PABPC1L2A

Summary

PABPC1L2A (poly(A) binding protein cytoplasmic 1 like 2A, HGNC:27989) is a protein-coding gene on chromosome Xq13.2, encoding Polyadenylate-binding protein 1-like 2 (Q5JQF8).

Predicted to enable mRNA 3’-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Located in extracellular exosome.

Source: NCBI Gene 340529 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001012977

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27989
Approved symbol	PABPC1L2A
Name	poly(A) binding protein cytoplasmic 1 like 2A
Location	Xq13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000186288
Ensembl biotype	protein_coding
Entrez	340529

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000373519

RefSeq mRNA: 1 — MANE Select: NM_001012977 NM_001012977

CCDS: CCDS35334

Canonical transcript exons

ENST00000373519 — 1 exons

Exon	Start	End
ENSE00001460745	73077276	73079512

Expression profiles

Bgee: expression breadth broad, 51 present calls, max score 82.07.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
superior frontal gyrus	UBERON:0002661	82.07	gold quality
prefrontal cortex	UBERON:0000451	80.61	gold quality
hypothalamus	UBERON:0001898	79.67	gold quality
frontal cortex	UBERON:0001870	78.78	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	78.51	gold quality
primary visual cortex	UBERON:0002436	78.44	gold quality
Brodmann (1909) area 9	UBERON:0013540	78.34	gold quality
cerebellum	UBERON:0002037	77.28	gold quality
cerebellar cortex	UBERON:0002129	77.22	gold quality
cerebellar hemisphere	UBERON:0002245	77.22	gold quality
right hemisphere of cerebellum	UBERON:0014890	76.82	gold quality
cerebral cortex	UBERON:0000956	76.55	gold quality
anterior cingulate cortex	UBERON:0009835	76.23	gold quality
right frontal lobe	UBERON:0002810	75.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.54	gold quality
brain	UBERON:0000955	73.30	gold quality
nucleus accumbens	UBERON:0001882	72.79	gold quality
Ammon’s horn	UBERON:0001954	70.94	gold quality
temporal lobe	UBERON:0001871	70.46	gold quality
amygdala	UBERON:0001876	70.38	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	70.37	gold quality
substantia nigra	UBERON:0002038	69.93	gold quality
caudate nucleus	UBERON:0001873	68.03	gold quality
putamen	UBERON:0001874	68.02	gold quality
pituitary gland	UBERON:0000007	62.36	gold quality
prostate gland	UBERON:0002367	61.85	gold quality
adenohypophysis	UBERON:0002196	61.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	60.47	gold quality
left testis	UBERON:0004533	57.77	gold quality
testis	UBERON:0000473	57.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

94 targeting PABPC1L2A, 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-8485	100.00	77.57	4731
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-6817-3P	99.79	68.35	2126

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	pabpc1a	ENSDARG00000017219
danio_rerio	pabpc1b	ENSDARG00000021140
mus_musculus	Pabpc1l2b	ENSMUSG00000084842
mus_musculus	Pabpc1l2a	ENSMUSG00000086524
rattus_norvegicus	Pabpc1l2a	ENSRNOG00000022267
rattus_norvegicus	Pabpc1l2a	ENSRNOG00000080500

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), RBM34 (ENSG00000188739), ELAVL3 (ENSG00000196361), RBM14 (ENSG00000239306), PABPC4L (ENSG00000254535)

Protein

Protein identifiers

Polyadenylate-binding protein 1-like 2 — Q5JQF8 (reviewed: Q5JQF8)

Alternative names: RNA-binding motif protein 32, RNA-binding protein 32

All UniProt accessions (1): Q5JQF8

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be not functional as it lacks the poly(A)-binding protein C-terminal (PABC) domain implicated in the mRNA stability and translation regulation.

RefSeq proteins (1): NP_001012995* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
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 (6 total): domain 2, chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JQF8-F1	89.94	0.76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): BENPORATH_ES_WITH_H3K27ME3, CACCAGC_MIR138, CCCAGAG_MIR326, GOCC_CYTOPLASMIC_STRESS_GRANULE, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_POLY_A_BINDING, GOMF_POLY_PYRIMIDINE_TRACT_BINDING, GOMF_MRNA_BINDING, GOMF_SINGLE_STRANDED_RNA_BINDING, GOMF_POLY_PURINE_TRACT_BINDING, GOMF_MRNA_3_UTR_BINDING, chrXq13, GOCC_SUPRAMOLECULAR_COMPLEX, MIR8485

GO Biological Process (0):

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), extracellular exosome (GO:0070062), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
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
cellular anatomical structure	1
cytoplasmic ribonucleoprotein granule	1
extracellular vesicle	1
protein-containing complex	1

