CPSF2

Summary

CPSF2 (cleavage and polyadenylation specific factor 2, HGNC:2325) is a protein-coding gene on chromosome 14q32.12, encoding Cleavage and polyadenylation specificity factor subunit 2 (Q9P2I0). Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3’-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. It is a common-essential gene (DepMap: required in 99.3% of cancer cell lines).

Predicted to enable RNA binding activity. Involved in mRNA 3’-end processing by stem-loop binding activity and cleavage. Located in membrane. Part of mRNA cleavage and polyadenylation specificity factor complex.

Source: NCBI Gene 53981 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 76 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 99.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_017437

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2325
Approved symbol	CPSF2
Name	cleavage and polyadenylation specific factor 2
Location	14q32.12
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1367, CPSF100
Ensembl gene	ENSG00000165934
Ensembl biotype	protein_coding
OMIM	606028
Entrez	53981

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000298875, ENST00000553427, ENST00000554290, ENST00000555244, ENST00000556622, ENST00000908829, ENST00000908830, ENST00000908831, ENST00000932645, ENST00000932646, ENST00000932647, ENST00000932648, ENST00000932649, ENST00000932650, ENST00000943809

RefSeq mRNA: 4 — MANE Select: NM_017437 NM_001322270, NM_001322271, NM_001322272, NM_017437

CCDS: CCDS9902

Canonical transcript exons

ENST00000298875 — 16 exons

Exon	Start	End
ENSE00001098228	92142164	92142351
ENSE00001098229	92157659	92157884
ENSE00001098230	92158983	92159282
ENSE00001098231	92155123	92155323
ENSE00001098233	92143004	92143294
ENSE00001098234	92156479	92156631
ENSE00001098236	92154358	92154458
ENSE00001260926	92135367	92135496
ENSE00001261020	92138232	92138347
ENSE00001313772	92134011	92134170
ENSE00001326336	92161652	92172145
ENSE00001332495	92130951	92131133
ENSE00001332498	92126122	92126180
ENSE00002533626	92121969	92122128
ENSE00003545625	92134250	92134355
ENSE00003788299	92161112	92161246

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 98.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.5291 / max 448.9475, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
141081	34.4394	1816
141082	0.0898	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	98.39	gold quality
tendon of biceps brachii	UBERON:0008188	95.47	gold quality
colonic epithelium	UBERON:0000397	94.91	gold quality
islet of Langerhans	UBERON:0000006	93.70	gold quality
tendon	UBERON:0000043	92.95	gold quality
adrenal tissue	UBERON:0018303	92.83	gold quality
stromal cell of endometrium	CL:0002255	92.72	gold quality
calcaneal tendon	UBERON:0003701	92.71	gold quality
upper arm skin	UBERON:0004263	92.21	gold quality
ventricular zone	UBERON:0003053	92.20	gold quality
vermiform appendix	UBERON:0001154	92.10	gold quality
monocyte	CL:0000576	91.95	gold quality
leukocyte	CL:0000738	91.77	gold quality
corpus callosum	UBERON:0002336	91.52	gold quality
caecum	UBERON:0001153	90.62	gold quality
bone marrow cell	CL:0002092	90.50	gold quality
tibialis anterior	UBERON:0001385	90.50	gold quality
medial globus pallidus	UBERON:0002477	90.42	gold quality
secondary oocyte	CL:0000655	90.39	gold quality
thymus	UBERON:0002370	90.16	gold quality
embryo	UBERON:0000922	89.82	gold quality
ganglionic eminence	UBERON:0004023	89.82	gold quality
muscle of leg	UBERON:0001383	89.39	gold quality
gastrocnemius	UBERON:0001388	89.25	gold quality
smooth muscle tissue	UBERON:0001135	89.17	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.05	gold quality
skeletal muscle organ	UBERON:0014892	89.02	gold quality
sperm	CL:0000019	88.97	gold quality
tonsil	UBERON:0002372	88.76	gold quality
cerebellar vermis	UBERON:0004720	88.67	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.85
E-MTAB-7606	no	494.98

