PABPN1L

Summary

PABPN1L (PABPN1 like, cytoplasmic, HGNC:37237) is a protein-coding gene on chromosome 16q24.3, encoding Embryonic polyadenylate-binding protein 2 (A6NDY0). Binds the poly(A) tail of mRNA.

Predicted to enable poly(A) binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay. Predicted to act upstream of or within maternal-to-zygotic transition of gene expression; negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process; and negative regulation of protein ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in nucleus.

Source: NCBI Gene 390748 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_001080487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37237
Approved symbol	PABPN1L
Name	PABPN1 like, cytoplasmic
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Aliases	ePABP2
Ensembl gene	ENSG00000205022
Ensembl biotype	protein_coding
Entrez	390748

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000411789, ENST00000419291, ENST00000547152

RefSeq mRNA: 3 — MANE Select: NM_001080487 NM_001080487, NM_001294328, NM_001385709

CCDS: CCDS45547, CCDS73925

Canonical transcript exons

ENST00000419291 — 7 exons

Exon	Start	End
ENSE00001477207	88865022	88865128
ENSE00001477208	88865563	88865630
ENSE00001477209	88865806	88865941
ENSE00002424687	88863333	88863795
ENSE00003487844	88864853	88864940
ENSE00003616063	88864237	88864379
ENSE00003978300	88866352	88866660

Expression profiles

Bgee: expression breadth broad, 98 present calls, max score 66.63.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	66.63	gold quality
cerebellar hemisphere	UBERON:0002245	66.18	gold quality
cerebellar cortex	UBERON:0002129	66.11	gold quality
cerebellum	UBERON:0002037	66.07	gold quality
apex of heart	UBERON:0002098	57.37	gold quality
right adrenal gland	UBERON:0001233	56.71	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	56.18	silver quality
right adrenal gland cortex	UBERON:0035827	56.06	gold quality
bone marrow	UBERON:0002371	55.90	gold quality
granulocyte	CL:0000094	55.57	gold quality
left adrenal gland cortex	UBERON:0035825	55.08	gold quality
left adrenal gland	UBERON:0001234	55.00	gold quality
adrenal gland	UBERON:0002369	53.92	gold quality
bone marrow cell	CL:0002092	53.66	gold quality
blood	UBERON:0000178	53.59	gold quality
spleen	UBERON:0002106	53.39	gold quality
monocyte	CL:0000576	53.38	gold quality
leukocyte	CL:0000738	52.80	gold quality
primary visual cortex	UBERON:0002436	51.89	gold quality
putamen	UBERON:0001874	51.71	gold quality
nucleus accumbens	UBERON:0001882	50.07	gold quality
right lobe of liver	UBERON:0001114	49.12	gold quality
right frontal lobe	UBERON:0002810	48.97	gold quality
cortical plate	UBERON:0005343	48.74	silver quality
ganglionic eminence	UBERON:0004023	48.46	gold quality
superior frontal gyrus	UBERON:0002661	48.31	gold quality
caudate nucleus	UBERON:0001873	47.89	gold quality
lymph node	UBERON:0000029	47.65	gold quality
prostate gland	UBERON:0002367	47.14	gold quality
body of pancreas	UBERON:0001150	46.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-3929	yes	496.40
E-ANND-3	no	0.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting PABPN1L, 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-3662	99.99	73.82	5684
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-3977	98.00	68.17	1500
HSA-MIR-5189-3P	97.52	66.33	487

Literature-anchored findings (GeneRIF, showing 2)

• Unique PABP2 gene plays a critical role in human embryo cleavage; cDNA has been isolated and sequenced. (PMID:18483763)
• Gene-level analysis further revealed a significant genome-wide association of a microRNA-encoding gene MIR1178 in both the discovery and replication cohorts. Another gene poly(A)-binding protein nuclear 1 like, cytoplasmic (PABPN1L) showed suggestive significance in the discovery cohort (p < 1 x 10(-4)) and was replicated in the replication cohort (p = 0.009). (PMID:31363184)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pabpn1l	ENSMUSG00000069867
rattus_norvegicus	Pabpn1l	ENSRNOG00000029558

Paralogs (1): PABPN1 (ENSG00000100836)

Protein

Protein identifiers

Embryonic polyadenylate-binding protein 2 — A6NDY0 (reviewed: A6NDY0)

Alternative names: Embryonic poly(A)-binding protein type II, Poly(A)-binding protein nuclear-like 1

All UniProt accessions (2): A6NDY0, A0A1C7CYY8

UniProt curated annotations — full annotation on UniProt →

Function. Binds the poly(A) tail of mRNA.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in various adult tissues.

