PABPC4L

Summary

PABPC4L (poly(A) binding protein cytoplasmic 4 like, HGNC:31955) is a protein-coding gene on chromosome 4q28.3, encoding Polyadenylate-binding protein 4-like (P0CB38). May bind RNA.

Predicted to enable mRNA 3’-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus.

Source: NCBI Gene 132430 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_001114734

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31955
Approved symbol	PABPC4L
Name	poly(A) binding protein cytoplasmic 4 like
Location	4q28.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000254535
Ensembl biotype	protein_coding
Entrez	132430

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000421491, ENST00000884201, ENST00000925025

RefSeq mRNA: 2 — MANE Select: NM_001114734 NM_001114734, NM_001363585

CCDS: CCDS47135

Canonical transcript exons

ENST00000421491 — 2 exons

Exon	Start	End
ENSE00001790557	134196333	134201245
ENSE00002221428	134201718	134201789

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 86.59.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0006 / max 64.6045, expressed in 722 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
53958	1.2077	514
53959	0.4816	261
53960	0.1730	79
53957	0.1383	66

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.59	silver quality
caput epididymis	UBERON:0004358	81.18	gold quality
placenta	UBERON:0001987	80.63	gold quality
endometrium	UBERON:0001295	77.92	gold quality
oviduct epithelium	UBERON:0004804	77.32	gold quality
cauda epididymis	UBERON:0004360	76.43	gold quality
buccal mucosa cell	CL:0002336	75.49	gold quality
seminal vesicle	UBERON:0000998	74.03	gold quality
stromal cell of endometrium	CL:0002255	73.89	gold quality
smooth muscle tissue	UBERON:0001135	72.08	gold quality
tibia	UBERON:0000979	71.91	gold quality
visceral pleura	UBERON:0002401	71.60	gold quality
parietal pleura	UBERON:0002400	70.37	gold quality
corpus epididymis	UBERON:0004359	69.69	gold quality
uterus	UBERON:0000995	69.10	gold quality
cartilage tissue	UBERON:0002418	68.94	silver quality
adrenal tissue	UBERON:0018303	67.14	gold quality
left ventricle myocardium	UBERON:0006566	66.60	gold quality
right atrium auricular region	UBERON:0006631	66.52	gold quality
cardiac atrium	UBERON:0002081	66.21	gold quality
fallopian tube	UBERON:0003889	66.20	gold quality
descending thoracic aorta	UBERON:0002345	65.99	gold quality
mucosa of stomach	UBERON:0001199	65.98	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.49	gold quality
female reproductive system	UBERON:0000474	65.48	gold quality
ventricular zone	UBERON:0003053	65.42	gold quality
pigmented layer of retina	UBERON:0001782	65.14	gold quality
epithelial cell of pancreas	CL:0000083	64.26	silver quality
thoracic aorta	UBERON:0001515	64.01	gold quality
ascending aorta	UBERON:0001496	63.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

155 targeting PABPC4L, 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-4692	100.00	67.32	2066
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-3163	100.00	77.23	8605
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-4514	99.99	67.10	1870
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910

Literature-anchored findings (GeneRIF, showing 1)

• Segregation and potential functional impact of a rare stop-gain PABPC4L variant in familial atypical Parkinsonism. (PMID:31537871)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pabpc4l	ENSMUSG00000090919
rattus_norvegicus	Pabpc4l	ENSRNOG00000075303

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), PABPC3 (ENSG00000151846), RBMS1 (ENSG00000153250), RBM45 (ENSG00000155636), ELAVL4 (ENSG00000162374), PABPC5 (ENSG00000174740), PUF60 (ENSG00000179950), PABPC1L2B (ENSG00000184388), PABPC1L2A (ENSG00000186288), RBM34 (ENSG00000188739), ELAVL3 (ENSG00000196361), RBM14 (ENSG00000239306)

Protein

Protein identifiers

Polyadenylate-binding protein 4-like — P0CB38 (reviewed: P0CB38)

All UniProt accessions (1): P0CB38

UniProt curated annotations — full annotation on UniProt →

Function. May bind RNA.

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

RefSeq proteins (2): NP_001108206, NP_001350514 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	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
IPR045305	RRM2_I_PABPs	Domain

Pfam: PF00076

UniProt features (8 total): domain 4, sequence variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CB38-F1	91.73	0.78

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, RICKMAN_HEAD_AND_NECK_CANCER_A, DODD_NASOPHARYNGEAL_CARCINOMA_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, SENESE_HDAC3_TARGETS_DN, GOCC_CYTOPLASMIC_STRESS_GRANULE, NAKAMURA_METASTASIS, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP, GOMF_POLY_A_BINDING, GOMF_POLY_PYRIMIDINE_TRACT_BINDING, GOMF_MRNA_BINDING

