PABPC1L

gene
On this page

Also known as dJ1069P2.3PABPC1L1ePAB

Summary

PABPC1L (poly(A) binding protein cytoplasmic 1 like, HGNC:15797) is a protein-coding gene on chromosome 20q13.12, encoding Polyadenylate-binding protein 1-like (Q4VXU2). Poly(A)-binding protein involved in oocyte maturation and early embryo development.

This gene belongs to the polyadenylate-binding protein type-1 family of proteins. Members of this family bind to the polyA tails of mRNAs to regulate mRNA stability and translation. The mouse ortholog of this gene is required for female fertility. In human, expression of a functional protein is regulated by alternative splicing. The protein-coding splice variant for this gene is abundantly expressed in human oocytes, while a noncoding splice variant subject to nonsense-mediated decay is the predominant splice variant expressed in somatic tissues.

Source: NCBI Gene 80336 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 121 total — 10 pathogenic
  • Phenotypes (HPO): 7
  • MANE Select transcript: NM_001372179

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15797
Approved symbolPABPC1L
Namepoly(A) binding protein cytoplasmic 1 like
Location20q13.12
Locus typegene with protein product
StatusApproved
AliasesdJ1069P2.3, PABPC1L1, ePAB
Ensembl geneENSG00000101104
Ensembl biotypeprotein_coding
OMIM621055
Entrez80336

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 7 protein_coding, 6 nonsense_mediated_decay, 4 retained_intron, 4 protein_coding_CDS_not_defined

ENST00000217073, ENST00000217074, ENST00000217075, ENST00000255136, ENST00000372819, ENST00000372822, ENST00000372824, ENST00000372826, ENST00000465761, ENST00000474208, ENST00000476056, ENST00000479873, ENST00000482486, ENST00000489068, ENST00000490798, ENST00000537323, ENST00000674244, ENST00000674318, ENST00000674382, ENST00000925475, ENST00000925476

RefSeq mRNA: 1 — MANE Select: NM_001372179 NM_001372179

CCDS: CCDS42878

Canonical transcript exons

ENST00000217073 — 15 exons

ExonStartEnd
ENSE000015953114493234244932432
ENSE000016214774491890644919045
ENSE000016934714491266044912853
ENSE000016995434493912644939316
ENSE000017105104491918344919277
ENSE000017429434491675644916871
ENSE000017913004492159444921731
ENSE000027265684491006044910336
ENSE000035043664493806144938191
ENSE000035154304492416144924256
ENSE000035303644493663744936730
ENSE000035535354493867444938748
ENSE000036258994493539144935497
ENSE000036471594493046044930726
ENSE000038986344493305744933185

Expression profiles

Bgee: expression breadth ubiquitous, 210 present calls, max score 96.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.1069 / max 232.4783, expressed in 1481 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1847628.10671461
1847630.5007273
1847640.4995261

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
body of pancreasUBERON:000115096.37gold quality
right lobe of liverUBERON:000111496.26gold quality
left lobe of thyroid glandUBERON:000112096.26gold quality
right lobe of thyroid glandUBERON:000111995.98gold quality
right uterine tubeUBERON:000130295.95gold quality
metanephros cortexUBERON:001053395.53gold quality
thyroid glandUBERON:000204695.25gold quality
adenohypophysisUBERON:000219693.89gold quality
lower esophagus mucosaUBERON:003583493.38gold quality
left ovaryUBERON:000211993.13gold quality
right ovaryUBERON:000211892.91gold quality
pituitary glandUBERON:000000792.89gold quality
pancreatic ductal cellCL:000207992.78silver quality
granulocyteCL:000009491.99gold quality
metanephrosUBERON:000008191.35gold quality
body of stomachUBERON:000116190.94gold quality
spleenUBERON:000210690.84gold quality
oocyteCL:000002390.78gold quality
cortex of kidneyUBERON:000122590.47gold quality
upper lobe of left lungUBERON:000895290.45gold quality
upper arm skinUBERON:000426390.32gold quality
stromal cell of endometriumCL:000225590.13gold quality
minor salivary glandUBERON:000183090.13gold quality
mucosa of transverse colonUBERON:000499189.66gold quality
descending thoracic aortaUBERON:000234589.53gold quality
small intestine Peyer’s patchUBERON:000345489.47gold quality
right lungUBERON:000216789.42gold quality
ascending aortaUBERON:000149689.32gold quality
right adrenal gland cortexUBERON:003582789.29gold quality
thoracic aortaUBERON:000151589.26gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.22

