PTBP3

Summary

PTBP3 (polypyrimidine tract binding protein 3, HGNC:10253) is a protein-coding gene on chromosome 9q32, encoding Polypyrimidine tract-binding protein 3 (O95758). RNA-binding protein that mediates pre-mRNA alternative splicing regulation.

The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 9991 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 63 total
• Druggable target: yes
• MANE Select transcript: NM_001163788

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10253
Approved symbol	PTBP3
Name	polypyrimidine tract binding protein 3
Location	9q32
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp781I1117
Ensembl gene	ENSG00000119314
Ensembl biotype	protein_coding
OMIM	607527
Entrez	9991

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 21 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000210227, ENST00000343327, ENST00000374255, ENST00000374257, ENST00000450374, ENST00000487997, ENST00000850864, ENST00000850866, ENST00000850867, ENST00000850868, ENST00000874007, ENST00000874008, ENST00000874009, ENST00000932749, ENST00000932750, ENST00000932751, ENST00000932752, ENST00000932753, ENST00000932754, ENST00000932755, ENST00000932756, ENST00000968727, ENST00000968728, ENST00000968729

RefSeq mRNA: 8 — MANE Select: NM_001163788 NM_001163788, NM_001163790, NM_001244896, NM_001244897, NM_001244898, NM_001375918, NM_001375920, NM_005156

CCDS: CCDS55332, CCDS55333, CCDS59140, CCDS59141, CCDS6784

Canonical transcript exons

ENST00000374257 — 14 exons

Exon	Start	End
ENSE00001462934	112218435	112223983
ENSE00001462940	112333470	112333619
ENSE00001601119	112231380	112231413
ENSE00001627411	112232099	112232238
ENSE00001688828	112224133	112224210
ENSE00001705448	112250929	112251103
ENSE00001715418	112234820	112234897
ENSE00001720829	112228380	112228472
ENSE00001721575	112252678	112252788
ENSE00001729161	112227411	112227627
ENSE00002202106	112275844	112276013
ENSE00003503329	112262435	112262599
ENSE00003623021	112268049	112268195
ENSE00004282550	112297832	112297916

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 98.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 68.4422 / max 1262.6114, expressed in 1824 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102066	52.7711	1824
102065	12.9779	1756
102063	1.3478	697
102064	1.3454	789

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelium of nasopharynx	UBERON:0001951	98.95	gold quality
nasopharynx	UBERON:0001728	98.93	gold quality
gingival epithelium	UBERON:0001949	98.81	gold quality
gingiva	UBERON:0001828	98.74	gold quality
esophagus squamous epithelium	UBERON:0006920	98.69	gold quality
trabecular bone tissue	UBERON:0002483	98.64	gold quality
oral cavity	UBERON:0000167	98.61	gold quality
corpus epididymis	UBERON:0004359	98.52	gold quality
upper leg skin	UBERON:0004262	98.45	gold quality
jejunal mucosa	UBERON:0000399	98.38	gold quality
bronchial epithelial cell	CL:0002328	98.35	gold quality
amniotic fluid	UBERON:0000173	98.35	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.35	gold quality
pharyngeal mucosa	UBERON:0000355	98.28	gold quality
caput epididymis	UBERON:0004358	98.21	gold quality
skin of hip	UBERON:0001554	98.02	gold quality
visceral pleura	UBERON:0002401	98.01	gold quality
mammalian vulva	UBERON:0000997	98.00	gold quality
colonic mucosa	UBERON:0000317	97.97	gold quality
renal medulla	UBERON:0000362	97.90	gold quality
pylorus	UBERON:0001166	97.89	gold quality
tibia	UBERON:0000979	97.75	gold quality
penis	UBERON:0000989	97.60	gold quality
superficial temporal artery	UBERON:0001614	97.26	gold quality
cauda epididymis	UBERON:0004360	97.13	gold quality
nipple	UBERON:0002030	97.09	gold quality
mammary duct	UBERON:0001765	97.08	gold quality
parietal pleura	UBERON:0002400	97.08	gold quality
superior surface of tongue	UBERON:0007371	96.97	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.73	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	29.97
E-HCAD-10	yes	21.71
E-ANND-3	yes	9.13
E-MTAB-6386	no	333.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

