CPED1

Summary

CPED1 (cadherin like and PC-esterase domain containing 1, HGNC:26159) is a protein-coding gene on chromosome 7q31.31, encoding Cadherin-like and PC-esterase domain-containing protein 1 (A4D0V7).

Located in endoplasmic reticulum.

Source: NCBI Gene 79974 — RefSeq curated summary.

At a glance

• GWAS associations: 45
• Clinical variants (ClinVar): 191 total
• MANE Select transcript: NM_024913

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26159
Approved symbol	CPED1
Name	cadherin like and PC-esterase domain containing 1
Location	7q31.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21986
Ensembl gene	ENSG00000106034
Ensembl biotype	protein_coding
OMIM	620637
Entrez	79974

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000310396, ENST00000340646, ENST00000423795, ENST00000428526, ENST00000443817, ENST00000450913, ENST00000466055, ENST00000495036, ENST00000520801, ENST00000521774, ENST00000942582, ENST00000942583, ENST00000942584, ENST00000942585, ENST00000942586

RefSeq mRNA: 2 — MANE Select: NM_024913 NM_001105533, NM_024913

CCDS: CCDS34739, CCDS47690

Canonical transcript exons

ENST00000310396 — 23 exons

Exon	Start	End
ENSE00000719130	121099926	121100094
ENSE00000719179	121124331	121124473
ENSE00000719188	121140827	121141013
ENSE00000719198	121266227	121266447
ENSE00000719203	121266707	121266808
ENSE00000719209	121267215	121267302
ENSE00000881968	121125820	121125892
ENSE00000881970	121128382	121128486
ENSE00000881971	121130125	121130294
ENSE00001188413	121127090	121127257
ENSE00001213884	121271284	121271430
ENSE00001214023	121295440	121297442
ENSE00001317337	121136040	121136090
ENSE00001326515	121141973	121142141
ENSE00001631458	120989391	120989870
ENSE00001893300	120988711	120988912
ENSE00003459186	121064238	121064313
ENSE00003480216	121046887	121046993
ENSE00003558798	121097699	121097831
ENSE00003607455	121244202	121244338
ENSE00003646517	121236714	121236831
ENSE00003649248	121015665	121015848
ENSE00003787920	121133823	121133893

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 98.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1925 / max 594.2183, expressed in 1269 samples.

FANTOM5 promoters (24 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80783	5.3806	1077
80805	3.1259	287
80784	2.1165	767
80786	1.0238	380
80785	0.5442	299
80804	0.4538	104
80799	0.3690	210
80797	0.3667	191
80787	0.2851	154
80809	0.2029	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cauda epididymis	UBERON:0004360	98.66	gold quality
saphenous vein	UBERON:0007318	98.24	gold quality
superficial temporal artery	UBERON:0001614	97.36	gold quality
seminal vesicle	UBERON:0000998	97.19	gold quality
urethra	UBERON:0000057	97.18	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.14	gold quality
right coronary artery	UBERON:0001625	96.07	gold quality
vena cava	UBERON:0004087	95.94	gold quality
synovial joint	UBERON:0002217	95.23	gold quality
biceps brachii	UBERON:0001507	95.16	gold quality
calcaneal tendon	UBERON:0003701	95.15	gold quality
popliteal artery	UBERON:0002250	94.87	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.86	gold quality
tibial artery	UBERON:0007610	94.85	gold quality
caput epididymis	UBERON:0004358	94.67	gold quality
artery	UBERON:0001637	94.62	gold quality
colonic epithelium	UBERON:0000397	94.12	gold quality
aorta	UBERON:0000947	93.83	gold quality
mammary duct	UBERON:0001765	93.40	gold quality
germinal epithelium of ovary	UBERON:0001304	93.06	gold quality
coronary artery	UBERON:0001621	92.78	gold quality
parietal pleura	UBERON:0002400	92.75	gold quality
left ovary	UBERON:0002119	92.57	gold quality
ascending aorta	UBERON:0001496	92.40	gold quality
thoracic aorta	UBERON:0001515	92.39	gold quality
heart right ventricle	UBERON:0002080	92.32	gold quality
corpus epididymis	UBERON:0004359	92.32	gold quality
left coronary artery	UBERON:0001626	92.27	gold quality
gall bladder	UBERON:0002110	91.96	gold quality
pericardium	UBERON:0002407	91.72	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-GEOD-180759	yes	1464.73
E-HCAD-10	yes	46.58
E-CURD-119	yes	14.25
E-MTAB-9388	yes	12.83
E-ANND-3	yes	7.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

