PABPC3

Summary

PABPC3 (poly(A) binding protein cytoplasmic 3, HGNC:8556) is a protein-coding gene on chromosome 13q12.13, encoding Polyadenylate-binding protein 3 (Q9H361). Binds the poly(A) tail of mRNA.

Messenger RNA stability and translation initiation are extensively under the control of poly(A)-binding proteins (PABP). See PABPC1 (MIM 604679) for background information.

Source: NCBI Gene 5042 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_030979

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8556
Approved symbol	PABPC3
Name	poly(A) binding protein cytoplasmic 3
Location	13q12.13
Locus type	gene with protein product
Status	Approved
Aliases	PABP3, tPABP
Ensembl gene	ENSG00000151846
Ensembl biotype	protein_coding
OMIM	604680
Entrez	5042

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000281589

RefSeq mRNA: 1 — MANE Select: NM_030979 NM_030979

CCDS: CCDS9311

Canonical transcript exons

ENST00000281589 — 1 exons

Exon	Start	End
ENSE00001425120	25096136	25099254

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 99.92.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5336 / max 120.3647, expressed in 199 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
206978	0.3249	164
134453	0.2063	23
134454	0.0023	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	99.92	gold quality
epithelium of nasopharynx	UBERON:0001951	99.81	gold quality
amniotic fluid	UBERON:0000173	99.80	gold quality
nasopharynx	UBERON:0001728	99.80	gold quality
pancreatic ductal cell	CL:0002079	99.78	gold quality
esophagus squamous epithelium	UBERON:0006920	99.78	gold quality
seminal vesicle	UBERON:0000998	99.75	gold quality
pylorus	UBERON:0001166	99.73	gold quality
cervix squamous epithelium	UBERON:0006922	99.73	gold quality
squamous epithelium	UBERON:0006914	99.71	gold quality
mammary duct	UBERON:0001765	99.68	gold quality
tongue squamous epithelium	UBERON:0006919	99.67	gold quality
buccal mucosa cell	CL:0002336	99.64	gold quality
oral cavity	UBERON:0000167	99.63	gold quality
mammalian vulva	UBERON:0000997	99.63	gold quality
epithelium of esophagus	UBERON:0001976	99.63	gold quality
epithelium of mammary gland	UBERON:0003244	99.63	gold quality
tibia	UBERON:0000979	99.60	gold quality
nipple	UBERON:0002030	99.59	gold quality
germinal epithelium of ovary	UBERON:0001304	99.58	gold quality
trabecular bone tissue	UBERON:0002483	99.56	gold quality
upper leg skin	UBERON:0004262	99.55	gold quality
urethra	UBERON:0000057	99.54	gold quality
cartilage tissue	UBERON:0002418	99.54	gold quality
penis	UBERON:0000989	99.53	gold quality
gingiva	UBERON:0001828	99.53	gold quality
mucosa of paranasal sinus	UBERON:0005030	99.53	gold quality
palpebral conjunctiva	UBERON:0001812	99.51	gold quality
pharyngeal mucosa	UBERON:0000355	99.50	gold quality
gingival epithelium	UBERON:0001949	99.50	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	19.55
E-CURD-11	no	0.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting PABPC3, 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-186-5P	99.99	70.83	3707
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-8061	99.63	69.44	1411
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-502-5P	98.77	66.51	906
HSA-MIR-6731-3P	98.61	67.86	749
HSA-MIR-6841-3P	98.08	66.54	604
HSA-MIR-8055	97.62	66.09	1023
HSA-MIR-4759	97.39	65.86	608
HSA-MIR-582-3P	96.69	67.38	1019
HSA-MIR-6760-3P	96.35	68.31	1001
HSA-MIR-423-3P	95.99	67.75	62
HSA-MIR-3117-3P	95.96	67.82	473
HSA-MIR-3200-3P	95.41	64.23	396
HSA-MIR-6503-3P	93.87	66.39	348
HSA-MIR-516A-5P	93.40	64.96	90

Literature-anchored findings (GeneRIF, showing 2)

• molecular cloning and expression in testis (PMID:11328870)
• PABPC3 decreased expression in in infertile men with non-obstructive azoospermia (PMID:26843391)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pabpc6	ENSMUSG00000046173
mus_musculus	Pabpc2	ENSMUSG00000051732
rattus_norvegicus	Pabpc2	ENSRNOG00000014527
rattus_norvegicus	Pabpc6	ENSRNOG00000017367