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

171 targeting CPSF2, 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-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-559	99.95	72.28	3609

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 4)

• Conserved residues in CPSF2 and CPSF-73 are required for assembly of the endonuclease activity that cleaves histone pre-mRNAs. (PMID:18688255)
• Decreased CPSF2 expression is associated with increased cellular invasion and cancer stem cell population, and more aggressive disease in papillary thyroid cancer. (PMID:24654752)
• CPSF2 and SYMPK, are RBFOX2 cofactors for both inclusion and exclusion of internal exons. (PMID:25921069)
• CPSF2 may have a role in Papillary Thyroid Carcinoma (PMID:26148673)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cpsf2	ENSDARG00000028971
mus_musculus	Cpsf2	ENSMUSG00000041781
rattus_norvegicus	Cpsf2	ENSRNOG00000005733
drosophila_melanogaster	Cpsf100	FBGN0027873
caenorhabditis_elegans		WBGENE00017313

Paralogs (3): INTS9 (ENSG00000104299), CPSF3 (ENSG00000119203), INTS11 (ENSG00000127054)

Protein

Protein identifiers

Cleavage and polyadenylation specificity factor subunit 2 — Q9P2I0 (reviewed: Q9P2I0)

Alternative names: Cleavage and polyadenylation specificity factor 100 kDa subunit

All UniProt accessions (4): Q9P2I0, G3V3T7, G3V5T3, H0YJF4

UniProt curated annotations — full annotation on UniProt →

Function. Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3’-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Involved in the histone 3’ end pre-mRNA processing.

Subunit / interactions. Component of the cleavage and polyadenylation specificity factor (CPSF) complex, composed of CPSF1, CPSF2, CPSF3, CPSF4 and FIP1L1. Interacts with CPSF3, CSTF2 and SYMPK. Interacts with ZC3H3.

Subcellular location. Nucleus.

Similarity. Belongs to the metallo-beta-lactamase superfamily. RNA-metabolizing metallo-beta-lactamase-like family. CPSF2/YSH1 subfamily.

RefSeq proteins (4): NP_001309199, NP_001309200, NP_001309201, NP_059133* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001279	Metallo-B-lactamas	Domain
IPR011108	RMMBL	Domain
IPR022712	Beta_Casp	Domain
IPR025069	Cpsf2_C	Domain
IPR027075	CPSF2	Family
IPR035639	CPSF2_MBL	Domain
IPR036866	RibonucZ/Hydroxyglut_hydro	Homologous_superfamily

Pfam: PF07521, PF10996, PF13299, PF16661

UniProt features (58 total): strand 28, helix 14, modified residue 4, mutagenesis site 3, compositionally biased region 3, sequence conflict 2, turn 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
9NH5	ELECTRON MICROSCOPY	2.82
9NH6	ELECTRON MICROSCOPY	2.82
6URG	ELECTRON MICROSCOPY	3
9NGO	ELECTRON MICROSCOPY	3.01
6V4X	ELECTRON MICROSCOPY	3.2
9NB1	ELECTRON MICROSCOPY	3.85

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2I0-F1	81.14	0.55

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): 419, 420, 423, 660

Mutagenesis-validated functional residues (3):

Position	Phenotype
289	does not inhibit histone 3’-end processing.
543	inhibits histone 3’-end processing.
67	inhibits histone 3’-end processing.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-72187	mRNA 3’-end processing
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-77595	Processing of Intronless Pre-mRNAs
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA

MSigDB gene sets: 196 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GGGNRMNNYCAT_UNKNOWN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, PATIL_LIVER_CANCER, INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP, WANG_LMO4_TARGETS_DN, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS, GOBP_MRNA_3_END_PROCESSING, KIM_GERMINAL_CENTER_T_HELPER_UP, GOBP_HISTONE_MRNA_METABOLIC_PROCESS, GOBP_HISTONE_MRNA_CATABOLIC_PROCESS, CCAGGGG_MIR331

