PTBP2

Summary

PTBP2 (polypyrimidine tract binding protein 2, HGNC:17662) is a protein-coding gene on chromosome 1p21.3, encoding Polypyrimidine tract-binding protein 2 (Q9UKA9). RNA-binding protein which binds to intronic polypyrimidine tracts and mediates negative regulation of exons splicing.

The protein encoded by this gene binds to intronic polypyrimidine clusters in pre-mRNA molecules and is implicated in controlling the assembly of other splicing-regulatory proteins. This protein is very similar to the polypyrimidine tract binding protein (PTB) but most of its isoforms are expressed primarily in the brain. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 58155 — RefSeq curated summary.

At a glance

• GWAS associations: 35
• Clinical variants (ClinVar): 64 total — 3 pathogenic
• MANE Select transcript: NM_021190

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17662
Approved symbol	PTBP2
Name	polypyrimidine tract binding protein 2
Location	1p21.3
Locus type	gene with protein product
Status	Approved
Aliases	brPTB, nPTB, PTB, PTBLP
Ensembl gene	ENSG00000117569
Ensembl biotype	protein_coding
OMIM	608449
Entrez	58155

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 17 protein_coding, 9 retained_intron, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000370197, ENST00000370198, ENST00000426398, ENST00000459735, ENST00000460706, ENST00000462433, ENST00000476419, ENST00000476783, ENST00000482253, ENST00000492905, ENST00000609116, ENST00000674579, ENST00000674951, ENST00000675080, ENST00000675365, ENST00000675401, ENST00000675735, ENST00000676096, ENST00000676292, ENST00000706595, ENST00000706596, ENST00000706597, ENST00000706598, ENST00000706599, ENST00000890857, ENST00000938887, ENST00000938888, ENST00000938889, ENST00000938890, ENST00000938891, ENST00000968497, ENST00000968498

RefSeq mRNA: 8 — MANE Select: NM_021190 NM_001300985, NM_001300986, NM_001300987, NM_001300988, NM_001300989, NM_001300990, NM_001410833, NM_021190

CCDS: CCDS72828, CCDS72829, CCDS72830, CCDS754, CCDS91005, CCDS91006

Canonical transcript exons

ENST00000674951 — 14 exons

Exon	Start	End
ENSE00003458415	96723564	96723594
ENSE00003464272	96751425	96751500
ENSE00003492375	96785059	96785254
ENSE00003511921	96769703	96769875
ENSE00003519797	96804800	96804939
ENSE00003525761	96806419	96806452
ENSE00003568917	96770708	96770851
ENSE00003584338	96812712	96812928
ENSE00003598607	96806866	96806958
ENSE00003628024	96813029	96813106
ENSE00003649021	96777836	96777946
ENSE00003688193	96777585	96777749
ENSE00003900845	96721784	96721872
ENSE00003902319	96813276	96815049

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 97.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.8587 / max 933.6806, expressed in 1785 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4140	32.6337	1785
4141	0.2250	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	97.25	gold quality
ganglionic eminence	UBERON:0004023	97.17	gold quality
corpus callosum	UBERON:0002336	96.69	gold quality
ventricular zone	UBERON:0003053	96.66	gold quality
embryo	UBERON:0000922	96.15	gold quality
calcaneal tendon	UBERON:0003701	95.29	gold quality
substantia nigra pars compacta	UBERON:0001965	95.26	gold quality
blood vessel layer	UBERON:0004797	95.19	gold quality
mucosa of stomach	UBERON:0001199	94.98	gold quality
secondary oocyte	CL:0000655	94.68	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.50	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.44	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.30	gold quality
superficial temporal artery	UBERON:0001614	93.75	gold quality
subthalamic nucleus	UBERON:0001906	93.55	gold quality
endocervix	UBERON:0000458	92.91	gold quality
body of uterus	UBERON:0009853	92.81	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	92.81	gold quality
tibia	UBERON:0000979	92.69	gold quality
inferior vagus X ganglion	UBERON:0005363	92.67	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.41	gold quality
saphenous vein	UBERON:0007318	92.40	gold quality
lower esophagus	UBERON:0013473	92.38	gold quality
superior vestibular nucleus	UBERON:0007227	92.36	gold quality
ectocervix	UBERON:0012249	91.93	gold quality
medulla oblongata	UBERON:0001896	91.90	gold quality
pons	UBERON:0000988	91.84	gold quality
left uterine tube	UBERON:0001303	91.83	gold quality
dorsal plus ventral thalamus	UBERON:0001897	91.81	gold quality
visceral pleura	UBERON:0002401	91.75	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-76312	yes	977.20
E-ANND-3	yes	11.54
E-MTAB-6911	no	369.44
E-MTAB-6386	no	125.39

