100277004 T>C), RS1000575637 (12:100251314 T>C), RS1000577170 (12:100239867 C>T), RS1000636505 (12:100264439 G>A), RS1000692366 (12:100264697 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
trichostatin A	decreases expression	1
beta-lapachone	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
epigallocatechin gallate	affects cotreatment, 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
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression	1
Phenylmercuric Acetate	affects cotreatment, decreases expression	1
Tretinoin	decreases expression	1

Clinical trials (associated diseases)

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