PCED1B

Summary

PCED1B (PC-esterase domain containing 1B, HGNC:28255) is a protein-coding gene on chromosome 12q13.11, encoding PC-esterase domain-containing protein 1B (Q96HM7).

This gene encodes a protein that belongs to the GDSL/SGNH-like acyl-esterase family. Members of this family are hydrolases thought to function in modification of biopolymers on the cell surface. Alternate splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 91523 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_138371

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28255
Approved symbol	PCED1B
Name	PC-esterase domain containing 1B
Location	12q13.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC16044
Ensembl gene	ENSG00000179715
Ensembl biotype	protein_coding
Entrez	91523

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 28 protein_coding

ENST00000432328, ENST00000546455, ENST00000548348, ENST00000549500, ENST00000549630, ENST00000551777, ENST00000872013, ENST00000872014, ENST00000872015, ENST00000872016, ENST00000872017, ENST00000872018, ENST00000872019, ENST00000872020, ENST00000872021, ENST00000872022, ENST00000872023, ENST00000872024, ENST00000872025, ENST00000872026, ENST00000872027, ENST00000872028, ENST00000872029, ENST00000929640, ENST00000962791, ENST00000962792, ENST00000962793, ENST00000962794

RefSeq mRNA: 2 — MANE Select: NM_138371 NM_001281429, NM_138371

CCDS: CCDS8752

Canonical transcript exons

ENST00000546455 — 4 exons

Exon	Start	End
ENSE00002351123	47216222	47216689
ENSE00002374553	47235007	47236660
ENSE00002413526	47104113	47104195
ENSE00003845606	47079621	47079725

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 93.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.2926 / max 539.1650, expressed in 1376 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125206	3.7325	315
125200	3.6130	1195
125205	3.0335	162
125199	0.4323	255
125208	0.2192	109
125204	0.1540	52
125209	0.1081	54

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	93.14	gold quality
right adrenal gland cortex	UBERON:0035827	92.91	gold quality
right adrenal gland	UBERON:0001233	92.32	gold quality
left adrenal gland	UBERON:0001234	91.74	gold quality
left adrenal gland cortex	UBERON:0035825	91.49	gold quality
adrenal cortex	UBERON:0001235	90.18	gold quality
adrenal gland	UBERON:0002369	89.72	gold quality
lymph node	UBERON:0000029	88.53	gold quality
blood	UBERON:0000178	88.37	gold quality
spleen	UBERON:0002106	88.11	gold quality
left ovary	UBERON:0002119	86.78	gold quality
right ovary	UBERON:0002118	85.16	gold quality
ileal mucosa	UBERON:0000331	84.62	silver quality
vermiform appendix	UBERON:0001154	84.46	gold quality
ovary	UBERON:0000992	83.75	gold quality
adrenal tissue	UBERON:0018303	83.52	gold quality
popliteal artery	UBERON:0002250	83.30	gold quality
tibial artery	UBERON:0007610	83.30	gold quality
right uterine tube	UBERON:0001302	82.65	gold quality
aorta	UBERON:0000947	81.30	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.25	gold quality
right coronary artery	UBERON:0001625	80.36	gold quality
left uterine tube	UBERON:0001303	80.05	gold quality
left coronary artery	UBERON:0001626	79.94	gold quality
stromal cell of endometrium	CL:0002255	79.85	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.60	gold quality
ascending aorta	UBERON:0001496	79.35	gold quality
thoracic aorta	UBERON:0001515	79.13	gold quality
right testis	UBERON:0004534	79.01	gold quality
bone marrow cell	CL:0002092	78.73	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-6	yes	90.89
E-MTAB-9067	yes	12.33
E-ANND-3	yes	10.30
E-MTAB-9801	yes	6.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting PCED1B, 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-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049
HSA-MIR-622	98.99	66.48	1050
HSA-MIR-4716-5P	98.82	68.57	1168
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-583	98.71	67.44	1791
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-4433B-3P	97.22	63.62	663

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam113	ENSDARG00000002685
mus_musculus	Pced1b	ENSMUSG00000044250
rattus_norvegicus	Pced1b	ENSRNOG00000022807
caenorhabditis_elegans	D2030.8	WBGENE00008418

Paralogs (1): PCED1A (ENSG00000132635)

Protein

Protein identifiers

PC-esterase domain-containing protein 1B — Q96HM7 (reviewed: Q96HM7)

Alternative names: Protein FAM113B

All UniProt accessions (4): Q96HM7, F8VRF7, F8VUD2, F8VYL8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PC-esterase family.