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NFKB

miRNA regulators (miRDB)

200 targeting PTBP2, 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-3064-3P	100.00	70.09	1254
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-7152-3P	99.97	67.47	849

Literature-anchored findings (GeneRIF, showing 17)

• The nPTB proximal promoter, although rich in G+C content and presenting putative binding sites for the transcription factors Sp1, NF-1, NF-kB and Oct-1, lacks a typical TATA box. (PMID:16002244)
• Study shows that PTB can function as an anti-repressor molecule to counteract the splicing inhibitory activity of SRp30c. (PMID:17548433)
• present fluorescence, NMR, and in vivo splicing data in support of a role of PTB in inducing RNA loops. We show that the RNA recognition motifs (RRMs) 3 and 4 of PTB can bind two distant pyrimidine tracts and bring their 5’ and 3’ ends in close proximity (PMID:20160105)
• Regulation of the mutually exclusive exons 8a and 8 in the CaV1.2 calcium channel transcript by polypyrimidine tract-binding protein. (PMID:21282112)
• Changes in miR-223/PTBP2 pathway could contribute of abnormal splicing in chronic myeloid leukemia. (PMID:23174904)
• Defining the multifunctional roles of PTB will contribute to the understanding of key regulatory events in gene expression. (PMID:24264039)
• In T98G glioma cells, the level of sumoylated PTBP2 was reduced compared to that of normal brain cells. Overall, this study shows that PTBP2 is posttranslationally modified by SUMO1. (PMID:24286314)
• MALAT1 binds to SFPQ releasing PTBP2 from the SFPQ/PTBP2 complex, the increased SFPQ-detached PTBP2 promotes cell proliferation and migration in colorectal cancer. (PMID:25025966)
• PTBP1 and PTBP2 impaired autoregulation of SRSF3 in oral squamous cell carcinoma cancer cells. (PMID:26416554)
• Data show that polypyrimidine tract-binding proteins nPTB and ROD1 interact with mitochondrial tRNA(Thr) in the cytoplasm outside of mitochondria. (PMID:26657638)
• It has been established that PTBP1 and PTBP2 are members of a family of cryptic exon repressors. (PMID:27681424)
• PTBP2 exon 10 inclusion is associated with the progression of CML and it is BCR-ABL1 dependent (PMID:30726713)
• LncRNA nuclear-enriched abundant transcript 1 shuttled by prostate cancer cells-secreted exosomes initiates osteoblastic phenotypes in the bone metastatic microenvironment via miR-205-5p/runt-related transcription factor 2/splicing factor proline- and glutamine-rich/polypyrimidine tract-binding protein 2 axis. (PMID:34459124)
• SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. (PMID:34548489)
• Associations between Gene-Gene Interaction and Overweight/Obesity of 12-Month-Old Chinese Infants. (PMID:35295960)
• Mapping PTBP2 binding in human brain identifies SYNGAP1 as a target for therapeutic splice switching. (PMID:37149717)
• KIS counteracts PTBP2 and regulates alternative exon usage in neurons. (PMID:38597390)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	ptbp2b	ENSDARG00000015901
danio_rerio	ptbp2a	ENSDARG00000101947
mus_musculus	Ptbp2	ENSMUSG00000028134
rattus_norvegicus	Ptbp2	ENSRNOG00000010827
drosophila_melanogaster	heph	FBGN0011224
caenorhabditis_elegans		WBGENE00004207

Paralogs (5): PTBP1 (ENSG00000011304), HNRNPL (ENSG00000104824), PTBP3 (ENSG00000119314), HNRNPLL (ENSG00000143889), RBM20 (ENSG00000203867)

Protein

Protein identifiers

Polypyrimidine tract-binding protein 2 — Q9UKA9 (reviewed: Q9UKA9)

Alternative names: Neural polypyrimidine tract-binding protein, Neurally-enriched homolog of PTB, PTB-like protein

All UniProt accessions (9): A0A6Q8PEZ3, A0A6Q8PFC0, A0A6Q8PFE6, A0A6Q8PFT8, A0A6Q8PH43, A0A6Q8PH82, A0A7I2RVZ4, B4DI28, Q9UKA9

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein which binds to intronic polypyrimidine tracts and mediates negative regulation of exons splicing. May antagonize in a tissue-specific manner the ability of NOVA1 to activate exon selection. In addition to its function in pre-mRNA splicing, plays also a role in the regulation of translation. Reduced affinity for RNA.