142 targeting CPED1, 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-3163	100.00	77.23	8605
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784

Literature-anchored findings (GeneRIF, showing 1)

• Variants at the CPED1 locus were strongly associated with bone mineral density at the skull and upper limb sites, but not with lower limb-bone mineral density. (PMID:24945404)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cped1	ENSDARG00000045747
mus_musculus	Cped1	ENSMUSG00000062980
rattus_norvegicus	Cped1	ENSRNOG00000021840

Protein

Protein identifiers

Cadherin-like and PC-esterase domain-containing protein 1 — A4D0V7 (reviewed: A4D0V7)

All UniProt accessions (6): A4D0V7, E7ENG7, E9PCC8, G5E9U2, H0YB19, Q5MJQ4

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PC-esterase family.

Isoforms (2)

UniProt ID	Names	Canonical?
A4D0V7-1	1	yes
A4D0V7-2	2

RefSeq proteins (2): NP_001099003, NP_079189* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025883	Cadherin-like_domain	Domain
IPR057106	NXPE4_C	Domain

Pfam: PF12733, PF24536

UniProt features (19 total): glycosylation site 6, sequence conflict 5, sequence variant 4, splice variant 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4D0V7-F1	73.08	0.28

Functional residue map

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

Glycosylation sites (6): 251, 404, 413, 737, 791, 985

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 113 (showing top): ATACCTC_MIR202, PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, ACATTCC_MIR1_MIR206, KUNINGER_IGF1_VS_PDGFB_TARGETS_DN, MODULE_48, MODULE_95, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP, CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN, LEIN_CHOROID_PLEXUS_MARKERS, chr7q31, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MODULE_163, STK33_SKM_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

490 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPED1	WNT16	Q9UBV4	702
CPED1	FAM3C	Q92520	655
CPED1	ING3	Q9NXR8	596
CPED1	TNFSF11	O14788	517
CPED1	MIMS1	Q96ND0	507
CPED1	EPDR1	Q9UM22	487
CPED1	IZUMO3	Q5VZ72	480
CPED1	PPP6R3	Q5H9R7	447
CPED1	GALNT3	Q14435	442
CPED1	MAMSTR	Q6ZN01	442
CPED1	C12orf43	Q96C57	435
CPED1	RIN3	Q8TB24	404
CPED1	TMEM263	Q8WUH6	394
CPED1	MEPE	Q9NQ76	392
CPED1	STARD3NL	O95772	383

IntAct

2 interactions, top by confidence:

A	B	Type	Score
gabP	CPED1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): CPED1 (Reconstituted Complex), CPED1 (Proximity Label-MS)

ESM2 similar proteins: A0A0D3QS98, A0A0D3QS99, A4D0V7, C5H5C4, F6Q1T7, O70309, O75354, P17405, P18084, P18424, P22413, P50747, P52850, P58242, P61642, P80747, Q04519, Q0VBD0, Q0VD19, Q13219, Q52KP5, Q58CQ9, Q5QQ51, Q5STE3, Q64687, Q6DFZ6, Q6KFX9, Q6MZW2, Q6P988, Q6UWX4, Q6YGZ1, Q6ZXD2, Q71RP1, Q812F8, Q8BJQ9, Q8C1F4, Q8C419, Q8N5D6, Q8N6G5, Q8R116