GO Biological Process (2): mRNA 3’-end processing by stem-loop binding and cleavage (GO:0006398), mRNA processing (GO:0006397)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (6): nucleoplasm (GO:0005654), mRNA cleavage and polyadenylation specificity factor complex (GO:0005847), membrane (GO:0016020), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Transport of Mature mRNAs Derived from Intronless Transcripts	1
Processing of Capped Intron-Containing Pre-mRNA	1
RNA Polymerase II Transcription	1
Processing of Capped Intronless Pre-mRNA	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
synapse	2
histone mRNA metabolic process	1
mRNA 3’-end processing	1
RNA processing	1
mRNA metabolic process	1
nucleic acid binding	1
binding	1
nuclear lumen	1
mRNA cleavage factor complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2654 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPSF2	CPSF4	O95639	999
CPSF2	CPSF1	Q10570	999
CPSF2	SYMPK	Q92797	997
CPSF2	WDR33	Q9C0J8	997
CPSF2	CPSF3	Q9UKF6	993
CPSF2	FIP1L1	Q6UN15	992
CPSF2	CSTF2	P33240	978
CPSF2	CSTF1	Q05048	920
CPSF2	THOC5	Q13769	920
CPSF2	CSTF3	Q12996	904
CPSF2	DCLRE1A	Q6PJP8	900
CPSF2	PCF11	O94913	866
CPSF2	CPSF7	Q8N684	833
CPSF2	NUDT21	O43809	824
CPSF2	CPSF6	Q16630	775

IntAct

99 interactions, top by confidence:

A	B	Type	Score
CPSF2	SYMPK	psi-mi:“MI:0915”(physical association)	0.850
SYMPK	CPSF2	psi-mi:“MI:0914”(association)	0.850
CPSF2	SYMPK	psi-mi:“MI:0914”(association)	0.850
SYMPK	CPSF2	psi-mi:“MI:0915”(physical association)	0.850
CPSF4	FIP1L1	psi-mi:“MI:0914”(association)	0.660
CPSF3	CPSF4	psi-mi:“MI:0914”(association)	0.640
CDC73	CSTF2	psi-mi:“MI:0914”(association)	0.580
CDC73	CSTF2	psi-mi:“MI:0915”(physical association)	0.580
CPSF1	CPSF4	psi-mi:“MI:0915”(physical association)	0.560
SYMPK	CPSF4	psi-mi:“MI:0914”(association)	0.530
TUT1	CSTF2	psi-mi:“MI:0914”(association)	0.530
WDR33	CPSF4	psi-mi:“MI:0914”(association)	0.530
ASB7	POLR3A	psi-mi:“MI:0914”(association)	0.530
CPSF3	CSTF2	psi-mi:“MI:0914”(association)	0.530
CDC73	CPSF4	psi-mi:“MI:0914”(association)	0.500
CPSF2	CSTF2	psi-mi:“MI:0914”(association)	0.500
CPSF2	CSTF2	psi-mi:“MI:0915”(physical association)	0.500
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
SYMPK	TUT1	psi-mi:“MI:0914”(association)	0.460
CPSF2	WWOX	psi-mi:“MI:0915”(physical association)	0.400
CPSF3	P4HA2	psi-mi:“MI:0914”(association)	0.350
CEP170P1	PCYT1A	psi-mi:“MI:0914”(association)	0.350
FIP1L1	WWP2	psi-mi:“MI:0914”(association)	0.350
RNPS1	CSNK2A1	psi-mi:“MI:0914”(association)	0.350
FOXL1	DDX39A	psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350

BioGRID (235): CPSF2 (Affinity Capture-Western), CPSF2 (Affinity Capture-MS), CPSF2 (Affinity Capture-MS), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CPSF2 (Co-fractionation), CSTF2 (Co-fractionation), FIP1L1 (Co-fractionation), ISY1-RAB43 (Co-fractionation)