GO Biological Process (3): positive regulation of gene expression (GO:0010628), 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 (5): nucleus (GO:0005634), cytosol (GO:0005829), cytoplasmic stress granule (GO:0010494), ribonucleoprotein complex (GO:1990904), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of metabolic process	2
cellular anatomical structure	2
gene expression	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
macromolecule metabolic process	1
primary metabolic process	1
mRNA binding	1
poly-purine tract binding	1
poly-pyrimidine tract binding	1
binding	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cytoplasmic ribonucleoprotein granule	1
protein-containing complex	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1548 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PABPC4L	PABPN1	Q86U42	874
PABPC4L	EIF4G1	Q04637	773
PABPC4L	EIF4E	P06730	686
PABPC4L	EIF4A1	P04765	643
PABPC4L	EIF4A2	Q14240	642
PABPC4L	TNRC6A	Q8NDV7	601
PABPC4L	PAN2	Q504Q3	565
PABPC4L	C1orf94	Q6P1W5	533
PABPC4L	ATXN2	Q99700	483
PABPC4L	PAIP2	Q9BPZ3	460
PABPC4L	XRN1	Q8IZH2	453
PABPC4L	COMP	P49747	429
PABPC4L	DCP2	Q8IU60	429
PABPC4L	SNW1	Q13573	424
PABPC4L	ENDOV	Q8N8Q3	418

IntAct

77 interactions, top by confidence:

A	B	Type	Score
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
NOP53	RRP8	psi-mi:“MI:0914”(association)	0.640
GSPT2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ZC3HAV1	KHNYN	psi-mi:“MI:0914”(association)	0.530
THAP3	CASC3	psi-mi:“MI:0914”(association)	0.530
PAIP2B	CASC3	psi-mi:“MI:0914”(association)	0.530
Rmdn3	DERL1	psi-mi:“MI:0914”(association)	0.350
Pqbp1	PRPF4	psi-mi:“MI:0914”(association)	0.350
Csde1	TXNDC9	psi-mi:“MI:0914”(association)	0.350
CSDE1	PABPC4L	psi-mi:“MI:0914”(association)	0.350
Rab3gap1	PABPC4L	psi-mi:“MI:0914”(association)	0.350
Chmp4c	SF1	psi-mi:“MI:0914”(association)	0.350
GPSM2	AASDH	psi-mi:“MI:0914”(association)	0.350
Sart1	PRPF4	psi-mi:“MI:0914”(association)	0.350
NP	KPNA4	psi-mi:“MI:0914”(association)	0.350
NP	HNRNPDL	psi-mi:“MI:0914”(association)	0.350
NP	HNRNPAB	psi-mi:“MI:0914”(association)	0.350
NP	KPNA6	psi-mi:“MI:0914”(association)	0.350
NP	HNRNPCL1	psi-mi:“MI:0914”(association)	0.350
NP	NKRF	psi-mi:“MI:0914”(association)	0.350
NP	IPO5	psi-mi:“MI:0914”(association)	0.350
NP	TRIM66	psi-mi:“MI:0914”(association)	0.350
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A2A5N3, A3LXL0, A5DM21, F1QB54, F4HT49, G5EFS2, O04319, O22173, O64380, O74968, P04147, P0CB38, P11940, P20965, P21187, P29341, P31209, P42731, P49960, P60047, P60048, P60049, P60050, P61286, P70318, Q05196, Q08BH5, Q0P4R6, Q13310, Q22708, Q4VXU2, Q503H1, Q54BM2, Q5JQF8, Q5R8F7, Q6BI95, Q6DCB7, Q6DEY7, Q6FKG4, Q6GR16

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 93 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
Eukaryotic Translation Termination	7	18.7×	4e-06
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	7	18.3×	4e-06
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	8	17.4×	3e-06
Processing of Capped Intron-Containing Pre-mRNA	8	14.6×	4e-06
Peptide chain elongation	5	14.1×	5e-04
Viral mRNA Translation	5	14.1×	5e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	5	13.9×	5e-04
SRP-dependent cotranslational protein targeting to membrane	6	13.4×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
NLS-bearing protein import into nucleus	5	54.2×	6e-06
RNA processing	6	17.8×	7e-05
cytoplasmic translation	6	15.0×	2e-04
negative regulation of translation	5	13.2×	1e-03
translation	9	12.5×	6e-06
rRNA processing	6	11.5×	5e-04
mRNA splicing, via spliceosome	6	7.4×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

213 predictions. Top by Δscore:

