PCED1A

Summary

PCED1A (PC-esterase domain containing 1A, HGNC:16212) is a protein-coding gene on chromosome 20p13, encoding PC-esterase domain-containing protein 1A (Q9H1Q7).

The protein encoded by this gene is a member of the GDSL/SGNH superfamily. Members of this family are hydrolytic enzymes with esterase and lipase activity and broad substrate specificity. This protein belongs to the Pmr5-Cas1p-esterase subfamily in that it contains the catalytic triad comprised of serine, aspartate and histidine and lacks two conserved regions (glycine after strand S2 and GxND motif). A pseudogene of this gene has been identified on the long arm of chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms.

Source: NCBI Gene 64773 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 74 total
• MANE Select transcript: NM_022760

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16212
Approved symbol	PCED1A
Name	PC-esterase domain containing 1A
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	bA12M19.1, FLJ22376
Ensembl gene	ENSG00000132635
Ensembl biotype	protein_coding
Entrez	64773

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 26 protein_coding, 1 retained_intron

ENST00000356872, ENST00000360652, ENST00000439542, ENST00000448755, ENST00000474714, ENST00000487501, ENST00000877260, ENST00000877261, ENST00000877262, ENST00000877263, ENST00000877264, ENST00000877265, ENST00000877266, ENST00000877267, ENST00000877268, ENST00000877269, ENST00000877270, ENST00000940412, ENST00000940413, ENST00000967738, ENST00000967739, ENST00000967740, ENST00000967741, ENST00000967742, ENST00000967743, ENST00000967744, ENST00000967745

RefSeq mRNA: 2 — MANE Select: NM_022760 NM_001271168, NM_022760

CCDS: CCDS13035, CCDS59442

Canonical transcript exons

ENST00000360652 — 8 exons

Exon	Start	End
ENSE00000858679	2836039	2836314
ENSE00001191737	2838844	2839082
ENSE00001874688	2840211	2840655
ENSE00003089902	2839192	2839271
ENSE00003094438	2839789	2839933
ENSE00003496190	2838596	2838746
ENSE00003508889	2835314	2835709
ENSE00003786629	2838232	2838478

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 97.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.3722 / max 169.5902, expressed in 1809 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186111	17.1747	1794
186113	2.8689	1286
186112	0.2961	106
186110	0.0325	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.77	gold quality
right lobe of thyroid gland	UBERON:0001119	97.06	gold quality
left lobe of thyroid gland	UBERON:0001120	96.87	gold quality
granulocyte	CL:0000094	96.30	gold quality
thyroid gland	UBERON:0002046	96.19	gold quality
right ovary	UBERON:0002118	95.82	gold quality
left ovary	UBERON:0002119	95.78	gold quality
endocervix	UBERON:0000458	95.66	gold quality
adenohypophysis	UBERON:0002196	95.57	gold quality
spleen	UBERON:0002106	95.48	gold quality
body of uterus	UBERON:0009853	95.45	gold quality
pituitary gland	UBERON:0000007	95.30	gold quality
left uterine tube	UBERON:0001303	95.18	gold quality
metanephros cortex	UBERON:0010533	94.80	gold quality
ectocervix	UBERON:0012249	94.23	gold quality
right lobe of liver	UBERON:0001114	94.08	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.99	gold quality
omental fat pad	UBERON:0010414	93.84	gold quality
peritoneum	UBERON:0002358	93.81	gold quality
lower esophagus mucosa	UBERON:0035834	93.63	gold quality
tibial nerve	UBERON:0001323	93.57	gold quality
right adrenal gland	UBERON:0001233	93.56	gold quality
mucosa of transverse colon	UBERON:0004991	93.49	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.48	gold quality
body of stomach	UBERON:0001161	93.42	gold quality
left adrenal gland cortex	UBERON:0035825	93.34	gold quality
right adrenal gland cortex	UBERON:0035827	93.28	gold quality
adipose tissue of abdominal region	UBERON:0007808	93.15	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.12	gold quality
left adrenal gland	UBERON:0001234	93.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting PCED1A, 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-4673	100.00	66.64	1490
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-1911-3P	99.15	66.17	528
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-5581-3P	98.55	70.31	1161
HSA-MIR-22-5P	97.67	68.92	1355
HSA-MIR-6872-3P	97.08	66.99	750
HSA-MIR-668-3P	96.18	65.80	673
HSA-MIR-6753-5P	94.70	64.08	470