386 targeting PTBP3, 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-4262	100.00	73.26	3931
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-8485	100.00	77.57	4731
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4668-3P	100.00	68.74	2635
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-190A-3P	100.00	80.35	5520

Literature-anchored findings (GeneRIF, showing 23)

• Regulator of differentiation 1 (ROD1) binds to the amphipathic C-terminal peptide of thrombospondin-4 and is involved in its mitogenic activity. (PMID:19441079)
• ROD1 and UPF1 associate with a significant number of common transcripts. (PMID:22575643)
• ROD1 is a bona fide seedless target of miR-210. (PMID:23024754)
• PTBP3 may promote proliferation and inhibit the differentiation of human gastric cancer MKN45 cells (PMID:25119103)
• We propose that miR-210 regulates cell proliferation and apoptosis in glioblastoma multiforme cells by targeting ROD1 (PMID:26443314)
• Data show that polypyrimidine tract-binding proteins nPTB and ROD1 interact with mitochondrial tRNA(Thr) in the cytoplasm outside of mitochondria. (PMID:26657638)
• Increased PTBP3 expression is associated with 5- fluorouracil resistance in gastric cancer. (PMID:28222070)
• Low PTBP1 expression is associated with Prostate Cancer Growth. (PMID:29187400)
• High PTBP3 expression is associated with Epithelial-Mesenchymal Transition in Breast Cancer. (PMID:29187406)
• the methylation profile combination of HKR1, ROD1, and NLRC5 could be a promising biomarker for aging in Hainan centenarians (PMID:29394898)
• findings provide experimental evidence that PTBP3 may function as a metastatic gene in gastric cancer by regulating CAV1 through alternative splicing. (PMID:29752441)
• RTqPCR revealed that the expression level of miR210 and ROD1 in the antimiR210 group was significantly reduced when compared with the NC and BL groups (P<0.05). MiR210 was overexpressed in the serum of prostate cancer patients and transfection with an miR210 inhibitor was able to effectively inhibit the proliferation of prostate cancer cells and promote apoptosis. (PMID:29901117)
• ROD1 directly interacts with AID, which jointly bind bidirectionally transcribed RNAs to facilitate genome-wide AID targeting to Ig and non-Ig loci, suggesting that cooperative binding of the ROD1-AID complex on RNA provides the targeting specificity for AID. (PMID:30143796)
• The Meg3-dependent association of PTBP3 with the promoters of p53 target genes suggests that Meg3 and PTBP3 restrain p53 activation. Our studies reveal a novel role of Meg3 and PTBP3 in regulating p53 signaling and endothelial function, which may serve as novel targets for therapies to restore endothelial homeostasis. (PMID:30476192)
• This proposed looping model is clearly correlated with the expression of PTBP3 and suggests that chromatin conformation changes are the main epigenetic mechanism that regulates PTBP3 expression in prostate cancer cells. (PMID:30634466)
• PTBP3 appears to be a novel oncogene of CRC through binding to the IRES region of HIF-1alpha mRNA, which regulates HIF-1alpha translation. PTBP3 can serve as a promising predictive biomarker for recurrence and prognosis in patients with CRC. (PMID:31291975)
• PTBP3 promotes malignancy and hypoxia-induced chemoresistance in pancreatic cancer cells by ATG12 up-regulation. (PMID:31989778)
• MiR-384 inhibits proliferation and migration of trophoblast cells via targeting PTBP3. (PMID:32512528)
• PTBP3 modulates P53 expression and promotes colorectal cancer cell proliferation by maintaining UBE4A mRNA stability. (PMID:35136024)
• PTBP3 mediates TGF-beta-induced EMT and metastasis of lung adenocarcinoma. (PMID:35323096)
• MiR-297 inhibits tumour progression of liver cancer by targeting PTBP3. (PMID:37633911)
• YTHDC1 promotes the malignant progression of gastric cancer by promoting ROD1 translocation to the nucleus. (PMID:38573528)
• PTBP3 Mediates IL-18 Exon Skipping to Promote Immune Escape in Gallbladder Cancer. (PMID:39116343)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ptbp3	ENSDARG00000043757
mus_musculus	Ptbp3	ENSMUSG00000028382
rattus_norvegicus	Ptbp3	ENSRNOG00000016334
drosophila_melanogaster	heph	FBGN0011224
caenorhabditis_elegans		WBGENE00004207