Protein interactions and networks

STRING

1172 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PABPC1L2A	PABPN1	Q86U42	871
PABPC1L2A	EIF4G1	Q04637	766
PABPC1L2A	EIF4E	P06730	676
PABPC1L2A	TNRC6A	Q8NDV7	608
PABPC1L2A	EIF4A1	P04765	594
PABPC1L2A	EIF4A2	Q14240	594
PABPC1L2A	PAN2	Q504Q3	537
PABPC1L2A	ATXN2	Q99700	482
PABPC1L2A	PAIP2	Q9BPZ3	452
PABPC1L2A	ENDOV	Q8N8Q3	430
PABPC1L2A	COMP	P49747	428
PABPC1L2A	SNW1	Q13573	424
PABPC1L2A	DCP2	Q8IU60	415
PABPC1L2A	XRN1	Q8IZH2	414
PABPC1L2A	FXR1	P51114	408

IntAct

6 interactions, top by confidence:

A	B	Type	Score
L	MYO1C	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
RYBP	PIPSL	psi-mi:“MI:0914”(association)	0.350
CACNA1C	SNRPGP15	psi-mi:“MI:0914”(association)	0.350

BioGRID (18): PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PTMA (Cross-Linking-MS (XL-MS)), PABPC1L2A (Protein-RNA), PABPC1L2A (Protein-RNA), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS), PABPC1L2A (Affinity Capture-MS)

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

116 predictions. Top by Δscore:

Variant	Effect	Δscore
X:73078771:T:TA	donor_gain	0.8400
X:73078800:T:TA	donor_gain	0.8200
X:73078393:C:A	donor_gain	0.7500
X:73078768:AGCT:A	donor_gain	0.6300
X:73078815:T:TA	donor_gain	0.6300
X:73078382:T:A	donor_gain	0.6200
X:73078379:CTCT:C	donor_gain	0.6000
X:73078784:T:TA	donor_gain	0.5800
X:73078996:AGC:A	donor_gain	0.5200
X:73079409:CAG:C	donor_gain	0.5100
X:73078964:AGATT:A	donor_gain	0.5000
X:73078968:T:TA	donor_gain	0.4900
X:73078989:A:T	donor_gain	0.4800
X:73078941:A:AC	donor_gain	0.4700
X:73078157:A:C	acceptor_gain	0.4500
X:73078375:A:AC	donor_gain	0.4500
X:73078725:TGTAA:T	donor_gain	0.4500
X:73078729:A:T	donor_gain	0.4400
X:73078992:C:CT	donor_gain	0.4400
X:73078769:G:C	donor_gain	0.4300
X:73078378:A:AC	donor_gain	0.4200
X:73078379:C:CC	donor_gain	0.4200
X:73078379:CT:C	donor_gain	0.4200
X:73078901:C:CA	donor_gain	0.4200
X:73078993:C:T	donor_gain	0.4200
X:73079411:G:C	donor_gain	0.4000
X:73078142:AAGCC:A	acceptor_loss	0.3900
X:73078143:AGCCT:A	acceptor_loss	0.3900
X:73078144:GCCTG:G	acceptor_loss	0.3900
X:73078145:CCTGT:C	acceptor_loss	0.3900

AlphaMissense

1320 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:73078988:G:C	F133L	0.999
X:73078988:G:T	F133L	0.999
X:73078990:A:G	F133L	0.999
X:73079046:C:A	G114V	0.999
X:73079244:A:T	V48D	0.999
X:73078895:G:C	F164L	0.998
X:73078895:G:T	F164L	0.998
X:73078897:A:G	F164L	0.998
X:73078980:A:G	F136S	0.998
X:73078986:A:T	V134E	0.998
X:73078992:C:T	G132E	0.998
X:73079250:G:T	A46E	0.998
X:73078905:A:T	V161D	0.997
X:73078979:G:C	F136L	0.997
X:73078979:G:T	F136L	0.997
X:73078981:A:G	F136L	0.997
X:73078993:C:A	G132W	0.997
X:73079106:A:T	I94N	0.997
X:73079112:A:T	V92D	0.997
X:73079251:C:G	A46P	0.997
X:73079310:C:T	G26E	0.997
X:73079311:C:A	G26W	0.997
X:73078954:C:G	A145P	0.996
X:73079047:C:G	G114R	0.996
X:73079070:A:G	L106P	0.996
X:73079108:G:C	F93L	0.996
X:73079108:G:T	F93L	0.996
X:73079110:A:G	F93L	0.996
X:73079334:A:G	L18P	0.996
X:73079334:A:T	L18Q	0.996

dbSNP variants (sampled 300 via entrez): RS1003842495 (X:73077385 T>C), RS1010699888 (X:73077333 A>T), RS1020592860 (X:73077334 A>T), RS1020664994 (X:73076786 A>G), RS1039247249 (X:73077248 T>C), RS11093406 (X:73077578 T>A,C), RS11093407 (X:73077702 T>C), RS1157179424 (X:73079505 G>A,C), RS115820229 (X:73076778 A>G), RS1158761618 (X:73078227 C>T), RS1160712980 (X:73079568 T>C,G), RS1162497758 (X:73077243 T>G), RS1162573335 (X:73078359 T>C), RS1163842186 (X:73079775 GCCGCCA>G), RS1166362789 (X:73077384 A>G)

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

1 associations (top):

Study	Trait	p-value
GCST008103_139	Bipolar disorder	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ethyl-p-hydroxybenzoate	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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