Isoforms (4)

UniProt ID	Names	Canonical?
A6NDY0-1	1	yes
A6NDY0-2	2
A6NDY0-4	4
A6NDY0-3	3

RefSeq proteins (3): NP_001073956, NP_001281257, NP_001372638 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (12 total): splice variant 5, region of interest 3, compositionally biased region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NDY0-F1	66.92	0.29

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9820841	M-decay: degradation of maternal mRNAs by maternally stored factors

MSigDB gene sets: 62 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOBP_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY, GOBP_SCF_DEPENDENT_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS

GO Biological Process (4): nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288), negative regulation of protein ubiquitination (GO:0031397), negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process (GO:0062026), maternal-to-zygotic transition of gene expression (GO:0160021)

GO Molecular Function (3): poly(A) binding (GO:0008143), nucleic acid binding (GO:0003676), RNA binding (GO:0003723)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Maternal to zygotic transition (MZT)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear-transcribed mRNA catabolic process	1
mRNA destabilization	1
protein ubiquitination	1
regulation of protein ubiquitination	1
negative regulation of protein modification by small protein conjugation or removal	1
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	1
negative regulation of proteasomal ubiquitin-dependent protein catabolic process	1
regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	1
regulation of gene expression	1
poly-purine tract binding	1
binding	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PABPN1L	BTG4	Q9NY30	606
PABPN1L	RBM22	Q9NW64	528
PABPN1L	TRA2A	Q13595	441
PABPN1L	CPSF4L	A6NMK7	440
PABPN1L	PUM1	Q14671	422
PABPN1L	KHDRBS2	Q5VWX1	420
PABPN1L	HNRNPCL1	O60812	419
PABPN1L	CNOT7	Q9UIV1	416
PABPN1L	FUBP3	Q96I24	411
PABPN1L	RBM15B	Q8NDT2	388
PABPN1L	SRSF9	Q13242	382
PABPN1L	RBMS2	Q15434	381
PABPN1L	RBM41	Q96IZ5	379
PABPN1L	MBD3L2	Q8NHZ7	376
PABPN1L	CNOT6L	Q96LI5	365

IntAct

5 interactions, top by confidence:

A	B	Type	Score
PABPN1L	CNOT1	psi-mi:“MI:0914”(association)	0.350
CEMP1	PABPN1L	psi-mi:“MI:0914”(association)	0.350

BioGRID (37): CNOT1 (Affinity Capture-MS), PMPCA (Affinity Capture-MS), BTG3 (Affinity Capture-MS), PMPCB (Affinity Capture-MS), EML4 (Affinity Capture-MS), CNOT11 (Affinity Capture-MS), C17orf70 (Affinity Capture-MS), RAVER1 (Affinity Capture-MS), CNOT8 (Affinity Capture-MS), TNKS1BP1 (Affinity Capture-MS), CDKN2AIP (Affinity Capture-MS), RQCD1 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT7 (Affinity Capture-MS), CNOT3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: A0A0D1C8Z4, A2Q848, A6NDY0, A8WLV5, B0BNE4, B3LYP1, B3P0D7, B4JUT1, B4KCD5, B4LZ88, O13620, O13741, O13845, O14327, O80678, P19683, P19684, P20397, P33240, P38922, P40561, P42696, P49313, P49314, Q00916, Q05AT9, Q05CL8, Q06106, Q08208, Q08937, Q09295, Q09301, Q10B98, Q1PEP5, Q28165, Q28ZX3, Q44554, Q44556, Q44560, Q4G0J3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	70
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1243 predictions. Top by Δscore:

Variant	Effect	Δscore
16:88864233:TCAC:T	donor_loss	1.0000
16:88864234:CACC:C	donor_loss	1.0000
16:88864235:ACCGG:A	donor_loss	1.0000
16:88864377:CAC:C	acceptor_gain	1.0000
16:88864379:CCTGG:C	acceptor_loss	1.0000
16:88864380:C:CC	acceptor_gain	1.0000
16:88864380:C:CG	acceptor_loss	1.0000
16:88864381:T:A	acceptor_loss	1.0000
16:88864822:ATGTT:A	donor_gain	1.0000
16:88864936:CATAA:C	acceptor_gain	1.0000
16:88864938:TAA:T	acceptor_gain	1.0000
16:88864939:AA:A	acceptor_gain	1.0000
16:88864941:C:CC	acceptor_gain	1.0000
16:88865020:ACC:A	donor_gain	1.0000
16:88865021:CCC:C	donor_gain	1.0000
16:88866346:TGTTA:T	donor_loss	1.0000
16:88866347:GTTAC:G	donor_loss	1.0000
16:88866348:TTACC:T	donor_loss	1.0000
16:88866349:TACC:T	donor_loss	1.0000
16:88866350:A:AT	donor_loss	1.0000
16:88866351:C:G	donor_loss	1.0000
16:88864231:A:AC	donor_gain	0.9900
16:88864232:C:CC	donor_gain	0.9900
16:88864235:A:AC	donor_gain	0.9900
16:88864236:C:CC	donor_gain	0.9900
16:88864375:AGCAC:A	acceptor_gain	0.9900
16:88864376:GCAC:G	acceptor_gain	0.9900
16:88864377:CACC:C	acceptor_gain	0.9900
16:88864378:AC:A	acceptor_gain	0.9900
16:88864379:CC:C	acceptor_gain	0.9900

AlphaMissense

1794 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:88864368:T:A	K222N	0.999
16:88864368:T:G	K222N	0.999
16:88864922:A:C	F195L	0.999
16:88864922:A:T	F195L	0.999
16:88864924:A:G	F195L	0.999
16:88865024:C:A	K188N	0.999
16:88865024:C:G	K188N	0.999
16:88864369:T:A	K222I	0.998
16:88864923:A:G	F195S	0.998
16:88864935:G:T	A191D	0.998
16:88865087:G:C	F167L	0.998
16:88865087:G:T	F167L	0.998
16:88865089:A:G	F167L	0.998
16:88864365:T:A	R223S	0.997
16:88864365:T:G	R223S	0.997
16:88864863:C:G	R215P	0.997
16:88864872:A:G	F212S	0.997
16:88864923:A:C	F195C	0.997
16:88865022:C:T	G189D	0.997
16:88865023:C:G	G189R	0.997
16:88865088:A:G	F167S	0.997
16:88865576:A:T	V149D	0.997
16:88864359:G:C	N225K	0.996
16:88864359:G:T	N225K	0.996
16:88864933:A:G	Y192H	0.996
16:88865055:A:G	I178T	0.996
16:88864366:C:G	R223T	0.994
16:88864857:A:T	I217N	0.994
16:88864896:G:T	A204D	0.994
16:88864924:A:C	F195V	0.994

dbSNP variants (sampled 300 via entrez): RS1000012962 (16:88869959 G>A,C), RS1000340685 (16:88866871 T>C), RS1000393007 (16:88866666 C>A,T), RS1000674599 (16:88867769 T>A,G), RS1000724791 (16:88867613 G>A), RS1000756839 (16:88867365 T>G), RS1000809042 (16:88867119 C>G,T), RS1001051381 (16:88863966 A>C,G), RS1001129213 (16:88867095 TG>T), RS1001243763 (16:88867274 CTG>C), RS1001310693 (16:88871133 C>A,T), RS1001568362 (16:88869387 A>T), RS1001870674 (16:88865821 T>C,G), RS1002138007 (16:88864752 C>A,G,T), RS1002206017 (16:88864016 C>G,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

4 associations (top):

Study	Trait	p-value
GCST002778_5	Parkinson disease and lewy body pathology	9.000000e-07
GCST003479_9	Hair color	1.000000e-07
GCST90016669_14	Pancreas volume	2.000000e-09
GCST90016675_8	Pancreas fat	6.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tebuconazole	decreases expression	1
abrine	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Endosulfan	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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