CPXM1

Summary

CPXM1 (carboxypeptidase X, M14 family member 1, HGNC:15771) is a protein-coding gene on chromosome 20p13, encoding Probable carboxypeptidase X1 (Q96SM3). May be involved in cell-cell interactions.

This gene likely encodes a member of the carboxypeptidase family of proteins. Cloning of a comparable locus in mouse indicates that the encoded protein contains a discoidin domain and a carboxypeptidase domain, but the protein appears to lack residues necessary for carboxypeptidase activity.

Source: NCBI Gene 56265 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 122 total
• MANE Select transcript: NM_019609

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15771
Approved symbol	CPXM1
Name	carboxypeptidase X, M14 family member 1
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	CPX-1, CPX1
Ensembl gene	ENSG00000088882
Ensembl biotype	protein_coding
OMIM	609555
Entrez	56265

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000380605, ENST00000867057, ENST00000867058, ENST00000921882, ENST00000921883, ENST00000921884, ENST00000948848

RefSeq mRNA: 2 — MANE Select: NM_019609 NM_001184699, NM_019609

CCDS: CCDS13033

Canonical transcript exons

ENST00000380605 — 14 exons

Exon	Start	End
ENSE00000561938	2794074	2794431
ENSE00000656574	2794537	2794639
ENSE00000656576	2795277	2795416
ENSE00000656578	2795599	2795896
ENSE00000656580	2795982	2796161
ENSE00000656584	2796527	2796650
ENSE00000656585	2797006	2797094
ENSE00000656588	2798152	2798291
ENSE00000656589	2798428	2798537
ENSE00001229858	2797192	2797342
ENSE00001229866	2797968	2798058
ENSE00001229894	2798726	2798893
ENSE00001229905	2796247	2796443
ENSE00001879799	2800401	2800627

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 99.54.

FANTOM5 (CAGE): breadth broad, TPM avg 19.7661 / max 353.7907, expressed in 834 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186105	18.9406	772
186107	0.4503	124
186106	0.2901	146
186108	0.0491	19
186101	0.0212	1
186103	0.0072	1
186102	0.0058	1
186104	0.0018	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	99.54	gold quality
gall bladder	UBERON:0002110	96.45	gold quality
cartilage tissue	UBERON:0002418	94.19	gold quality
omental fat pad	UBERON:0010414	92.61	gold quality
peritoneum	UBERON:0002358	92.54	gold quality
endocervix	UBERON:0000458	91.91	gold quality
adipose tissue of abdominal region	UBERON:0007808	91.82	gold quality
ectocervix	UBERON:0012249	91.46	gold quality
smooth muscle tissue	UBERON:0001135	91.32	gold quality
body of uterus	UBERON:0009853	90.97	gold quality
parietal pleura	UBERON:0002400	90.81	gold quality
left uterine tube	UBERON:0001303	89.77	gold quality
ganglionic eminence	UBERON:0004023	89.29	gold quality
germinal epithelium of ovary	UBERON:0001304	88.99	gold quality
ventricular zone	UBERON:0003053	87.34	gold quality
uterine cervix	UBERON:0000002	87.23	gold quality
myometrium	UBERON:0001296	87.22	gold quality
uterus	UBERON:0000995	86.77	gold quality
left ovary	UBERON:0002119	86.77	gold quality
right ovary	UBERON:0002118	86.47	gold quality
adipose tissue	UBERON:0001013	86.00	gold quality
ovary	UBERON:0000992	85.84	gold quality
subcutaneous adipose tissue	UBERON:0002190	85.58	gold quality
right uterine tube	UBERON:0001302	85.06	gold quality
endometrium	UBERON:0001295	85.01	gold quality
female reproductive system	UBERON:0000474	84.74	gold quality
skin of hip	UBERON:0001554	83.89	gold quality
vagina	UBERON:0000996	82.67	gold quality
mucosa of paranasal sinus	UBERON:0005030	82.55	silver quality
placenta	UBERON:0001987	82.23	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-124472	yes	2735.49
E-MTAB-6678	yes	1255.16
E-MTAB-6701	yes	868.86
E-MTAB-10287	yes	327.78
E-HCAD-10	yes	21.14
E-ANND-3	yes	15.76
E-CURD-112	no	2.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting CPXM1, 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-3663-3P	99.84	70.39	798
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-3127-3P	98.94	67.34	1055
HSA-MIR-6756-3P	98.94	66.79	1104
HSA-MIR-5088-5P	97.97	64.28	487
HSA-MIR-6849-3P	97.25	64.57	1371

Literature-anchored findings (GeneRIF, showing 3)

• This paper deals with mouse CPXM. (PMID:10073577)
• These findings establish CPX-1 as a positive regulator of adipogenesis situated downstream of FGF-1/BAMBI that may contribute to hyperplastic adipose tissue expansion via affecting extracellular matrix remodeling. (PMID:27006448)
• Role of CPXM1 in Impaired Glucose Metabolism and Ovarian Dysfunction in Polycystic Ovary Syndrome. (PMID:35697923)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cpxm1a	ENSDARG00000073716
danio_rerio	cpxm1b	ENSDARG00000098158
mus_musculus	Cpxm1	ENSMUSG00000027408
rattus_norvegicus	Cpxm1	ENSRNOG00000021220