Variant	Effect	Δscore
4:134200040:T:TA	donor_gain	0.9300
4:134201666:CGGA:C	donor_gain	0.9300
4:134199905:T:A	donor_gain	0.9100
4:134200055:A:C	donor_gain	0.8900
4:134201672:G:T	donor_gain	0.8700
4:134200355:A:AC	donor_gain	0.8000
4:134201507:G:A	donor_gain	0.8000
4:134201669:A:AC	donor_gain	0.8000
4:134201670:C:CC	donor_gain	0.8000
4:134200201:AG:A	donor_gain	0.7800
4:134201711:GGCTC:G	donor_loss	0.7400
4:134201712:GCTC:G	donor_loss	0.7400
4:134201713:CTCAC:C	donor_loss	0.7400
4:134201714:TCA:T	donor_loss	0.7400
4:134201715:C:CG	donor_loss	0.7400
4:134201717:C:CT	donor_loss	0.7400
4:134201289:C:A	donor_gain	0.7300
4:134201710:GGGC:G	donor_loss	0.7300
4:134200397:T:TA	donor_gain	0.7200
4:134201284:T:A	donor_gain	0.7200
4:134201288:T:TA	donor_gain	0.7200
4:134201709:GGGGC:G	donor_loss	0.7200
4:134201716:A:AC	donor_gain	0.7000
4:134201717:C:CC	donor_gain	0.7000
4:134201511:G:C	donor_gain	0.6600
4:134201668:G:T	donor_gain	0.6500
4:134201717:CCGG:C	donor_gain	0.6500
4:134201312:T:TA	donor_gain	0.6400
4:134201502:A:T	donor_gain	0.6400
4:134201718:C:G	donor_loss	0.6400

AlphaMissense

2485 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:134200504:G:C	F172L	0.997
4:134200504:G:T	F172L	0.997
4:134200506:A:G	F172L	0.997
4:134200597:A:C	F141L	0.997
4:134200597:A:T	F141L	0.997
4:134200599:A:G	F141L	0.997
4:134200318:A:C	F234L	0.996
4:134200318:A:T	F234L	0.996
4:134200320:A:G	F234L	0.996
4:134200324:A:C	F232L	0.995
4:134200324:A:T	F232L	0.995
4:134200326:A:G	F232L	0.995
4:134200595:A:T	V142E	0.995
4:134200601:G:T	A140E	0.995
4:134200859:G:T	A54D	0.995
4:134200970:A:G	L17S	0.995
4:134200453:G:C	F189L	0.994
4:134200453:G:T	F189L	0.994
4:134200455:A:G	F189L	0.994
4:134200563:C:G	A153P	0.994
4:134200589:A:G	F144S	0.994
4:134200292:G:T	A243D	0.993
4:134200588:A:C	F144L	0.993
4:134200588:A:T	F144L	0.993
4:134200590:A:G	F144L	0.993
4:134200715:A:T	I102N	0.993
4:134200860:C:G	A54P	0.993
4:134200322:C:T	G233D	0.992
4:134200776:G:T	R82S	0.992
4:134200847:A:G	F58S	0.992

dbSNP variants (sampled 300 via entrez): RS1000001625 (4:134163879 CAAAATCATAGTTA>C), RS1000028957 (4:134123922 T>C), RS1000049820 (4:134090662 C>T), RS1000054305 (4:134117529 T>A), RS1000057020 (4:134131113 C>A,G,T), RS1000063376 (4:133974549 T>C), RS10000682 (4:133951554 G>A), RS1000075316 (4:134177640 C>T), RS1000078872 (4:134171934 A>G), RS1000082003 (4:134090340 T>C), RS1000083350 (4:134040803 G>T), RS1000102203 (4:134200961 T>A), RS1000110124 (4:133963911 A>T), RS1000113308 (4:134027777 A>G,T), RS1000126796 (4:134034320 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

8 associations (top):

Study	Trait	p-value
GCST002063_10	Sexual dimorphism in anthropometric traits	8.000000e-06
GCST002826_11	Urate levels (BMI interaction)	9.000000e-07
GCST004071_9	Cerebrospinal T-tau levels	7.000000e-06
GCST008362_216	Birth weight	2.000000e-13
GCST009103_3	Resistance to antihypertensive treatment in hypertension	2.000000e-06
GCST009379_266	Type 2 diabetes	4.000000e-08
GCST009936_8	Venous thromboembolism	9.000000e-06
GCST011909_2	Hypertensive renal disease	6.000000e-07

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0005951	sexual dimorphism
EFO:0004340	body mass index
EFO:0004531	urate measurement
EFO:0004760	t-tau measurement
EFO:0004344	birth weight
EFO:1002006	treatment-resistant hypertension

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, affects cotreatment	6
sodium arsenite	decreases expression, affects expression	2
Panobinostat	affects cotreatment, increases expression	2
Benzo(a)pyrene	increases methylation, increases mutagenesis	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
trichostatin A	increases expression	1
hydroquinone	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
licochalcone B	decreases expression	1
Temozolomide	increases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression	1
Ribonucleotides	affects binding	1
Silicon Dioxide	decreases expression	1
Tretinoin	increases expression	1
Cyclosporine	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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