Paralogs (5): PTBP1 (ENSG00000011304), HNRNPL (ENSG00000104824), PTBP2 (ENSG00000117569), HNRNPLL (ENSG00000143889), RBM20 (ENSG00000203867)

Protein

Protein identifiers

Polypyrimidine tract-binding protein 3 — O95758 (reviewed: O95758)

Alternative names: Regulator of differentiation 1

All UniProt accessions (3): B1ALY4, O95758, X6R242

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein that mediates pre-mRNA alternative splicing regulation. Plays a role in the regulation of cell proliferation, differentiation and migration. Positive regulator of EPO-dependent erythropoiesis. Participates in cell differentiation regulation by repressing tissue-specific exons. Promotes FAS exon 6 skipping. Binds RNA, preferentially to both poly(G) and poly(U).

Subunit / interactions. Interacts with THBS4 (via the acidic amphipathic C-terminus).

Tissue specificity. Expressed in several hematopoietic cell lines examined.

Isoforms (7)

UniProt ID	Names	Canonical?
O95758-3	3	yes
O95758-1	1
O95758-2	2
O95758-4	4
O95758-5	5
O95758-6	6
O95758-7	7

RefSeq proteins (8): NP_001157260, NP_001157262, NP_001231825, NP_001231826, NP_001231827, NP_001362847, NP_001362849, NP_005147 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR006536	HnRNP-L/PTB	Family
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR021790	PTBP1-like_RRM2	Domain
IPR033110	PTBP3_RRM4	Domain
IPR034326	ROD1_RRM1	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR055204	HNRNPL_RRM	Domain

Pfam: PF11835, PF13893, PF22976

UniProt features (23 total): modified residue 7, splice variant 5, domain 4, cross-link 2, region of interest 2, chain 1, sequence conflict 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95758-F1	70.48	0.10

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 (9): 127, 138, 423, 454, 65, 216, 1, 1, 17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 336 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, TGGTGCT_MIR29A_MIR29B_MIR29C, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_MYELOID_CELL_HOMEOSTASIS, GOBP_MYELOID_CELL_DEVELOPMENT, GOBP_ERYTHROCYTE_HOMEOSTASIS, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, PATIL_LIVER_CANCER, GTGCCTT_MIR506, AGTCTTA_MIR499, GOBP_ANATOMICAL_STRUCTURE_MATURATION, MARTINEZ_RB1_TARGETS_UP, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN

GO Biological Process (8): mRNA processing (GO:0006397), RNA splicing (GO:0008380), anatomical structure morphogenesis (GO:0009653), negative regulation of RNA splicing (GO:0033119), erythrocyte maturation (GO:0043249), regulation of RNA splicing (GO:0043484), regulation of cell differentiation (GO:0045595), cell differentiation (GO:0030154)

GO Molecular Function (3): RNA binding (GO:0003723), mRNA binding (GO:0003729), nucleic acid binding (GO:0003676)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
RNA splicing	2
mRNA metabolic process	1
developmental process	1
anatomical structure development	1
negative regulation of gene expression	1
regulation of RNA splicing	1
cell maturation	1
erythrocyte development	1
regulation of gene expression	1
regulation of primary metabolic process	1
cell differentiation	1
regulation of developmental process	1
regulation of cellular process	1
cellular developmental process	1
nucleic acid binding	1
RNA binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1524 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTBP3	NEDD4L	Q96PU5	721
PTBP3	RAVER1	Q8IY67	672
PTBP3	CCT4	P50991	609
PTBP3	CTHRC1	Q96CG8	588
PTBP3	RAVER2	Q9HCJ3	588
PTBP3	CELF1	Q92879	586
PTBP3	KHSRP	Q92945	581
PTBP3	HMMR	O75330	554
PTBP3	HNRNPC	P07910	513
PTBP3	HNRNPDL	O14979	510
PTBP3	ZEB1	P37275	483
PTBP3	THBS4	P35443	463
PTBP3	IQGAP3	Q86VI3	446
PTBP3	BCL2	P10415	434
PTBP3	RBMS1	P29558	431