Paralogs (24): ELAVL1 (ENSG00000066044), PABPC1 (ENSG00000070756), RBMS2 (ENSG00000076067), PABPC4 (ENSG00000090621), PABPC1L (ENSG00000101104), ELAVL2 (ENSG00000107105), RBM24 (ENSG00000112183), TARDBP (ENSG00000120948), HNRNPR (ENSG00000125944), RBM38 (ENSG00000132819), SYNCRIP (ENSG00000135316), SF3B4 (ENSG00000143368), RBMS3 (ENSG00000144642), RBMS1 (ENSG00000153250), RBM45 (ENSG00000155636), ELAVL4 (ENSG00000162374), PABPC5 (ENSG00000174740), PUF60 (ENSG00000179950), PABPC1L2B (ENSG00000184388), PABPC1L2A (ENSG00000186288), RBM34 (ENSG00000188739), ELAVL3 (ENSG00000196361), RBM14 (ENSG00000239306), PABPC4L (ENSG00000254535)

Protein

Protein identifiers

Polyadenylate-binding protein 3 — Q9H361 (reviewed: Q9H361)

Alternative names: Testis-specific poly(A)-binding protein

All UniProt accessions (2): Q9H361, Q5VX58

UniProt curated annotations — full annotation on UniProt →

Function. Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Binds poly(A) with a slightly lower affinity as compared to PABPC1.

Subcellular location. Cytoplasm.

Tissue specificity. Testis specific.

Similarity. Belongs to the polyadenylate-binding protein type-1 family.

RefSeq proteins (1): NP_112241* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR002004	PABP_HYD_C	Domain
IPR003954	RRM_euk-type	Domain
IPR006515	PABP_1234	Family
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034364	PABP_RRM1	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR036053	PABP-dom	Homologous_superfamily
IPR045305	RRM2_I_PABPs	Domain

Pfam: PF00076, PF00658

UniProt features (24 total): modified residue 9, domain 5, helix 5, sequence conflict 2, chain 1, cross-link 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
4IVE	X-RAY DIFFRACTION	2.3
2D9P	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H361-F1	76.92	0.49

Functional residue map

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

Post-translational modifications (10): 426, 430, 449, 501, 513, 361, 140, 315, 361, 364

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, SP3_Q3, GCAAGGA_MIR502, BLALOCK_ALZHEIMERS_DISEASE_UP, ATTCTTT_MIR186, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, HNF1_01, MODULE_48, ACCGAGC_MIR423, MODULE_95, GRADE_COLON_AND_RECTAL_CANCER_UP, GOCC_CYTOPLASMIC_STRESS_GRANULE, SPZ1_01, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOCC_RIBONUCLEOPROTEIN_COMPLEX

GO Biological Process (1): mRNA metabolic process (GO:0016071)

GO Molecular Function (6): mRNA 3’-UTR binding (GO:0003730), poly(A) binding (GO:0008143), poly(U) RNA binding (GO:0008266), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), cytoplasmic stress granule (GO:0010494), extracellular exosome (GO:0070062), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cellular anatomical structure	2
RNA metabolic process	1
mRNA binding	1
poly-purine tract binding	1
poly-pyrimidine tract binding	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoplasm	1
cytoplasmic ribonucleoprotein granule	1
extracellular vesicle	1
protein-containing complex	1

Protein interactions and networks

STRING

1934 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PABPC3	PABPN1	Q86U42	856
PABPC3	EIF4G1	Q04637	801
PABPC3	EIF4E	P06730	715
PABPC3	PAIP1	Q9H074	668
PABPC3	EIF4A1	P04765	654
PABPC3	EIF4A2	Q14240	653
PABPC3	TNRC6A	Q8NDV7	610
PABPC3	PAN2	Q504Q3	548
PABPC3	RRM1	P23921	523
PABPC3	PAIP2	Q9BPZ3	521
PABPC3	TDRD7	Q8NHU6	503
PABPC3	ACTB	P02570	490
PABPC3	KPNB1	Q14974	490
PABPC3	HSPA9	P30036	481
PABPC3	UBA1	P22314	477

IntAct

70 interactions, top by confidence:

A	B	Type	Score
ATXN2	PABPC1	psi-mi:“MI:0915”(physical association)	0.820
YBX1	HNRNPR	psi-mi:“MI:0914”(association)	0.770
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
RUVBL1	POLR3A	psi-mi:“MI:0914”(association)	0.640
TENT5D	PABPC3	psi-mi:“MI:0915”(physical association)	0.560
PABPC3	WFS1	psi-mi:“MI:0915”(physical association)	0.560
PABPC3	JPH3	psi-mi:“MI:0915”(physical association)	0.560
GALK2	POTEF	psi-mi:“MI:0914”(association)	0.530
DDX6	MCRIP1	psi-mi:“MI:0914”(association)	0.510
rep	PABPC3	psi-mi:“MI:0915”(physical association)	0.490
PABPC3	CALR	psi-mi:“MI:0915”(physical association)	0.400
	GNAT3	psi-mi:“MI:0915”(physical association)	0.400
EIF4ENIF1	RPLP0	psi-mi:“MI:0915”(physical association)	0.400
EIF4ENIF1	PABPC1	psi-mi:“MI:0915”(physical association)	0.400
EIF4ENIF1	MCRIP1	psi-mi:“MI:0915”(physical association)	0.400
DCP1B	PABPC1	psi-mi:“MI:0915”(physical association)	0.400
ACTA1	PABPC1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (122): PABPC3 (Affinity Capture-MS), NHP2L1 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PABPC3 (Co-fractionation), PAN3 (Co-fractionation), PAPOLA (Co-fractionation), PEBP1 (Co-fractionation), PABPC3 (Affinity Capture-MS), PABPC3 (Affinity Capture-MS)