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

  • Human EPAB mRNA is detected in ovaries, testes and several somatic tissues including pancreas, liver and thymus, and EPAB is the predominant poly(A) binding protein in immature (germinal vesicle) and mature (metaphase II) oocytes. (PMID:18716053)
  • EPAB decreased expression in in infertile men with non-obstructive azoospermia (PMID:26843391)
  • Identification of nonfunctional PABPC1L causing oocyte maturation abnormalities and early embryonic arrest in female primary infertility. (PMID:37723834)
  • Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage. (PMID:38177974)
  • PABPC1L Induces IDO1 to Promote Tryptophan Metabolism and Immune Suppression in Renal Cell Carcinoma. (PMID:38382068)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriopabpc1lENSDARG00000002597
mus_musculusPabpc1lENSMUSG00000054582
rattus_norvegicusPabpc1lENSRNOG00000012750

Paralogs (24): ELAVL1 (ENSG00000066044), PABPC1 (ENSG00000070756), RBMS2 (ENSG00000076067), PABPC4 (ENSG00000090621), ELAVL2 (ENSG00000107105), RBM24 (ENSG00000112183), TARDBP (ENSG00000120948), HNRNPR (ENSG00000125944), RBM38 (ENSG00000132819), SYNCRIP (ENSG00000135316), SF3B4 (ENSG00000143368), RBMS3 (ENSG00000144642), PABPC3 (ENSG00000151846), 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 1-likeQ4VXU2 (reviewed: Q4VXU2)

Alternative names: Embryonic poly(A)-binding protein, Poly(A) binding protein cytoplasmic 1 like

All UniProt accessions (10): Q4VXU2, A0A6I8PIK9, A0A6I8PL98, A0A6I8PLA1, A0A6I8PS38, A0A6Q8JFT6, A0A6Q8JFV4, H0Y386, Q4VXT5, Q4VXT8

UniProt curated annotations — full annotation on UniProt →

Function. Poly(A)-binding protein involved in oocyte maturation and early embryo development. It is required for cytosolic mRNA polyadenylation and translational activation of maternally stored mRNA in oocytes.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in ovary and testis. Also expressed in pancreas, liver and thymus, and at lower levels in other somatic tissues including brain and lung.

Disease relevance. Oocyte/zygote/embryo maturation arrest 22 (OZEMA22) [MIM:621093] An autosomal recessive, female infertility disorder characterized by oocyte maturation arrest, primarily at the germinal vesicle or metaphase I stages. In some cases, oocyte reaching the metaphase II stage can be fertilized, but embryo development is arrested before the 4-cell stage. The disease is caused by variants affecting the gene represented in this entry.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q4VXU2-11yes
Q4VXU2-22

RefSeq proteins (1): NP_001359108* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR002004PABP_HYD_CDomain
IPR003954RRM_euk-typeDomain
IPR006515PABP_1234Family
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR034364PABP_RRM1Domain
IPR035979RBD_domain_sfHomologous_superfamily
IPR036053PABP-domHomologous_superfamily
IPR045305RRM2_I_PABPsDomain

Pfam: PF00076, PF00658

UniProt features (19 total): sequence variant 10, domain 5, splice variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q4VXU2-F176.410.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): GOBP_OOGENESIS, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_ANATOMICAL_STRUCTURE_MATURATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_CELL_MATURATION, TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_OOCYTE_MATURATION, GOBP_OOCYTE_DIFFERENTIATION, GOBP_FEMALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_POSITIVE_REGULATION_OF_TRANSLATION, GOCC_CYTOPLASMIC_STRESS_GRANULE, GOBP_REGULATION_OF_TRANSLATION

GO Biological Process (6): oocyte maturation (GO:0001556), positive regulation of translation (GO:0045727), cell differentiation (GO:0030154), oogenesis (GO:0048477), regulation of macromolecule metabolic process (GO:0060255), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (5): 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)

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of metabolic process2
cellular anatomical structure2
developmental process involved in reproduction1
cell maturation1
oocyte development1
translation1
regulation of translation1
positive regulation of gene expression1
positive regulation of protein metabolic process1
cellular developmental process1
germ cell development1
female gamete generation1
macromolecule metabolic process1
primary metabolic process1
mRNA binding1
poly-purine tract binding1
poly-pyrimidine tract binding1
binding1
nucleic acid binding1
intracellular membrane-bounded organelle1
cytoplasm1
cytoplasmic ribonucleoprotein granule1
extracellular vesicle1
protein-containing complex1
intracellular anatomical structure1

Protein interactions and networks

STRING

1662 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PABPC1LPABPN1Q86U42870
PABPC1LEIF4G1Q04637798
PABPC1LCPEB1Q9BZB8762
PABPC1LTENT2Q6PIY7719
PABPC1LEIF4EP06730703
PABPC1LPARNO95453680
PABPC1LSYMPKQ92797654
PABPC1LEIF4E1BA6NMX2648
PABPC1LEIF4A1P04765642
PABPC1LEIF4A2Q14240642
PABPC1LDDX6P26196634
PABPC1LLSM14BQ9BX40616
PABPC1LPNLDC1Q8NA58602
PABPC1LTNRC6AQ8NDV7601
PABPC1LPAN2Q504Q3554
PABPC1LPAIP2Q9BPZ3554