Paralogs (7): AEBP1 (ENSG00000106624), CPD (ENSG00000108582), CPE (ENSG00000109472), CPZ (ENSG00000109625), CPN1 (ENSG00000120054), CPXM2 (ENSG00000121898), CPM (ENSG00000135678)

Protein

Protein identifiers

Probable carboxypeptidase X1 — Q96SM3 (reviewed: Q96SM3)

Alternative names: Metallocarboxypeptidase CPX-1

All UniProt accessions (1): Q96SM3

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in cell-cell interactions. No carboxypeptidase activity was found yet.

Subcellular location. Secreted.

Cofactor. Binds 1 zinc ion per subunit.

Similarity. Belongs to the peptidase M14 family.

RefSeq proteins (2): NP_001171628, NP_062555* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000421	FA58C	Domain
IPR000834	Peptidase_M14	Domain
IPR008969	CarboxyPept-like_regulatory	Homologous_superfamily
IPR008979	Galactose-bd-like_sf	Homologous_superfamily
IPR050753	Peptidase_M14_domain	Family
IPR057246	CARBOXYPEPT_ZN_1	Binding_site
IPR057247	CARBOXYPEPT_ZN_2	Binding_site

Pfam: PF00246, PF00754, PF13620

UniProt features (20 total): glycosylation site 6, sequence conflict 3, binding site 3, domain 2, signal peptide 1, chain 1, disulfide bond 1, region of interest 1, compositionally biased region 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96SM3-F1	84.78	0.73

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): 591 (proton donor/acceptor)

Ligand- & substrate-binding residues (3): 360; 363; 498

Disulfide bonds (1): 115–274

Glycosylation sites (6): 57, 210, 220, 318, 428, 472

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 98 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, TSENG_IRS1_TARGETS_UP, GOMF_METALLOPEPTIDASE_ACTIVITY, HUMMERICH_SKIN_CANCER_PROGRESSION_UP, HOWLIN_PUBERTAL_MAMMARY_GLAND, TGCTGAY_UNKNOWN, DOUGLAS_BMI1_TARGETS_UP, NERF_Q2, CUI_TCF21_TARGETS_2_UP, GOBP_PROTEOLYSIS, GOMF_CARBOXYPEPTIDASE_ACTIVITY, GOMF_METALLOEXOPEPTIDASE_ACTIVITY, GOMF_METALLOCARBOXYPEPTIDASE_ACTIVITY, GOMF_PEPTIDASE_ACTIVITY, GOMF_EXOPEPTIDASE_ACTIVITY

GO Biological Process (1): proteolysis (GO:0006508)

GO Molecular Function (7): metallocarboxypeptidase activity (GO:0004181), zinc ion binding (GO:0008270), carboxypeptidase activity (GO:0004180), peptidase activity (GO:0008233), metallopeptidase activity (GO:0008237), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein metabolic process	1
carboxypeptidase activity	1
metalloexopeptidase activity	1
transition metal ion binding	1
exopeptidase activity	1
hydrolase activity	1
catalytic activity, acting on a protein	1
peptidase activity	1
catalytic activity	1
cation binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

664 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPXM1	SMIM24	O75264	639
CPXM1	NYNRIN	Q9P2P1	621
CPXM1	BEX3	Q00994	547
CPXM1	ARHGAP22	Q7Z5H3	544
CPXM1	LAPTM4B	Q86VI4	518
CPXM1	MMRN1	Q13201	440
CPXM1	ZBTB46	Q86UZ6	438
CPXM1	TMEM176A	Q96HP8	438
CPXM1	EMP1	P54849	434
CPXM1	TMEM176B	Q3YBM2	433
CPXM1	GDAP1L1	Q96MZ0	433
CPXM1	TMEM47	Q9BQJ4	429
CPXM1	KLF9	Q13886	412
CPXM1	ZNF177	Q13360	399
CPXM1	GDAP1	Q8TB36	394

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CPXM1	MAPK3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): IGF2R (Cross-Linking-MS (XL-MS)), CPXM1 (Affinity Capture-RNA), CPXM1 (Two-hybrid)

ESM2 similar proteins: A2RUV9, F8W3R9, O18738, O43278, O54858, O88393, O97827, P00734, P00735, P0C5J5, P12259, P18292, P26342, P35054, P51511, Q08629, Q08E66, Q09101, Q14118, Q24567, Q24568, Q28685, Q29243, Q5R537, Q5RD69, Q62165, Q62288, Q640N1, Q66K79, Q701R2, Q7TQN3, Q80TS3, Q8BKV0, Q8IUX7, Q8N436, Q8R4V4, Q8TEU8, Q91ZV2, Q91ZV3, Q92563