ESM2 similar proteins: A1CRM1, A1D4K4, A2Q848, A3LXL0, A4QUF0, A5DM21, A5DW14, F1QB54, O22173, O43390, O60506, O64380, P04147, P0CP46, P0CP47, P11940, P20965, P21187, P29341, P31209, P42731, P61286, Q05196, Q0CR95, Q0U1G2, Q13310, Q1DXH0, Q2GSX8, Q2UK72, Q4P8R9, Q4WK03, Q54BM2, Q5AI15, Q5B630, Q5R8F7, Q6BI95, Q6CDH3, Q6CSV3, Q6DEY7, Q6FKG4

Diamond homologs: A0A0D1C8Z4, A1A5R1, A2A5N3, A3LXL0, A4F5G6, A5A6M3, A5DW14, A6NFN3, A6QPR6, F1QB54, F4HT49, O04319, O13845, O35698, O43251, O93235, P0CB38, P11940, P19682, P19683, P19684, P20965, P28644, P29341, P38159, P42731, P49313, P49314, P60824, P60825, P60826, P61286, P62995, P62996, P62997, Q04836, Q08935, Q08937, Q09511, Q0VD23

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
PABPC3	“up-regulates quantity by stabilization”	“messenger RNA”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 70 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Extra-nuclear estrogen signaling	5	16.1×	4e-03
PIP3 activates AKT signaling	7	8.8×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of translation	6	18.4×	6e-04
regulation of apoptotic process	6	7.8×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

4153 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:25097138:T:C	F314L	0.970
13:25097140:T:A	F314L	0.970
13:25097140:T:G	F314L	0.970
13:25097207:T:C	F337L	0.966
13:25097209:T:A	F337L	0.966
13:25097209:T:G	F337L	0.966
13:25097201:T:C	F335L	0.961
13:25097203:T:A	F335L	0.961
13:25097203:T:G	F335L	0.961
13:25096895:T:C	F233L	0.956
13:25096897:T:A	F233L	0.956
13:25096897:T:G	F233L	0.956
13:25097216:T:C	F340L	0.928
13:25097218:C:A	F340L	0.928
13:25097218:C:G	F340L	0.928
13:25097205:G:A	G336D	0.923
13:25097147:T:C	F317L	0.918
13:25097149:T:A	F317L	0.918
13:25097149:T:G	F317L	0.918
13:25097211:T:A	V338E	0.910
13:25096901:T:C	F235L	0.907
13:25096903:T:A	F235L	0.907
13:25096903:T:G	F235L	0.907
13:25097139:T:C	F314S	0.883
13:25097091:T:A	V298E	0.878
13:25097094:A:T	K299I	0.876
13:25096910:T:C	F238L	0.872
13:25096912:T:A	F238L	0.872
13:25096912:T:G	F238L	0.872
13:25096373:T:C	F59L	0.870

dbSNP variants (sampled 300 via entrez): RS1000034110 (13:25094767 C>G,T), RS1000635311 (13:25096005 G>A,T), RS1002673588 (13:25096048 C>A), RS1003216540 (13:25094897 T>A,C,G), RS1003621733 (13:25094608 G>A), RS1004483660 (13:25095735 A>C), RS1004813992 (13:25095501 T>G), RS1005111952 (13:25099287 C>T), RS1005575626 (13:25099519 T>A), RS1005773294 (13:25095182 G>A), RS1008966264 (13:25099656 G>A), RS1009243830 (13:25094400 C>T), RS1009259939 (13:25099147 C>G,T), RS1009746122 (13:25099612 C>G), RS1009968412 (13:25097795 C>A,G)

Disease associations

OMIM: gene MIM:604680 | 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
GCST005576_20	Intracranial aneurysm	7.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases abundance, decreases expression, affects cotreatment, decreases methylation	3
ginger extract	affects cotreatment, affects expression, increases abundance	1
lead acetate	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
sodium arsenite	increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
cupric oxide	decreases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
CGP 52608	increases reaction, affects binding	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Decitabine	affects reaction, decreases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation, increases methylation	1
Arsenic	increases expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Catechin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diazinon	decreases methylation	1
Furaldehyde	affects localization, increases expression, affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Oils, Volatile	affects cotreatment, affects expression, increases abundance	1
Phthalic Acids	decreases methylation	1
Sodium Chloride	affects cotreatment, affects localization, decreases expression, increases expression	1
Vitamin E	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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