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	143
Likely benign	14
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

4593 predictions. Top by Δscore:

Variant	Effect	Δscore
7:121015659:TCTTA:T	acceptor_loss	1.0000
7:121015660:CTTAG:C	acceptor_loss	1.0000
7:121015661:TTA:T	acceptor_loss	1.0000
7:121015663:A:T	acceptor_loss	1.0000
7:121015664:G:A	acceptor_loss	1.0000
7:121046961:G:GT	donor_gain	1.0000
7:121046976:T:G	donor_gain	1.0000
7:121046989:AAAAG:A	donor_loss	1.0000
7:121046990:AAAGG:A	donor_loss	1.0000
7:121046991:AAGG:A	donor_loss	1.0000
7:121046992:AGGT:A	donor_loss	1.0000
7:121046994:G:A	donor_loss	1.0000
7:121046995:T:A	donor_loss	1.0000
7:121097697:A:AG	acceptor_gain	1.0000
7:121097698:G:GG	acceptor_gain	1.0000
7:121097698:GA:G	acceptor_gain	1.0000
7:121097698:GAA:G	acceptor_gain	1.0000
7:121097698:GAACT:G	acceptor_gain	1.0000
7:121097827:CAGCT:C	donor_gain	1.0000
7:121097828:AGCT:A	donor_gain	1.0000
7:121097829:GCT:G	donor_gain	1.0000
7:121097829:GCTG:G	donor_gain	1.0000
7:121097830:CT:C	donor_gain	1.0000
7:121097831:TGTAA:T	donor_loss	1.0000
7:121097832:G:GG	donor_gain	1.0000
7:121097832:GT:G	donor_loss	1.0000
7:121097833:TAAG:T	donor_loss	1.0000
7:121097837:C:G	donor_gain	1.0000
7:121099922:TTAG:T	acceptor_loss	1.0000
7:121099923:TAG:T	acceptor_loss	1.0000

AlphaMissense

6773 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:121244207:T:A	W727R	0.999
7:121244207:T:C	W727R	0.999
7:121244209:G:C	W727C	0.998
7:121244209:G:T	W727C	0.998
7:121244254:G:C	W742C	0.998
7:121244254:G:T	W742C	0.998
7:121266762:T:A	W863R	0.997
7:121266762:T:C	W863R	0.997
7:121244252:T:A	W742R	0.996
7:121244252:T:C	W742R	0.996
7:121244267:T:A	W747R	0.996
7:121244267:T:C	W747R	0.996
7:121244269:G:C	W747C	0.996
7:121244269:G:T	W747C	0.996
7:121266242:G:C	D776H	0.996
7:121266243:A:T	D776V	0.996
7:121244221:C:G	C731W	0.994
7:121266243:A:C	D776A	0.994
7:121267247:A:T	K889I	0.994
7:121244246:T:A	C740S	0.993
7:121244246:T:C	C740R	0.993
7:121244247:G:A	C740Y	0.993
7:121244247:G:C	C740S	0.993
7:121266240:G:T	G775V	0.993
7:121266764:G:C	W863C	0.993
7:121266764:G:T	W863C	0.993
7:121244219:T:C	C731R	0.992
7:121266243:A:G	D776G	0.992
7:121266438:T:C	L841P	0.992
7:121267264:T:C	F895L	0.992

dbSNP variants (sampled 300 via entrez): RS1000011022 (7:121228799 C>T), RS1000016988 (7:121106183 A>C), RS1000042491 (7:121133904 A>T), RS1000044197 (7:121232689 G>A,C), RS1000052255 (7:121039719 C>G,T), RS1000061072 (7:121031344 C>T), RS1000062119 (7:121062637 A>G), RS1000074288 (7:121057018 C>A), RS1000088998 (7:121209994 C>A), RS1000097692 (7:121003581 G>T), RS1000113775 (7:121073147 A>G), RS1000113847 (7:121149386 A>G), RS1000120603 (7:121174973 T>A), RS1000136697 (7:121012956 C>T), RS1000154474 (7:121239757 C>G)