IntAct

60 interactions, top by confidence:

A	B	Type	Score
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
ZNRD2	MYO9A	psi-mi:“MI:0914”(association)	0.530
PTBP3	HNRNPC	psi-mi:“MI:0914”(association)	0.480
PTBP3	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440
TAS2R39	PTBP3	psi-mi:“MI:0915”(physical association)	0.400
UGT1A8	PTBP3	psi-mi:“MI:0915”(physical association)	0.400
	PTBP3	psi-mi:“MI:0914”(association)	0.350
NOTCH1	CNOT1	psi-mi:“MI:0914”(association)	0.350
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
CACNA1C	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
CAPZB	ENAH	psi-mi:“MI:0914”(association)	0.350
COPB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
COPE	ESYT2	psi-mi:“MI:0914”(association)	0.350
	GTPBP10	psi-mi:“MI:0914”(association)	0.350
	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
	EIF3F	psi-mi:“MI:0914”(association)	0.350
PABPC5	APOBEC3DE	psi-mi:“MI:0914”(association)	0.350
	SUPT5H	psi-mi:“MI:0914”(association)	0.350
PTBP3	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
	POLRMT	psi-mi:“MI:0914”(association)	0.350
CCT8L2	DVL2	psi-mi:“MI:0914”(association)	0.350
	DDX3X	psi-mi:“MI:0914”(association)	0.350

BioGRID (236): PTBP3 (Affinity Capture-MS), CHEK1 (Co-fractionation), PTBP3 (Co-fractionation), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS), PTBP3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IEW8, A4QNI8, B5DF91, O01671, O09032, O17310, O61374, O64380, O95758, O97018, P16914, P19339, P26378, P26599, P42731, P70372, P86049, Q12926, Q14576, Q15717, Q1JQ73, Q24668, Q28FX0, Q28GD4, Q29099, Q5R9H4, Q5R9Z6, Q5U259, Q5YD48, Q60899, Q60900, Q61701, Q6DEY7, Q6GLB5, Q6GR16, Q6YZW2, Q7SZT7, Q8CH84, Q8GZ26, Q8LFS6

Diamond homologs: E9PT37, O95758, P0DW16, P17225, P26599, Q00438, Q14966, Q29099, Q3UQS8, Q5T481, Q61464, Q66H20, Q8BHD7, Q8WN55, Q91Z31, Q9FGL9, Q9UKA9, Q9ULV3, Q9Z118, P40567, P43243, P43244, Q15233, Q5FVM4, Q5RFL9, Q6ICX4, Q8K310, Q99K48, Q9MAC5, O74452, A2Y0J7, B8AM21, O22922, O74968, P08579, P09012, P43332, P45429, Q06AA4, Q0DKM4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 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.

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of translation	5	16.3×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2567 predictions. Top by Δscore:

Variant	Effect	Δscore
9:112224131:A:AC	donor_gain	1.0000
9:112224132:C:CC	donor_gain	1.0000
9:112227409:A:AC	donor_gain	1.0000
9:112227410:C:CC	donor_gain	1.0000
9:112227410:CGGA:C	donor_gain	1.0000
9:112227410:CGGAA:C	donor_gain	1.0000
9:112227623:CATTG:C	acceptor_gain	1.0000
9:112227625:TTG:T	acceptor_gain	1.0000
9:112227631:G:GC	acceptor_gain	1.0000
9:112227634:C:CT	acceptor_gain	1.0000
9:112227635:A:AC	acceptor_gain	1.0000
9:112227635:A:C	acceptor_gain	1.0000
9:112227635:A:T	acceptor_gain	1.0000
9:112228376:GTACC:G	donor_loss	1.0000
9:112228377:TAC:T	donor_loss	1.0000
9:112228379:CCT:C	donor_loss	1.0000
9:112228379:CCTAG:C	donor_gain	1.0000
9:112228383:G:C	donor_gain	1.0000
9:112228388:G:C	donor_gain	1.0000
9:112228470:CTC:C	acceptor_gain	1.0000
9:112228470:CTCCT:C	acceptor_loss	1.0000
9:112228473:C:CC	acceptor_gain	1.0000
9:112228477:T:C	acceptor_gain	1.0000
9:112228477:T:TC	acceptor_gain	1.0000
9:112250924:CTCA:C	donor_loss	1.0000
9:112250925:TCA:T	donor_loss	1.0000
9:112250926:CA:C	donor_loss	1.0000
9:112250927:ACCA:A	donor_loss	1.0000
9:112252786:TAT:T	acceptor_gain	1.0000
9:112252789:C:CC	acceptor_gain	1.0000