IntAct

19 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
PAIP2BCASC3psi-mi:“MI:0914”(association)0.530
GSPT2IGF2BP3psi-mi:“MI:0914”(association)0.530
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
NPHNRNPCL1psi-mi:“MI:0914”(association)0.350
PAIP1H2AXpsi-mi:“MI:0914”(association)0.350
BMI1MEIS3P1psi-mi:“MI:0914”(association)0.350
ESR2psi-mi:“MI:0914”(association)0.350
GCM1LONP1psi-mi:“MI:0914”(association)0.350
PABPC5APOBEC3DEpsi-mi:“MI:0914”(association)0.350
PAIP1CASC3psi-mi:“MI:0914”(association)0.350
ESR1TUBAL3psi-mi:“MI:0914”(association)0.350

BioGRID (48): PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-RNA), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS), PABPC1L (Affinity Capture-MS)

ESM2 similar proteins: A2A5N3, F1QB54, F4HT49, G5EFS2, O04319, O22173, O43347, O64380, P11940, P20965, P21187, P29341, P31209, P42731, P61286, P70318, P86049, Q05196, Q08BH5, Q0P4R6, Q13310, Q22708, Q4VXU2, Q503H1, Q54BM2, Q5R8F7, Q5R9H4, Q5YD48, Q61474, Q6DCB7, Q6DEY7, Q6GR16, Q6IP09, Q6IQE0, Q7T1H5, Q8GZ26, Q8K3P4, Q8LFS6, Q8TBY0, Q920Q6

Diamond homologs: A0A0D1DWZ5, A0JM51, A1CRM1, A1D4K4, A2A5N3, A2Q848, A3LXL0, A4IIM2, A4QUF0, A5DW14, F4HT49, O04319, O14102, O22173, O57406, O64380, O95319, O97018, P04147, P0CB38, P0CP46, P0CP47, P20965, P21187, P28659, P29558, P31209, P32588, P39697, P42731, P60047, P60048, P60049, P60050, Q08E07, Q09442, Q0CR95, Q0U1G2, Q13310, Q15427

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic10
Likely pathogenic0
Uncertain significance84
Likely benign7
Benign1

Top pathogenic / likely-pathogenic (10)

Variant IDHGVSClassification
1172840NM_001372179.1(PABPC1L):c.1037C>T (p.Ala346Val)Pathogenic
3602609NM_001372179.1(PABPC1L):c.290G>A (p.Gly97Asp)Pathogenic
3602610NM_001372179.1(PABPC1L):c.526C>T (p.Arg176Ter)Pathogenic
3602611NM_001372179.1(PABPC1L):c.958dup (p.Ile320fs)Pathogenic
3602612NM_001372179.1(PABPC1L):c.410C>T (p.Ser137Phe)Pathogenic
3602613NM_001372179.1(PABPC1L):c.1121G>A (p.Arg374Gln)Pathogenic
3602614NM_001372179.1(PABPC1L):c.536G>A (p.Arg179Gln)Pathogenic
3602615NM_001372179.1(PABPC1L):c.793C>T (p.Arg265Trp)Pathogenic
3602616NM_001372179.1(PABPC1L):c.1201C>T (p.Gln401Ter)Pathogenic
3602617A346VPathogenic

SpliceAI

3683 predictions. Top by Δscore:

VariantEffectΔscore
20:44910333:GACG:Gdonor_gain1.0000
20:44910334:ACGGT:Adonor_loss1.0000
20:44910335:CGGT:Cdonor_loss1.0000
20:44910336:GGT:Gdonor_loss1.0000
20:44910337:G:GGdonor_gain1.0000
20:44910337:GTGAG:Gdonor_loss1.0000
20:44910338:T:Adonor_loss1.0000
20:44912653:T:Aacceptor_gain1.0000
20:44912654:GTCCA:Gacceptor_loss1.0000
20:44912655:TCCAG:Tacceptor_loss1.0000
20:44912656:CCAGC:Cacceptor_loss1.0000
20:44912657:CAGCG:Cacceptor_loss1.0000
20:44912658:A:AGacceptor_gain1.0000
20:44912658:AG:Aacceptor_loss1.0000
20:44912658:AGC:Aacceptor_gain1.0000
20:44912658:AGCG:Aacceptor_gain1.0000
20:44912659:G:GTacceptor_gain1.0000
20:44912659:GC:Gacceptor_gain1.0000
20:44912659:GCG:Gacceptor_gain1.0000
20:44912659:GCGG:Gacceptor_gain1.0000
20:44912659:GCGGA:Gacceptor_gain1.0000
20:44912661:G:Aacceptor_gain1.0000
20:44912806:GCTT:Gdonor_gain1.0000
20:44912850:CAAGG:Cdonor_loss1.0000
20:44912851:AAG:Adonor_loss1.0000
20:44912852:AG:Adonor_loss1.0000
20:44912853:GG:Gdonor_loss1.0000
20:44912854:GTAGA:Gdonor_loss1.0000
20:44912855:T:Gdonor_loss1.0000
20:44916870:GT:Gdonor_gain1.0000