Disease associations

OMIM: gene MIM:620637 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

45 associations (top):

Study	Trait	p-value
GCST001482_32	Lumbar spine bone mineral density	2.000000e-11
GCST001594_2	Bone mineral density	1.000000e-10
GCST002492_1	Bone mineral density (paediatric, lower limb)	3.000000e-11
GCST002492_10	Bone mineral density (paediatric, lower limb)	1.000000e-09
GCST002493_15	Bone mineral density (paediatric, skull)	3.000000e-22
GCST002493_16	Bone mineral density (paediatric, skull)	2.000000e-28
GCST002494_15	Bone mineral density (paediatric, total body less head)	2.000000e-15
GCST002494_3	Bone mineral density (paediatric, total body less head)	6.000000e-20
GCST002496_11	Bone mineral density (paediatric, upper limb)	1.000000e-37
GCST002496_7	Bone mineral density (paediatric, upper limb)	3.000000e-32
GCST002952_2	Pediatric bone mineral content (radius)	6.000000e-07
GCST002952_3	Pediatric bone mineral content (radius)	3.000000e-08
GCST002953_1	Pediatric areal bone mineral density (radius)	2.000000e-11
GCST002953_2	Pediatric areal bone mineral density (radius)	3.000000e-10
GCST004175_1	Pediatric bone mineral content (radius)	1.000000e-07
GCST004175_10	Pediatric bone mineral content (radius)	7.000000e-09
GCST004176_1	Pediatric areal bone mineral density (radius)	4.000000e-12
GCST004176_2	Pediatric areal bone mineral density (radius)	9.000000e-12
GCST004179_5	Pediatric bone mineral content (femoral neck)	2.000000e-08
GCST004771_6	TB-LM or TBLH-BMD (pleiotropy)	3.000000e-20
GCST004772_6	Bone mineral density (paediatric, total body less head)	5.000000e-17
GCST006247_1	Pediatric areal bone mineral density (radius vs spine & hip discordant skeletal phenotype)	3.000000e-11
GCST006247_2	Pediatric areal bone mineral density (radius vs spine & hip discordant skeletal phenotype)	4.000000e-12
GCST006247_3	Pediatric areal bone mineral density (radius vs spine & hip discordant skeletal phenotype)	5.000000e-12
GCST006247_4	Pediatric areal bone mineral density (radius vs spine & hip discordant skeletal phenotype)	4.000000e-12
GCST006288_104	Heel bone mineral density	7.000000e-12
GCST006288_105	Heel bone mineral density	2.000000e-06
GCST006288_652	Heel bone mineral density	1.000000e-19
GCST006288_653	Heel bone mineral density	3.000000e-13
GCST006288_758	Heel bone mineral density	2.000000e-09

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0007621	bone mineral content measurement
EFO:0007933	radius bone mineral density
EFO:0004995	lean body mass
EFO:0009270	heel bone mineral density
EFO:0007006	depressive symptom measurement
EFO:0009262	nicotine dependence symptom count
EFO:0004346	neuroimaging measurement
EFO:0010701	mean reticulocyte volume
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	8
bisphenol A	affects cotreatment, decreases expression, affects methylation	3
Benzo(a)pyrene	decreases expression, increases methylation	3
Tetrachlorodibenzodioxin	affects expression, decreases expression	3
trichostatin A	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Acetaminophen	decreases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	decreases expression	1
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
sulforaphane	decreases expression	1
sodium arsenite	increases expression	1
3,4,5,3’,4’-pentachlorobiphenyl	decreases expression	1
potassium chromate(VI)	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Vorinostat	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Allergens	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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