CDCP2

Summary

CDCP2 (CUB domain containing protein 2, HGNC:27297) is a protein-coding gene on chromosome 1p32.3, encoding CUB domain-containing protein 2 (Q5VXM1).

Predicted to be located in membrane.

Source: NCBI Gene 200008 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 94 total
• MANE Select transcript: NM_001353655

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27297
Approved symbol	CDCP2
Name	CUB domain containing protein 2
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000157211
Ensembl biotype	protein_coding
OMIM	612320
Entrez	200008

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000371330, ENST00000530059

RefSeq mRNA: 2 — MANE Select: NM_001353655 NM_001353655, NM_201546

CCDS: CCDS588, CCDS85977

Canonical transcript exons

ENST00000530059 — 6 exons

Exon	Start	End
ENSE00001454959	54141098	54141433
ENSE00001454960	54144466	54144813
ENSE00003795668	54136630	54136808
ENSE00003795881	54139753	54140106
ENSE00003978268	54132687	54133294
ENSE00003978269	54152844	54153000

Expression profiles

Bgee: expression breadth broad, 19 present calls, max score 45.05.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	45.05	silver quality
bone marrow cell	CL:0002092	41.95	gold quality
prefrontal cortex	UBERON:0000451	41.16	gold quality
ganglionic eminence	UBERON:0004023	40.88	gold quality
bone marrow	UBERON:0002371	40.53	gold quality
sural nerve	UBERON:0015488	40.09	gold quality
spleen	UBERON:0002106	39.97	gold quality
ventricular zone	UBERON:0003053	39.81	gold quality
lower esophagus mucosa	UBERON:0035834	39.56	gold quality
ectocervix	UBERON:0012249	39.31	gold quality
urinary bladder	UBERON:0001255	39.20	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
uterine cervix	UBERON:0000002	36.88	silver quality
cortical plate	UBERON:0005343	36.47	gold quality
skeletal muscle tissue	UBERON:0001134	36.09	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.39	gold quality
muscle tissue	UBERON:0002385	35.28	gold quality
frontal cortex	UBERON:0001870	35.26	silver quality
liver	UBERON:0002107	35.16	gold quality
omental fat pad	UBERON:0010414	34.66	silver quality
myometrium	UBERON:0001296	34.40	gold quality
mucosa of transverse colon	UBERON:0004991	34.29	gold quality
metanephros cortex	UBERON:0010533	33.75	silver quality
primary visual cortex	UBERON:0002436	33.36	gold quality
endocervix	UBERON:0000458	33.32	gold quality
adipose tissue	UBERON:0001013	33.13	silver quality
left adrenal gland cortex	UBERON:0035825	33.06	silver quality
superior frontal gyrus	UBERON:0002661	33.03	gold quality
mucosa of stomach	UBERON:0001199	32.76	gold quality
smooth muscle tissue	UBERON:0001135	32.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting CDCP2, 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-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-516A-3P	99.46	67.96	1378
HSA-MIR-516B-3P	99.46	67.96	1378
HSA-MIR-7162-5P	99.46	68.08	1368
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-1264	99.25	66.81	1317
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-4716-5P	98.82	68.57	1168
HSA-MIR-5590-5P	98.81	68.78	969

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdcp2	ENSDARG00000075866
mus_musculus	Cdcp2	ENSMUSG00000047636
rattus_norvegicus	Cdcp2	ENSRNOG00000009221

Paralogs (35): NRXN3 (ENSG00000021645), TLL1 (ENSG00000038295), CP (ENSG00000047457), DCBLD2 (ENSG00000057019), HEPH (ENSG00000089472), TLL2 (ENSG00000095587), NRP1 (ENSG00000099250), PCOLCE (ENSG00000106333), CNTNAP3 (ENSG00000106714), CUBN (ENSG00000107611), CNTNAP1 (ENSG00000108797), NRXN2 (ENSG00000110076), MEP1A (ENSG00000112818), NRP2 (ENSG00000118257), CUZD1 (ENSG00000138161), MFGE8 (ENSG00000140545), MEP1B (ENSG00000141434), PDGFC (ENSG00000145431), CNTNAP4 (ENSG00000152910), CNTNAP3B (ENSG00000154529), CNTNAP5 (ENSG00000155052), PCOLCE2 (ENSG00000163710), EDIL3 (ENSG00000164176), NETO1 (ENSG00000166342), BMP1 (ENSG00000168487), PDGFD (ENSG00000170962), NETO2 (ENSG00000171208), CNTNAP2 (ENSG00000174469), NRXN1 (ENSG00000179915), HEPHL1 (ENSG00000181333), F8 (ENSG00000185010), ASTL (ENSG00000188886), F5 (ENSG00000198734), MFRP (ENSG00000235718), CNTNAP3C (ENSG00000283378)