AlphaMissense

4055 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:44916796:T:AV143D1.000
20:44924181:G:CK299N1.000
20:44924181:G:TK299N1.000
20:44930490:T:CF335L1.000
20:44930492:T:AF335L1.000
20:44930492:T:GF335L1.000
20:44930496:T:CF337L1.000
20:44930498:T:AF337L1.000
20:44930498:T:GF337L1.000
20:44916790:G:AG141D0.999
20:44916792:T:CF142L0.999
20:44916794:T:AF142L0.999
20:44916794:T:GF142L0.999
20:44924171:T:GL296W0.999
20:44924173:T:GY297D0.999
20:44924177:T:AV298E0.999
20:44924179:A:GK299E0.999
20:44924184:T:AN300K0.999
20:44924184:T:GN300K0.999
20:44924213:T:CL310P0.999
20:44924224:T:CF314L0.999
20:44924225:T:CF314S0.999
20:44924226:C:AF314L0.999
20:44924226:C:GF314L0.999
20:44924237:G:AG318E0.999
20:44930494:G:AG336D0.999
20:44930497:T:CF337S0.999
20:44930497:T:GF337C0.999
20:44930500:T:AV338E0.999
20:44930590:C:AA368D0.999

dbSNP variants (sampled 300 via entrez): RS1000083379 (20:44928237 A>T), RS1000089307 (20:44916116 G>A), RS1000114583 (20:44927936 G>A), RS1000160191 (20:44914506 C>CATG), RS1000220458 (20:44937332 C>A,T), RS1000261530 (20:44917189 G>A,T), RS1000472941 (20:44922600 A>G), RS1000537729 (20:44910628 C>G), RS1000792824 (20:44934181 T>C), RS1001004140 (20:44928369 G>A), RS1001051874 (20:44910289 G>A), RS1001248942 (20:44917777 G>A,T), RS1001362876 (20:44917458 A>G), RS1001379593 (20:44939657 T>C), RS1001500048 (20:44917345 C>T)

Disease associations

OMIM: gene MIM:621055 | disease phenotypes: MIM:615774, MIM:621093

GenCC curated gene-disease

Mondo (2): female infertility due to zona pellucida defect (MONDO:0014342), oocyte/zygote/embryo maturation arrest 22 (MONDO:0976137)

Orphanet (1): Female infertility due to zona pellucida defect (Orphanet:404466)

HPO phenotypes

7 total (7 of 7 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0008222Female infertility
HP:0011462Young adult onset
HP:0025708Early young adult onset
HP:0031516Metaphase I oocyte maturation arrest
HP:0033712Repeated implantation failure
HP:0034914Oocyte maturation arrest

GWAS associations

5 associations (top):

StudyTraitp-value
GCST004618_52White blood cell count (basophil)7.000000e-09
GCST006947_59Feeling fed-up1.000000e-08
GCST007565_171Morning person4.000000e-15
GCST007576_251Chronotype4.000000e-15
GCST008103_18Bipolar disorder1.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0005090basophil count
EFO:0009588feeling “fed-up” measurement
EFO:0008328chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression4
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression3
bisphenol Faffects cotreatment, increases methylation, decreases expression2
bisphenol Aaffects expression, decreases methylation2
Air Pollutantsaffects expression, increases abundance, increases expression2
Arsenicaffects methylation, affects cotreatment, increases abundance, increases expression2
Benzo(a)pyrenedecreases methylation, increases expression2
Silicon Dioxideincreases expression, decreases expression2
Tetrachlorodibenzodioxindecreases expression2
Valproic Acidincreases expression2
Cadmium Chloridedecreases expression, increases abundance2
Particulate Matterincreases abundance, increases expression, affects cotreatment, affects expression, decreases expression2
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
trichostatin Aincreases expression1
beta-lapachonedecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydeincreases expression1
isobutyl alcoholincreases abundance, affects cotreatment, decreases expression1
perfluorooctane sulfonic acidincreases expression1
ICG 001increases expression1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideincreases expression1
jinfukangaffects cotreatment, increases expression1
NSC 689534affects binding, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Ethanolincreases expression1

Clinical trials (associated diseases)

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