RefSeq proteins (2): NP_001268358, NP_612380* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR036514	SGNH_hydro_sf	Homologous_superfamily

UniProt features (4 total): region of interest 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96HM7-F1	72.31	0.51

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): MODULE_255, MODULE_317, BRUECKNER_TARGETS_OF_MIRLET7A3_DN, LEE_NAIVE_T_LYMPHOCYTE, AML_Q6, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP, MODULE_69, STAT1_02, MEISSNER_NPC_HCP_WITH_H3K4ME2, STAT1_03, MODULE_37, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_UP, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, E2F5_TARGET_GENES, RYBP_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

322 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCED1B	OR51F1	A6NGY5	392
PCED1B	OR8B8	Q15620	371
PCED1B	NXPE1	Q8N323	353
PCED1B	HDDC2	Q7Z4H3	348
PCED1B	HEPACAM2	A8MVW5	348
PCED1B	SLX4IP	Q5VYV7	343
PCED1B	XTBD1	Q96HQ2	328
PCED1B	SNX13	Q9Y5W8	316
PCED1B	ZNF500	O60304	310
PCED1B	OR2B6	P58173	310
PCED1B	HYI	Q5T013	307
PCED1B	ENTREP2	O60320	303
PCED1B	NXPE4	Q6UWF7	303
PCED1B	OVCA2	Q8WZ82	302
PCED1B	DPH6	Q7L8W6	300
PCED1B	NXPE3	Q969Y0	300

IntAct

10 interactions, top by confidence:

A	B	Type	Score
NOTCH2NLA	PCED1B	psi-mi:“MI:0915”(physical association)	0.560
PCED1B	NOTCH2NLA	psi-mi:“MI:0915”(physical association)	0.560
PCED1B	S100PBP	psi-mi:“MI:0915”(physical association)	0.500
PCED1B	S100PBP	psi-mi:“MI:0914”(association)	0.500
PCED1B	S100PBP	psi-mi:“MI:0915”(physical association)	0.400
ALB	CNOT1	psi-mi:“MI:0914”(association)	0.350
PCED1B	tyrS	psi-mi:“MI:0915”(physical association)	0.000
PCED1B	mnmG	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): NOTCH2NL (Two-hybrid), ZFR (Affinity Capture-MS), S100PBP (Affinity Capture-MS), NME7 (Affinity Capture-MS), S100PBP (Affinity Capture-MS), PCED1B (Positive Genetic), PCED1B (Affinity Capture-RNA), S100PBP (Affinity Capture-MS), ZFR (Affinity Capture-MS), PCED1B (Affinity Capture-MS)

ESM2 similar proteins: A0A8M9QN10, A2ARM1, A6QL70, E7F654, O08653, O15178, O43147, P20293, P23611, P33242, P50569, P56524, P59114, P79779, P87377, P97499, Q02556, Q04752, Q0VD00, Q15306, Q1LVK9, Q28HY0, Q2M1K5, Q32N92, Q4VC12, Q5U263, Q64287, Q6DHF9, Q6NZM9, Q6NZR5, Q6P1Z5, Q6ZUJ8, Q7Z3E5, Q80U12, Q80U38, Q8BGX1, Q8C2B3, Q8R151, Q96HM7, Q96SI1

Diamond homologs: A6QL70, Q2M1K5, Q6P1Z5, Q8BGX1, Q96HM7, Q9H1Q7

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	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2208 predictions. Top by Δscore:

Variant	Effect	Δscore
12:47079460:A:AC	donor_gain	1.0000
12:47079461:C:CC	donor_gain	1.0000
12:47079461:CGGTG:C	donor_gain	1.0000
12:47161131:C:G	donor_gain	1.0000
12:47079432:TAGCA:T	donor_gain	0.9900
12:47079433:AGCAA:A	donor_gain	0.9900
12:47079461:CG:C	donor_gain	0.9900
12:47104196:G:GG	donor_gain	0.9900
12:47105161:G:T	donor_gain	0.9900
12:47105180:G:T	donor_gain	0.9900
12:47155038:GAGAC:G	donor_gain	0.9900
12:47155121:A:G	donor_gain	0.9900
12:47212587:A:AG	acceptor_gain	0.9900
12:47216357:G:GT	donor_gain	0.9900
12:47235005:A:AG	acceptor_gain	0.9900
12:47235006:G:GG	acceptor_gain	0.9900
12:47079434:G:C	donor_gain	0.9800
12:47079455:AACTC:A	donor_loss	0.9800
12:47079457:CTCA:C	donor_loss	0.9800
12:47079460:A:T	donor_loss	0.9800
12:47079461:C:A	donor_loss	0.9800
12:47079511:T:TA	donor_gain	0.9800
12:47079721:TGAAG:T	donor_loss	0.9800
12:47079723:AAGG:A	donor_loss	0.9800
12:47079724:AGG:A	donor_loss	0.9800
12:47079725:GG:G	donor_loss	0.9800
12:47079726:G:A	donor_loss	0.9800
12:47079727:T:G	donor_loss	0.9800
12:47080713:A:G	donor_gain	0.9800
12:47104193:TAT:T	donor_gain	0.9800