Protein

Protein identifiers

CUB domain-containing protein 2 — Q5VXM1 (reviewed: Q5VXM1)

All UniProt accessions (1): Q5VXM1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5VXM1-3	1	yes
Q5VXM1-1	2

RefSeq proteins (2): NP_001340584, NP_963840 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000859	CUB_dom	Domain
IPR035914	Sperma_CUB_dom_sf	Homologous_superfamily
IPR055356	ZP-N	Domain

Pfam: PF00431, PF23344

UniProt features (22 total): disulfide bond 6, glycosylation site 5, domain 3, splice variant 2, topological domain 2, signal peptide 1, chain 1, sequence variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VXM1-F1	82.43	0.43

Functional residue map

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

Disulfide bonds (6): 30–56, 83–106, 145–171, 198–218, 257–283, 314–336

Glycosylation sites (5): 377, 435, 436, 40, 267

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): TGACCTY_ERR1_Q2, TGGAAA_NFAT_Q4_01, LINDGREN_BLADDER_CANCER_CLUSTER_1_DN, CHEN_METABOLIC_SYNDROM_NETWORK, NABA_ECM_GLYCOPROTEINS, MIR2467_5P, MIR6874_3P, MIR148B_5P, MIR331_3P, NABA_CORE_MATRISOME, NABA_MATRISOME, chr1p32, GSE3720_UNSTIM_VS_LPS_STIM_VD2_GAMMADELTA_TCELL_DN, GSE19941_UNSTIM_VS_LPS_AND_IL10_STIM_IL10_KO_NFKBP50_KO_MACROPHAGE_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

440 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDCP2	USP24	Q9UPU5	890
CDCP2	HIVEP3	Q5T1R4	847
CDCP2	EIF2B3	Q9NR50	776
CDCP2	ELAVL4	P26378	763
CDCP2	ZNF852	Q6ZMS4	697
CDCP2	CCDC73	Q6ZRK6	561
CDCP2	MROH7	Q68CQ1	541
CDCP2	WDR27	A2RRH5	508
CDCP2	PRDM15	P57071	486
CDCP2	ANKRD65	E5RJM6	476
CDCP2	SCLT1	Q96NL6	451
CDCP2	JPH4	Q96JJ6	451
CDCP2	ZDBF2	Q9HCK1	451
CDCP2	FAM111B	Q6SJ93	450
CDCP2	FOXI3	A8MTJ6	428

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CDCP2	EDEM1	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): EDEM1 (Affinity Capture-MS), CDC6 (Affinity Capture-MS), EHD4 (Affinity Capture-MS)

ESM2 similar proteins: A0JNA2, A2RRU4, A6QM06, C0HL12, D3ZTD8, O14514, O54693, O60241, O60242, O75077, O75462, P08138, P97260, Q0GA42, Q13591, Q29RN8, Q3TMX7, Q3UHD1, Q4V7F2, Q4V9Z5, Q53EL9, Q5R7Y0, Q5VXM1, Q62217, Q6GQT6, Q6UXD5, Q6ZRP7, Q7TSK2, Q7TSQ1, Q7TT36, Q80ZF8, Q8BQC3, Q8BQH6, Q8CGM1, Q8IVU1, Q8IWK6, Q91XD7, Q924S4, Q92838, Q96MU8

Diamond homologs: A0A0C5PRQ1, A0FKN6, A0JNA2, A8Q2D1, C6K2K4, C9D7R3, D2KBH9, D5FM34, D5FM37, D5FM38, K7Z9Q9, O16977, O17264, O35276, O35375, O43897, O57382, O57460, O60462, O60494, O70244, P07584, P0DM61, P0DM62, P13497, P28825, P28826, P31579, P31580, P31581, P42674, P55112, P55113, P55114, P55115, P84748, P91828, P98060, P98061, P98068

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1210 predictions. Top by Δscore:

Variant	Effect	Δscore
1:54140104:CTC:C	acceptor_gain	1.0000
1:54144583:T:TA	donor_gain	1.0000
1:54144584:C:A	donor_gain	1.0000
1:54139754:T:TA	donor_gain	0.9900
1:54140102:TTCTC:T	acceptor_gain	0.9900
1:54140105:TC:T	acceptor_gain	0.9900
1:54140106:CC:C	acceptor_gain	0.9900
1:54140106:CCTGG:C	acceptor_loss	0.9900
1:54140107:C:CC	acceptor_gain	0.9900
1:54140111:A:C	acceptor_gain	0.9900
1:54140118:A:AC	acceptor_gain	0.9900
1:54140118:A:C	acceptor_gain	0.9900
1:54140126:G:C	acceptor_gain	0.9900
1:54141092:TCCTA:T	donor_loss	0.9900
1:54141093:CCTA:C	donor_loss	0.9900
1:54141094:CTAC:C	donor_loss	0.9900
1:54141095:TACC:T	donor_loss	0.9900
1:54141096:ACCTG:A	donor_loss	0.9900
1:54141097:CCTG:C	donor_loss	0.9900
1:54141431:CAT:C	acceptor_gain	0.9900
1:54144496:TGGC:T	donor_gain	0.9900
1:54144572:G:A	donor_gain	0.9900
1:54153084:T:TA	donor_gain	0.9900
1:54153094:A:AC	donor_gain	0.9900
1:54153095:C:CC	donor_gain	0.9900
1:54153298:C:A	donor_gain	0.9900
1:54153642:T:TA	donor_gain	0.9900
1:54140103:TCTC:T	acceptor_gain	0.9800
1:54140104:CTCC:C	acceptor_gain	0.9800
1:54140105:TCCT:T	acceptor_gain	0.9800

AlphaMissense

3516 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:54141118:A:C	F248C	0.999
1:54141118:A:G	F248S	0.999
1:54141145:G:A	S239F	0.999
1:54141259:T:A	D201V	0.999
1:54141349:C:G	C171S	0.999
1:54141350:A:T	C171S	0.999
1:54141387:A:C	S158R	0.999
1:54141387:A:T	S158R	0.999
1:54141389:T:G	S158R	0.999
1:54144486:A:G	F136S	0.999
1:54144636:T:A	D86V	0.999
1:54139762:A:C	Y370D	0.998
1:54140022:C:G	C283S	0.998
1:54140023:A:T	C283S	0.998
1:54140060:G:C	S270R	0.998
1:54140060:G:T	S270R	0.998
1:54140062:T:G	S270R	0.998
1:54141117:G:C	F248L	0.998
1:54141117:G:T	F248L	0.998
1:54141119:A:G	F248L	0.998
1:54141142:T:A	D240V	0.998
1:54141260:C:A	D201Y	0.998
1:54141260:C:G	D201H	0.998
1:54141301:A:C	F187C	0.998
1:54141342:C:A	W173C	0.998
1:54141342:C:G	W173C	0.998
1:54144485:A:C	F136L	0.998
1:54144485:A:T	F136L	0.998
1:54144486:A:C	F136C	0.998
1:54144487:A:G	F136L	0.998

dbSNP variants (sampled 300 via entrez): RS1000175520 (1:54138312 A>G), RS1000249456 (1:54144019 G>T), RS1000265132 (1:54134207 C>A,T), RS1000294561 (1:54144267 C>T), RS1000526750 (1:54152153 GGGA>G), RS1000628871 (1:54142891 T>C), RS1000784867 (1:54137327 A>G), RS1000934805 (1:54154457 C>T), RS1001022187 (1:54149163 C>T), RS1001191284 (1:54137656 G>C,T), RS1001264396 (1:54135578 G>A), RS1001297053 (1:54135306 G>A), RS1001325740 (1:54147151 C>A,T), RS1001437442 (1:54147372 C>T), RS1001494229 (1:54148838 C>T)

Disease associations

OMIM: gene MIM:612320 | 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
GCST012335_13	Hodgkin’s lymphoma	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
ethylbenzene	increases expression, affects cotreatment, decreases methylation	1
alpha phellandrene	increases expression	1
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenite	increases abundance, increases expression	1
CGP 52608	affects binding, increases reaction	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases methylation, increases expression	1
Benzo(a)pyrene	increases methylation	1
Copper	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Toluene	increases expression, affects cotreatment, decreases methylation	1
Xylenes	affects cotreatment, decreases methylation, increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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