ESM2 similar proteins: A0JN39, D2SW95, O00178, O35218, O43242, P11029, P11497, P23514, P53618, Q07G98, Q0JNK5, Q10568, Q13085, Q28559, Q2KJA6, Q4FZT2, Q4R5Z4, Q53PC7, Q58DN4, Q5F3X4, Q5R4F9, Q5R8R4, Q5R922, Q5SWU9, Q5VQ78, Q5XGS8, Q5ZIA5, Q5ZKK2, Q66HV4, Q68FK8, Q69YN2, Q6DFF4, Q6NUC2, Q7QG73, Q8BVQ5, Q8IWZ6, Q8K114, Q8K2G4, Q8L828, Q92889

Diamond homologs: A8XUS3, O17403, O35218, Q10568, Q55BS1, Q652P4, Q9LKF9, Q9P2I0, Q9V3D6, Q9W799, O74740, Q2YDM2, Q3MHC2, Q503E1, Q5NVE6, Q5TA45, Q5ZIH0, Q9CWS4, Q9VAH9, O13794

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CPSF2	“form complex”	“CPSF complex”	binding

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
Processing of Intronless Pre-mRNAs	9	73.4×	7e-14
mRNA 3’-end processing	14	39.4×	3e-17
RNA Polymerase II Transcription Termination	12	37.6×	1e-14
mRNA Polyadenylation	23	28.9×	1e-25
Transport of Mature mRNA Derived from an Intronless Transcript	6	23.3×	8e-06
Processing of Capped Intron-Containing Pre-mRNA	16	18.8×	1e-14
mRNA Splicing	10	15.7×	3e-08
Dengue Virus-Host Interactions	23	15.0×	4e-19

GO biological processes:

GO term	Partners	Fold	FDR
mRNA 3’-end processing	7	46.8×	3e-08
regulation of alternative mRNA splicing, via spliceosome	6	17.4×	1e-04
mRNA splicing, via spliceosome	15	16.4×	1e-11
mRNA transport	5	15.7×	1e-03
negative regulation of translation	6	14.0×	4e-04
regulation of RNA splicing	5	13.0×	2e-03
mRNA processing	11	10.3×	1e-06
RNA splicing	8	8.4×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3425 predictions. Top by Δscore:

Variant	Effect	Δscore
14:92122348:GCCC:G	donor_gain	1.0000
14:92126181:G:GG	donor_gain	1.0000
14:92130942:ATTT:A	acceptor_gain	1.0000
14:92130943:T:G	acceptor_gain	1.0000
14:92130945:T:TA	acceptor_gain	1.0000
14:92130946:GAAA:G	acceptor_loss	1.0000
14:92130948:AAG:A	acceptor_loss	1.0000
14:92130949:A:G	acceptor_gain	1.0000
14:92130950:G:GG	acceptor_gain	1.0000
14:92131129:AGGAA:A	donor_gain	1.0000
14:92131130:GGAA:G	donor_gain	1.0000
14:92131130:GGAAG:G	donor_gain	1.0000
14:92131131:GAA:G	donor_gain	1.0000
14:92131131:GAAG:G	donor_gain	1.0000
14:92131131:GAAGT:G	donor_loss	1.0000
14:92131132:AAGT:A	donor_loss	1.0000
14:92131133:AGT:A	donor_loss	1.0000
14:92131134:G:GG	donor_gain	1.0000
14:92131134:G:T	donor_loss	1.0000
14:92131135:TAA:T	donor_loss	1.0000
14:92134050:T:TA	acceptor_gain	1.0000
14:92134246:TTA:T	acceptor_loss	1.0000
14:92134248:A:AG	acceptor_gain	1.0000
14:92134248:AGTCT:A	acceptor_loss	1.0000
14:92134249:G:GT	acceptor_gain	1.0000
14:92134249:GT:G	acceptor_gain	1.0000
14:92134249:GTCTC:G	acceptor_gain	1.0000
14:92134356:G:A	donor_loss	1.0000
14:92134357:T:G	donor_loss	1.0000
14:92134372:GTA:G	donor_gain	1.0000