AlphaMissense

2804 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:47235547:T:A	W162R	0.996
12:47235547:T:C	W162R	0.996
12:47235334:T:C	F91L	0.992
12:47235336:T:A	F91L	0.992
12:47235336:T:G	F91L	0.992
12:47235158:A:C	D32A	0.991
12:47235301:C:A	R80S	0.991
12:47235156:G:C	K31N	0.990
12:47235156:G:T	K31N	0.990
12:47235307:T:C	F82L	0.990
12:47235309:C:A	F82L	0.990
12:47235309:C:G	F82L	0.990
12:47235549:G:C	W162C	0.990
12:47235549:G:T	W162C	0.990
12:47235709:T:C	F216L	0.990
12:47235711:C:A	F216L	0.990
12:47235711:C:G	F216L	0.990
12:47235229:T:C	F56L	0.989
12:47235231:C:A	F56L	0.989
12:47235231:C:G	F56L	0.989
12:47235340:T:C	F93L	0.989
12:47235342:C:A	F93L	0.989
12:47235342:C:G	F93L	0.989
12:47235442:G:C	D127H	0.989
12:47235157:G:C	D32H	0.987
12:47235661:A:C	S200R	0.987
12:47235663:C:A	S200R	0.987
12:47235663:C:G	S200R	0.987
12:47235238:G:C	D59H	0.986
12:47235112:T:C	F17L	0.985

dbSNP variants (sampled 300 via entrez): RS1000004723 (12:47100899 G>A), RS1000026851 (12:47120990 A>C), RS1000030231 (12:47227687 C>G,T), RS1000055331 (12:47101548 T>A), RS1000061531 (12:47227970 C>G), RS1000071932 (12:47079799 G>A,T), RS1000075757 (12:47094655 G>A), RS1000092617 (12:47221893 G>A), RS1000099059 (12:47136977 A>C), RS1000108466 (12:47180578 A>T), RS1000112569 (12:47198528 A>G), RS1000128701 (12:47127589 C>G), RS1000139606 (12:47180211 T>C), RS1000149007 (12:47118888 C>A,T), RS1000165218 (12:47145553 G>A)

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

9 associations (top):

Study	Trait	p-value
GCST000310_2	Alzheimer’s disease	3.000000e-07
GCST004748_23	Lung cancer	4.000000e-06
GCST005790_25	Rosacea symptom severity	3.000000e-07
GCST007259_5	Severe skin toxicity response to cetuximab in colorectal cancer	2.000000e-06
GCST008151_1	Waist circumference	5.000000e-06
GCST008160_46	Waist circumference	5.000000e-06
GCST009724_95	Vertical cup-disc ratio (multi-trait analysis)	2.000000e-10
GCST90000025_964	Appendicular lean mass	2.000000e-11
GCST90026415_8	Mild obesity-related type 2 diabetes	9.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0009180	rosacea severity measurement
EFO:0007682	response to cetuximab
EFO:0006939	cup-to-disc ratio measurement
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	affects cotreatment, increases expression, decreases expression	2
Formaldehyde	decreases expression, increases expression	2
Nickel	increases expression	2
pirinixic acid	increases activity, affects binding, decreases expression	1
bisphenol A	decreases methylation	1
terbufos	decreases methylation	1
mono-(2-ethylhexyl)phthalate	increases expression	1
afimoxifene	decreases expression, decreases reaction	1
sulforaphane	decreases expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
Zoledronic Acid	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation	1
Cytarabine	decreases expression	1
Fonofos	decreases methylation	1
Estrogens	decreases expression, decreases reaction	1
Lipopolysaccharides	affects cotreatment, decreases expression	1
Parathion	decreases methylation	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Vincristine	decreases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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