Subunit / interactions. Monomer. Interacts with NOVA1; the interaction is direct. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Part of a ternary complex containing KHSRP and HNRPH1. Interacts with NOVA2; the interaction is direct.

Subcellular location. Nucleus.

Tissue specificity. Mainly expressed in brain although also detected in other tissues like heart and skeletal muscle. Isoform 1 and isoform 2 are specifically expressed in neuronal tissues. Isoform 3 and isoform 4 are expressed in non-neuronal tissues. Isoform 5 and isoform 6 are truncated forms expressed in non-neuronal tissues.

Isoforms (6)

UniProt ID	Names	Canonical?
Q9UKA9-1	1, nPTB1	yes
Q9UKA9-2	2, nPTB2, PTBPLP-L
Q9UKA9-3	3, nPTB3, PTBPLP-L'
Q9UKA9-4	4, nPTB4
Q9UKA9-5	5, nPTB5, nPTB7, PTBPLP-S
Q9UKA9-6	6, nPTB6, nPTB8, PTBPLP-S'

RefSeq proteins (8): NP_001287914, NP_001287915, NP_001287916, NP_001287917, NP_001287918, NP_001287919, NP_001397762, NP_067013* (*=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
IPR034799	PTBP2_RRM3	Domain
IPR034800	PTBP2_RRM4	Domain
IPR035002	PTBP2_RRM1	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR055204	HNRNPL_RRM	Domain

Pfam: PF11835, PF13893, PF22976

UniProt features (44 total): strand 17, helix 8, turn 6, domain 4, splice variant 4, modified residue 4, chain 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
4CQ1	X-RAY DIFFRACTION	1.69
2CQ1	SOLUTION NMR
2MJU	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UKA9-F1	73.84	0.28

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 (4): 1, 26, 27, 308

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 243 (showing top): GOBP_SPINAL_CORD_DEVELOPMENT, GGGACCA_MIR133A_MIR133B, RNGTGGGC_UNKNOWN, GOBP_HINDBRAIN_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, GGTGTGT_MIR329, GCM_ZNF198, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GCM_PPM1D, GOBP_NEURAL_PRECURSOR_CELL_PROLIFERATION, GTGCCTT_MIR506, AGTCTTA_MIR499, YY1_02, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION

GO Biological Process (8): mRNA splice site recognition (GO:0006376), spinal cord development (GO:0021510), cerebellum development (GO:0021549), negative regulation of RNA splicing (GO:0033119), regulation of RNA splicing (GO:0043484), regulation of neural precursor cell proliferation (GO:2000177), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA binding (GO:0003729), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), spliceosomal complex (GO:0005681), growth cone (GO:0030426), neuronal cell body (GO:0043025), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anatomical structure development	2
RNA splicing	2
RNA processing	2
binding	2
spliceosomal complex assembly	1
protein-RNA complex assembly	1
central nervous system development	1
metencephalon development	1
negative regulation of gene expression	1
regulation of RNA splicing	1
regulation of gene expression	1
regulation of primary metabolic process	1
regulation of cell population proliferation	1
neural precursor cell proliferation	1
mRNA metabolic process	1
nucleic acid binding	1
RNA binding	1
intracellular membrane-bounded organelle	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
site of polarized growth	1
distal axon	1
somatodendritic compartment	1
cell body	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1388 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTBP2	SFPQ	P23246	989
PTBP2	SRRM4	A7MD48	926
PTBP2	NOVA2	Q9UNW9	888
PTBP2	NOVA1	P51513	861
PTBP2	RAVER1	Q8IY67	843
PTBP2	KHSRP	Q92945	811
PTBP2	HNRNPH1	P31943	776
PTBP2	HNRNPDL	O14979	755
PTBP2	HNRNPC	P07910	729
PTBP2	MORF4L1	Q9UBU8	721
PTBP2	HNRNPA1	P09651	710
PTBP2	CELF2	O95319	698
PTBP2	SRSF3	P23152	694
PTBP2	DAAM1	Q9Y4D1	684
PTBP2	KHDRBS1	Q07666	670
PTBP2	TPM1	P09493	670

IntAct

44 interactions, top by confidence:

A	B	Type	Score
IGF2BP1	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
RBM10	PTBP2	psi-mi:“MI:0915”(physical association)	0.550
PTBP2	QKI	psi-mi:“MI:0915”(physical association)	0.550
	NHERF1	psi-mi:“MI:0914”(association)	0.530
PTBP2	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
PTBP2	PTBP1	psi-mi:“MI:0915”(physical association)	0.370
PTBP2	CCDC106	psi-mi:“MI:0915”(physical association)	0.370
PTBP2		psi-mi:“MI:0915”(physical association)	0.370
TOM1	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
EIF5A2	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
CALCOCO2	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
SNRPA	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
PUF60	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
ELAVL1	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
PTBP2	HNRNPC	psi-mi:“MI:0915”(physical association)	0.370
PTBP2	HNRNPAB	psi-mi:“MI:0915”(physical association)	0.370
PTBP2	RBM4	psi-mi:“MI:0915”(physical association)	0.370
MATR3	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
HNRNPD	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
PTBP2	KHDRBS3	psi-mi:“MI:0915”(physical association)	0.370
KHDRBS1	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
GOLGA2	PTBP2	psi-mi:“MI:0915”(physical association)	0.370
JUN		psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
IGF2BP1	DDX3X	psi-mi:“MI:0914”(association)	0.350
STAT1	KPNA6	psi-mi:“MI:0914”(association)	0.350
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
TRAF2	TMEM178B	psi-mi:“MI:0914”(association)	0.350

BioGRID (111): PTBP2 (Two-hybrid), PTBP2 (Two-hybrid), PTBP2 (Two-hybrid), PTBP2 (Two-hybrid), MATR3 (Two-hybrid), PTBP2 (Affinity Capture-MS), PTBP2 (Affinity Capture-RNA), PTBP2 (Two-hybrid), PTBP2 (Affinity Capture-MS), PTBP2 (Affinity Capture-MS), PTBP2 (Affinity Capture-MS), PTBP2 (Affinity Capture-MS), PTBP2 (Synthetic Lethality), PTBP2 (Affinity Capture-MS), PTBP2 (Affinity Capture-MS)

ESM2 similar proteins: A2Y0J7, B5DF91, B8AM21, O22922, O95758, P09012, P17225, P26368, P26369, P26599, P43332, P45429, P70372, Q00438, Q06AA4, Q08E07, Q0DKM4, Q10MR0, Q12926, Q14576, Q15717, Q24562, Q28FX0, Q29099, Q2KIR1, Q39244, Q54J05, Q5R9Z6, Q5SZQ8, Q60899, Q60900, Q62189, Q66H20, Q6GLB5, Q8BHD7, Q8BHN5, Q8CFD1, Q8CH84, Q8CIN6, Q8H1S6

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

3 interactions.

A	Effect	B	Mechanism
PTBP2	“down-regulates quantity by repression”	SRC	“post transcriptional regulation”
PTBP2	“up-regulates activity”	KHSRP	binding
PTBP2	“up-regulates activity”	HNRNPH1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 47 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
mRNA Polyadenylation	6	16.0×	2e-04
Processing of Capped Intron-Containing Pre-mRNA	6	14.9×	2e-04
mRNA Splicing - Major Pathway	7	11.6×	2e-04
Dengue Virus-Host Interactions	6	8.3×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
regulation of alternative mRNA splicing, via spliceosome	6	35.7×	7e-06
negative regulation of translation	5	23.9×	5e-04
mRNA processing	6	11.5×	1e-03
RNA splicing	5	10.8×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	37
Likely benign	1
Benign	3

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
442387	GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)	Pathogenic
4528354	NM_021190.4(PTBP2):c.2T>C (p.Met1Thr)	Pathogenic
4528355	NM_021190.4(PTBP2):c.41G>C (p.Arg14Thr)	Pathogenic

SpliceAI

3331 predictions. Top by Δscore:

Variant	Effect	Δscore
1:96751422:T:G	acceptor_gain	1.0000
1:96751423:A:AG	acceptor_gain	1.0000
1:96751424:G:GG	acceptor_gain	1.0000
1:96751424:GA:G	acceptor_gain	1.0000
1:96751424:GAGA:G	acceptor_gain	1.0000
1:96769701:A:AG	acceptor_gain	1.0000
1:96769702:G:GA	acceptor_gain	1.0000
1:96769702:GCC:G	acceptor_gain	1.0000
1:96769702:GCCA:G	acceptor_gain	1.0000
1:96769792:G:GT	donor_gain	1.0000
1:96769792:G:T	donor_gain	1.0000
1:96770704:TCAG:T	acceptor_loss	1.0000
1:96770705:CA:C	acceptor_loss	1.0000
1:96770706:A:AG	acceptor_gain	1.0000
1:96770706:A:C	acceptor_loss	1.0000
1:96770707:G:GA	acceptor_loss	1.0000
1:96770707:G:GG	acceptor_gain	1.0000
1:96770707:GGC:G	acceptor_gain	1.0000
1:96770848:CCAA:C	donor_gain	1.0000
1:96770849:CAA:C	donor_gain	1.0000
1:96770849:CAAG:C	donor_loss	1.0000
1:96770852:G:C	donor_loss	1.0000
1:96770852:G:GG	donor_gain	1.0000
1:96770853:T:A	donor_loss	1.0000
1:96770854:AA:A	donor_loss	1.0000
1:96777584:GCGT:G	acceptor_gain	1.0000
1:96777746:CCAA:C	donor_gain	1.0000
1:96777746:CCAAG:C	donor_loss	1.0000
1:96777748:AAGTA:A	donor_loss	1.0000
1:96777749:AGTAA:A	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000002728 (1:96776300 A>C), RS1000011396 (1:96740060 A>G), RS1000020033 (1:96784345 C>T), RS1000020869 (1:96722035 C>G,T), RS1000029168 (1:96758499 A>C), RS1000060480 (1:96744023 T>C), RS1000071003 (1:96784659 T>C), RS1000093032 (1:96814882 T>C,G), RS1000110485 (1:96782573 G>A), RS1000112457 (1:96733153 G>A,T), RS1000140282 (1:96803290 T>G), RS1000146260 (1:96823051 C>T), RS1000184840 (1:96799941 T>A), RS1000264236 (1:96760629 T>C), RS1000264688 (1:96778281 T>G)

Disease associations

OMIM: gene MIM:608449 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

35 associations (top):

Study	Trait	p-value
GCST000434_3	Schizophrenia	6.000000e-07
GCST000830_27	Body mass index	4.000000e-10
GCST001565_8	Schizophrenia	5.000000e-07
GCST002783_439	Body mass index	1.000000e-13
GCST002783_515	Body mass index	2.000000e-12
GCST002783_7	Body mass index	6.000000e-09
GCST002783_87	Body mass index	4.000000e-07
GCST004065_83	Waist circumference	6.000000e-06
GCST004065_84	Waist circumference	5.000000e-09
GCST004066_105	Hip circumference	8.000000e-07
GCST004066_64	Hip circumference	3.000000e-10
GCST004495_75	BMI (adjusted for smoking behaviour)	3.000000e-08
GCST004495_88	BMI (adjusted for smoking behaviour)	1.000000e-06
GCST004497_31	Body mass index (joint analysis main effects and smoking interaction)	1.000000e-06
GCST004557_150	Body mass index	3.000000e-07
GCST004558_50	Body mass index (joint analysis main effects and physical activity interaction)	4.000000e-06
GCST004558_69	Body mass index (joint analysis main effects and physical activity interaction)	4.000000e-08
GCST004560_35	Body mass index in physically inactive individuals	3.000000e-06
GCST004904_105	Body mass index	4.000000e-10
GCST005337_25	Headache	2.000000e-08
GCST006268_490	Reaction time	2.000000e-08
GCST006921_11	Regular attendance at a pub or social club	5.000000e-10
GCST007326_23	Number of sexual partners	3.000000e-08
GCST007327_11	Smoking status (ever vs never smokers)	2.000000e-08
GCST007556_22	Autism spectrum disorder	4.000000e-08
GCST007576_305	Chronotype	5.000000e-13
GCST007576_74	Chronotype	5.000000e-13
GCST007816_3	Trunk fat mass adjusted for trunk lean mass	7.000000e-10
GCST008465_6	Anorexia nervosa	3.000000e-08
GCST010266_1	Femoral neck bone mineral density and trunk fat mass adjusted by trunk lean mass	4.000000e-09

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004318	smoking behavior
EFO:0008002	physical activity measurement
EFO:0008393	reaction time measurement
EFO:0009592	social interaction measurement
EFO:0008328	chronotype measurement
EFO:0007785	femoral neck bone mineral density
EFO:0009819	comparative body size at age 10, self-reported
EFO:0007828	daytime rest measurement
EFO:0009749	age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	7
bisphenol A	decreases methylation, affects cotreatment, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression, increases expression	1
methylmercuric chloride	decreases expression	1
testosterone undecanoate	affects cotreatment, decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
sodium arsenite	decreases expression, increases abundance	1
manganese chloride	decreases expression, increases abundance	1
obeticholic acid	decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Cuprizone	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diethylstilbestrol	increases expression	1
Doxorubicin	decreases expression	1
Gold	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Nicotine	increases expression	1

Clinical trials (associated diseases)

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