Diamond homologs: A2RUV9, A5A6K7, O14786, O17754, O18806, O35276, O35375, O35474, O43854, O54858, O54991, O60462, O75976, O88783, O89001, P00451, P02886, P02887, P02888, P04836, P12259, P12263, P14384, P15087, P15169, P16870, P21956, P28824, P29068, P37892, P39041, P42787, P70490, P78357, P79385, P79795, P83852, P97333, P97846, P98092

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	12
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2233 predictions. Top by Δscore:

Variant	Effect	Δscore
20:2794536:C:CA	donor_gain	1.0000
20:2795597:A:AC	donor_gain	1.0000
20:2795597:ACT:A	donor_gain	1.0000
20:2795598:C:CC	donor_gain	1.0000
20:2795598:CT:C	donor_gain	1.0000
20:2795598:CTC:C	donor_gain	1.0000
20:2795978:TCA:T	donor_loss	1.0000
20:2795979:CACG:C	donor_loss	1.0000
20:2795980:A:AC	donor_gain	1.0000
20:2795980:ACG:A	donor_loss	1.0000
20:2795981:C:CA	donor_gain	1.0000
20:2795981:C:CT	donor_loss	1.0000
20:2795981:CG:C	donor_gain	1.0000
20:2795981:CGG:C	donor_gain	1.0000
20:2795981:CGGT:C	donor_gain	1.0000
20:2796526:CCCAG:C	donor_gain	1.0000
20:2796530:G:C	donor_gain	1.0000
20:2796534:ATGCT:A	donor_gain	1.0000
20:2796539:C:CA	donor_gain	1.0000
20:2796540:C:A	donor_gain	1.0000
20:2796570:CAG:C	donor_gain	1.0000
20:2796648:CAG:C	acceptor_gain	1.0000
20:2797239:C:A	donor_gain	1.0000
20:2797344:T:G	acceptor_loss	1.0000
20:2797966:A:AC	donor_gain	1.0000
20:2797967:C:CC	donor_gain	1.0000
20:2798288:CTGA:C	acceptor_gain	1.0000
20:2798292:C:CC	acceptor_gain	1.0000
20:2798424:TGA:T	donor_loss	1.0000
20:2798534:CAGC:C	acceptor_gain	1.0000

AlphaMissense

4782 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:2795316:C:A	W607C	0.999
20:2795316:C:G	W607C	0.999
20:2795615:C:A	W568C	0.999
20:2795615:C:G	W568C	0.999
20:2795837:A:C	S494R	0.999
20:2795837:A:T	S494R	0.999
20:2795839:T:G	S494R	0.999
20:2794410:C:G	R662P	0.998
20:2795296:A:G	L614P	0.998
20:2795356:C:G	C594S	0.998
20:2795356:C:T	C594Y	0.998
20:2795357:A:T	C594S	0.998
20:2795400:G:C	S579R	0.998
20:2795400:G:T	S579R	0.998
20:2795402:T:G	S579R	0.998
20:2795408:C:G	D577H	0.998
20:2795667:C:G	C551S	0.998
20:2795668:A:T	C551S	0.998
20:2795713:A:C	Y536D	0.998
20:2795720:G:C	S533R	0.998
20:2795720:G:T	S533R	0.998
20:2795722:T:G	S533R	0.998
20:2795866:A:G	W485R	0.998
20:2795866:A:T	W485R	0.998
20:2796093:A:C	F437L	0.998
20:2796093:A:T	F437L	0.998
20:2796094:A:C	F437C	0.998
20:2796094:A:G	F437S	0.998
20:2796095:A:G	F437L	0.998
20:2796141:C:A	W421C	0.998

dbSNP variants (sampled 300 via entrez): RS1000138124 (20:2799536 C>G,T), RS1000321194 (20:2799113 G>C), RS1000372240 (20:2794116 G>A,T), RS1000654985 (20:2797830 C>A,T), RS1001086455 (20:2795540 G>A,T), RS1001161109 (20:2800208 C>A,T), RS1001212089 (20:2800427 G>A), RS1001495086 (20:2795029 C>A,G,T), RS1001807255 (20:2800282 A>C,G,T), RS1001867650 (20:2801775 A>G), RS1002382493 (20:2796480 T>G), RS1004232939 (20:2800909 G>A), RS1004343442 (20:2795780 G>A), RS1004378491 (20:2799396 T>C), RS1004386946 (20:2799068 A>G)

Disease associations

OMIM: gene MIM:609555 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST005580_255	Intraocular pressure	2.000000e-10
GCST005580_295	Intraocular pressure	2.000000e-09
GCST006394_51	Intraocular pressure	2.000000e-08
GCST010397_18	Gut microbiota (bacterial taxa, rank normal transformation method)	1.000000e-06
GCST90000654_70	Central corneal thickness	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0007874	gut microbiome measurement
EFO:0005213	central corneal thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — M14: Carboxypeptidase A

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance	2
Doxorubicin	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol A	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases reaction, increases expression	1
beta-methylcholine	affects expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Decitabine	increases expression	1
Sunitinib	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	increases expression	1
Fluorouracil	affects expression	1
Lead	affects expression	1
Lipopolysaccharides	increases expression, decreases reaction	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	decreases methylation	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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