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	fam113	ENSDARG00000002685
mus_musculus	Pced1a	ENSMUSG00000037773
rattus_norvegicus	Pced1a	ENSRNOG00000021221
caenorhabditis_elegans	D2030.8	WBGENE00008418

Paralogs (1): PCED1B (ENSG00000179715)

Protein

Protein identifiers

PC-esterase domain-containing protein 1A — Q9H1Q7 (reviewed: Q9H1Q7)

Alternative names: Protein FAM113A, Sarcoma antigen NY-SAR-23

All UniProt accessions (4): Q9H1Q7, S4R3X0, X6RC47, X6RFT7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PC-esterase family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9H1Q7-1	1	yes
Q9H1Q7-2	2
Q9H1Q7-3	3
Q9H1Q7-4	4

RefSeq proteins (2): NP_001258097, NP_073597* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR059235	Pced1a_dom	Domain

UniProt features (8 total): splice variant 4, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H1Q7-F1	70.52	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): RNGTGGGC_UNKNOWN, GGGTGGRR_PAX4_03, GGAANCGGAANY_UNKNOWN, USF_01, ELK1_01, USF_02, ACEVEDO_LIVER_CANCER_UP, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, MYCMAX_03, MAX_01, ARNT_01, WHITFIELD_CELL_CYCLE_G2, CIITA_TARGET_GENES, ELF2_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

270 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCED1A	SLX4IP	Q5VYV7	589
PCED1A	RBM26	Q5T8P6	538
PCED1A	VPS50	Q96JG6	507
PCED1A	RNF24	Q9Y225	498
PCED1A	POF1B	Q8WVV4	471
PCED1A	ESF1	Q9H501	459
PCED1A	ATRN	O75882	450
PCED1A	TRERF1	Q96PN7	418
PCED1A	VPS16	Q9H269	418
PCED1A	ZNF711	Q9Y462	418
PCED1A	PSMA8	Q8TAA3	398
PCED1A	APOOL	Q6UXV4	398
PCED1A	PPAN	Q9NQ55	396
PCED1A	PTPRA	P18433	380
PCED1A	ZNF326	Q5BKZ1	373

IntAct

26 interactions, top by confidence:

A	B	Type	Score
	PCED1A	psi-mi:“MI:0915”(physical association)	0.560
PCED1A	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
PCED1A	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.560
PCED1A	NOTCH2NLA	psi-mi:“MI:0915”(physical association)	0.560
PCED1A		psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	PCED1A	psi-mi:“MI:0915”(physical association)	0.560
env	PCED1A	psi-mi:“MI:0915”(physical association)	0.490
PCED1A	env	psi-mi:“MI:0915”(physical association)	0.490
PCED1A	FXR1	psi-mi:“MI:0915”(physical association)	0.370
PLSCR1	PCED1A	psi-mi:“MI:0915”(physical association)	0.370
PCED1A	HSPD1	psi-mi:“MI:0914”(association)	0.350
CAV1	PCED1A	psi-mi:“MI:0915”(physical association)	0.000
	PCED1A	psi-mi:“MI:0915”(physical association)	0.000
CDK2	PCED1A	psi-mi:“MI:0915”(physical association)	0.000
TNFRSF14	PCED1A	psi-mi:“MI:0915”(physical association)	0.000
UBE2M	PCED1A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (15): KRTAP10-7 (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-3 (Two-hybrid), NOTCH2NL (Two-hybrid), PCED1A (Two-hybrid), PCED1A (Affinity Capture-MS), PCED1A (Affinity Capture-MS), PCED1A (Two-hybrid), PKP2 (Affinity Capture-MS), RAP1B (Affinity Capture-MS), S100PBP (Affinity Capture-MS), LONP1 (Affinity Capture-MS), TEX10 (Affinity Capture-MS), CPSF7 (Affinity Capture-MS), HSPD1 (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	2
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1634 predictions. Top by Δscore:

Variant	Effect	Δscore
20:2838627:T:A	donor_gain	1.0000
20:2838744:TAT:T	acceptor_gain	1.0000
20:2839272:C:CC	acceptor_gain	1.0000
20:2839787:A:AC	donor_gain	1.0000
20:2839788:C:CA	donor_gain	1.0000
20:2839813:A:AC	donor_gain	1.0000
20:2839814:C:CC	donor_gain	1.0000
20:2838366:C:CT	acceptor_gain	0.9900
20:2838628:C:A	donor_gain	0.9900
20:2838742:CATAT:C	acceptor_gain	0.9900
20:2838743:ATAT:A	acceptor_gain	0.9900
20:2838746:TC:T	acceptor_loss	0.9900
20:2838747:C:CC	acceptor_gain	0.9900
20:2838750:T:TC	acceptor_gain	0.9900
20:2838754:A:C	acceptor_gain	0.9900
20:2838758:C:CT	acceptor_gain	0.9900
20:2838854:C:A	donor_gain	0.9900
20:2838946:G:GC	acceptor_gain	0.9900
20:2839185:C:A	donor_gain	0.9900
20:2839186:CCTCA:C	donor_loss	0.9900
20:2839187:CTCAC:C	donor_loss	0.9900
20:2839189:CA:C	donor_loss	0.9900
20:2839190:A:C	donor_loss	0.9900
20:2839270:AACTG:A	acceptor_loss	0.9900
20:2839271:ACTG:A	acceptor_loss	0.9900
20:2839272:CTGG:C	acceptor_loss	0.9900
20:2839273:T:A	acceptor_loss	0.9900
20:2839781:GCACT:G	donor_loss	0.9900
20:2839782:CACTC:C	donor_loss	0.9900
20:2839783:AC:A	donor_loss	0.9900

AlphaMissense

2957 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:2838331:G:C	H248D	0.999
20:2838652:A:G	W180R	0.999
20:2838652:A:T	W180R	0.999
20:2838855:C:A	W144C	0.999
20:2838855:C:G	W144C	0.999
20:2838857:A:G	W144R	0.999
20:2838857:A:T	W144R	0.999
20:2838951:G:C	F112L	0.999
20:2838951:G:T	F112L	0.999
20:2838953:A:G	F112L	0.999
20:2838998:G:T	R97S	0.999
20:2838328:A:G	W249R	0.998
20:2838328:A:T	W249R	0.998
20:2838422:A:C	S217R	0.998
20:2838422:A:T	S217R	0.998
20:2838424:T:G	S217R	0.998
20:2838853:T:G	D145A	0.998
20:2838952:A:G	F112S	0.998
20:2838957:G:C	F110L	0.998
20:2838957:G:T	F110L	0.998
20:2838959:A:G	F110L	0.998
20:2838997:C:G	R97P	0.998
20:2839002:C:A	E95D	0.998
20:2839002:C:G	E95D	0.998
20:2839010:A:G	Y93H	0.998
20:2839061:C:G	D76H	0.998
20:2839252:C:A	K48N	0.998
20:2839252:C:G	K48N	0.998
20:2839264:C:A	R44S	0.998
20:2839264:C:G	R44S	0.998

dbSNP variants (sampled 300 via entrez): RS1000067326 (20:2841068 C>T), RS1000133986 (20:2840141 G>A), RS1000250978 (20:2835310 G>A), RS1000390265 (20:2840592 G>A), RS1000523206 (20:2840764 C>T), RS1000677106 (20:2840464 A>C,G,T), RS1001117525 (20:2839977 G>A), RS1001191158 (20:2838343 G>GT), RS1001280369 (20:2841583 C>T), RS1001284692 (20:2836047 G>A), RS1001403895 (20:2836380 C>T), RS1001639528 (20:2836289 C>T), RS1001791816 (20:2841916 G>A), RS1001797836 (20:2842171 A>G), RS1002145430 (20:2842442 C>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

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation	1
beta-lapachone	decreases expression	1
sodium arsenite	decreases expression, increases abundance	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression	1
benzo(e)pyrene	increases methylation	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	decreases expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Manganese	increases abundance, increases expression	1
Methapyrilene	increases methylation	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Sodium Dodecyl Sulfate	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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