AlphaMissense

5186 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:92131052:T:C	L23P	1.000
14:92134030:G:C	A57P	1.000
14:92134037:T:A	L59Q	1.000
14:92134117:G:C	A86P	1.000
14:92134127:C:A	P89H	1.000
14:92134127:C:G	P89R	1.000
14:92134141:G:A	G94R	1.000
14:92134141:G:C	G94R	1.000
14:92134142:G:A	G94E	1.000
14:92134142:G:T	G94V	1.000
14:92134156:T:C	Y99H	1.000
14:92134160:A:T	D100V	1.000
14:92134250:T:C	S104P	1.000
14:92134298:G:C	D120H	1.000
14:92134299:A:C	D120A	1.000
14:92134299:A:G	D120G	1.000
14:92134299:A:T	D120V	1.000
14:92135388:T:A	I146N	1.000
14:92135406:G:A	G152D	1.000
14:92135417:G:C	G156R	1.000
14:92135418:G:A	G156D	1.000
14:92135418:G:T	G156V	1.000
14:92135429:T:A	W160R	1.000
14:92135429:T:C	W160R	1.000
14:92135436:T:A	I162K	1.000
14:92135436:T:G	I162R	1.000
14:92135482:C:A	N177K	1.000
14:92135482:C:G	N177K	1.000
14:92138276:T:C	L197P	1.000
14:92138279:T:C	L198P	1.000

dbSNP variants (sampled 300 via entrez): RS1000040093 (14:92157249 T>C), RS1000066590 (14:92122001 C>G,T), RS1000102024 (14:92146690 A>G), RS1000218911 (14:92147770 C>T), RS1000308397 (14:92152339 G>C), RS1000377952 (14:92143474 G>A), RS1000385790 (14:92150584 C>A), RS1000402319 (14:92139754 G>A,T), RS1000522496 (14:92131847 A>G,T), RS1000647485 (14:92136844 T>G), RS1000657521 (14:92152617 A>G), RS1001010600 (14:92125976 C>T), RS1001025527 (14:92128525 A>G), RS1001046532 (14:92150924 T>C), RS1001090160 (14:92170322 G>C)

Disease associations

OMIM: gene MIM:606028 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST000175_32	Height	1.000000e-10
GCST001066_5	Dialysis-related mortality	2.000000e-06
GCST001762_579	Obesity-related traits	3.000000e-06
GCST003996_30	Monobrow	4.000000e-21
GCST003997_5	Myopia	4.000000e-14
GCST005965_3	B cell acute lymphoblastic leukaemia (normal cytogenetics)	6.000000e-09
GCST005966_3	B cell acute lymphoblastic leukaemia (hyperdiploid negative)	2.000000e-06
GCST005967_3	B cell acute lymphoblastic leukaemia (Philadelphia chromosome negative)	3.000000e-06
GCST007674_2	3-month functional outcome in lacunar ischaemic stroke (modified Rankin score)	8.000000e-06
GCST009614_3	LDL cholesterol levels x loop diuretics use interaction	4.000000e-07
GCST010002_158	Refractive error	4.000000e-24
GCST012490_47	Femur bone mineral density x serum urate levels interaction	1.000000e-11
GCST012490_606	Femur bone mineral density x serum urate levels interaction	6.000000e-09

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004730	hormone measurement
EFO:0007906	synophrys measurement
EFO:0009603	stroke outcome severity measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066175 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	5
trichostatin A	affects cotreatment, decreases expression, affects expression	3
Nickel	decreases expression, increases expression	3
bisphenol A	decreases methylation, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
decabromobiphenyl ether	decreases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
jinfukang	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants, Occupational	decreases expression	1
Caffeine	increases phosphorylation	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	increases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Thiram	decreases expression	1

ChEMBL screening assays

6 unique, capped per target: 6 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5697237	Binding	Inhibition of CPSF2 (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Clinical trials (associated diseases)

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