AlphaMissense

3426 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:112223869:G:C	F547L	1.000
9:112223869:G:T	F547L	1.000
9:112223870:A:G	F547S	1.000
9:112223871:A:G	F547L	1.000
9:112223874:A:G	S546P	1.000
9:112223876:A:T	V545D	1.000
9:112223878:T:A	R544S	1.000
9:112223878:T:G	R544S	1.000
9:112223879:C:G	R544T	1.000
9:112223882:A:G	L543P	1.000
9:112223882:A:T	L543H	1.000
9:112223924:A:G	L529P	1.000
9:112223963:A:G	L516P	1.000
9:112223966:G:T	A515E	1.000
9:112223967:C:G	A515P	1.000
9:112223968:C:A	M514I	1.000
9:112223968:C:G	M514I	1.000
9:112223968:C:T	M514I	1.000
9:112223969:A:C	M514R	1.000
9:112223969:A:G	M514T	1.000
9:112227416:G:C	N481K	1.000
9:112227416:G:T	N481K	1.000
9:112227423:A:C	L479R	1.000
9:112227423:A:G	L479P	1.000
9:112227423:A:T	L479H	1.000
9:112227425:A:C	H478Q	1.000
9:112227425:A:T	H478Q	1.000
9:112227426:T:C	H478R	1.000
9:112227427:G:C	H478D	1.000
9:112227427:G:T	H478N	1.000

dbSNP variants (sampled 300 via entrez): RS1000031079 (9:112332247 C>A,G), RS1000044660 (9:112325613 G>A,T), RS1000045806 (9:112303427 A>G,T), RS1000051948 (9:112322153 A>AG), RS1000101589 (9:112373933 C>G), RS1000104790 (9:112264176 A>G), RS1000115715 (9:112322705 C>G,T), RS1000119838 (9:112344915 C>T), RS1000140567 (9:112289008 C>A,T), RS1000168383 (9:112369782 G>C), RS1000197821 (9:112243011 T>G), RS1000211944 (9:112368497 C>A,G), RS1000250585 (9:112362124 A>T), RS1000253782 (9:112297939 G>A), RS1000255654 (9:112377551 T>G)

Disease associations

OMIM: gene MIM:607527 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004227_12	Obstetric antiphospholipid syndrome	8.000000e-06
GCST009525_3	Panic disorder	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066398 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.74	Kd	18.1	nM	CHEMBL5653589
7.74	ED50	18.1	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149142: Binding affinity to human PTBP3 incubated for 45 mins by Kinobead based pull down assay	kd	0.0181	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, decreases expression	3
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	3
Aflatoxin B1	affects expression, decreases methylation, increases expression	3
cobaltous chloride	decreases expression, increases expression	2
Weichang’an	decreases expression	2
Tobacco Smoke Pollution	decreases methylation, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
geldanamycin	increases expression	1
urushiol	increases expression	1
2,4,6-tribromophenol	decreases expression	1
methylmercuric chloride	increases expression	1
alpha phellandrene	increases expression	1
decabromobiphenyl ether	decreases expression	1
sodium arsenite	increases expression	1
tetrabromobisphenol A	decreases expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol S	increases expression	1
jinfukang	decreases expression	1
Arsenic Trioxide	increases expression	1
Vorinostat	decreases expression	1
Caffeine	decreases phosphorylation	1
Cisplatin	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652184	Binding	Binding affinity to human PTBP3 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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