PCIF1

Summary

PCIF1 (phosphorylated CTD interacting factor 1, HGNC:16200) is a protein-coding gene on chromosome 20q13.12, encoding mRNA (2’-O-methyladenosine-N(6)-)-methyltransferase (Q9H4Z3). Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2’-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs.

Enables RNA polymerase II C-terminal domain phosphoserine binding activity; S-adenosyl-L-methionine binding activity; and mRNA (2’-O-methyladenosine-N6-)-methyltransferase activity. Involved in mRNA processing; negative regulation of translation; and positive regulation of translation. Located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm.

Source: NCBI Gene 63935 — RefSeq curated summary.

At a glance

• GWAS associations: 57
• Clinical variants (ClinVar): 90 total
• Druggable target: yes
• MANE Select transcript: NM_022104

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16200
Approved symbol	PCIF1
Name	phosphorylated CTD interacting factor 1
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	bA465L10.1, PPP1R121, CAPAM, MT-A70
Ensembl gene	ENSG00000100982
Ensembl biotype	protein_coding
OMIM	618626
Entrez	63935

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 23 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000372409, ENST00000479348, ENST00000616084, ENST00000904032, ENST00000904033, ENST00000904034, ENST00000904035, ENST00000904036, ENST00000904037, ENST00000904038, ENST00000904039, ENST00000904040, ENST00000920263, ENST00000920264, ENST00000920265, ENST00000920266, ENST00000944654, ENST00000944655, ENST00000944656, ENST00000944657, ENST00000944658, ENST00000944659, ENST00000944660, ENST00000944661

RefSeq mRNA: 1 — MANE Select: NM_022104 NM_022104

CCDS: CCDS13388

Canonical transcript exons

ENST00000372409 — 17 exons

Exon	Start	End
ENSE00000662456	45940475	45940612
ENSE00000845079	45940809	45940939
ENSE00000845084	45944868	45945030
ENSE00000845088	45947263	45947438
ENSE00001042750	45937418	45937585
ENSE00001124282	45943666	45943765
ENSE00001124288	45943340	45943423
ENSE00001124294	45943097	45943244
ENSE00001124299	45941053	45941207
ENSE00001124316	45939215	45939339
ENSE00001457731	45947524	45948020
ENSE00001457741	45938981	45939123
ENSE00001457747	45934683	45934804
ENSE00003719351	45946029	45946115
ENSE00003726432	45945711	45945883
ENSE00003730055	45947073	45947166
ENSE00003736241	45946200	45946384

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 94.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.9423 / max 224.4358, expressed in 1814 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184971	27.9423	1814

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of stomach	UBERON:0001199	94.49	gold quality
body of uterus	UBERON:0009853	93.73	gold quality
left uterine tube	UBERON:0001303	93.29	gold quality
apex of heart	UBERON:0002098	93.18	gold quality
popliteal artery	UBERON:0002250	93.17	gold quality
tibial artery	UBERON:0007610	93.17	gold quality
left ovary	UBERON:0002119	93.14	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.93	gold quality
right ovary	UBERON:0002118	92.85	gold quality
cerebellar hemisphere	UBERON:0002245	92.81	gold quality
cerebellar cortex	UBERON:0002129	92.73	gold quality
skin of leg	UBERON:0001511	92.69	gold quality
granulocyte	CL:0000094	92.63	gold quality
ganglionic eminence	UBERON:0004023	92.63	gold quality
right lung	UBERON:0002167	92.61	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	92.59	gold quality
endocervix	UBERON:0000458	92.58	gold quality
lower esophagus muscularis layer	UBERON:0035833	92.41	gold quality
lower esophagus	UBERON:0013473	92.39	gold quality
aorta	UBERON:0000947	92.28	gold quality
left lobe of thyroid gland	UBERON:0001120	92.27	gold quality
gastrocnemius	UBERON:0001388	92.24	gold quality
ectocervix	UBERON:0012249	92.20	gold quality
skin of abdomen	UBERON:0001416	92.04	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.98	gold quality
ventricular zone	UBERON:0003053	91.66	gold quality
muscle layer of sigmoid colon	UBERON:0035805	91.64	gold quality
muscle of leg	UBERON:0001383	91.62	gold quality
upper lobe of left lung	UBERON:0008952	91.53	gold quality
tibial nerve	UBERON:0001323	91.50	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PDX1

miRNA regulators (miRDB)

33 targeting PCIF1, 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-5193	100.00	67.26	1744
HSA-MIR-3646	100.00	73.56	5283
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-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-942-3P	98.81	69.04	876
HSA-MIR-4742-3P	98.73	69.82	1803
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-6787-5P	97.54	63.85	457
HSA-MIR-6515-5P	97.08	65.48	1219
HSA-MIR-6815-5P	96.05	65.55	662
HSA-MIR-6865-5P	96.05	65.58	675
HSA-MIR-10396B-5P	94.99	63.57	358
HSA-MIR-1908-5P	94.99	63.41	352

Literature-anchored findings (GeneRIF, showing 18)

• Data suggest that phosphorylated CTD interacting factor 1 (PCIF1) may play a role in mRNA synthesis by modulating RNA polymerase II activity. (PMID:12565871)
• These data suggest that icariin exerts its potent osteogenic effect through induction of Runx2 expression, production of BMP-4 and activation of BMP signaling. (PMID:18294453)
• These results suggest that Pin1 may have overlapping cellular function with PCIF1. (PMID:19682092)
• PCIF1/CAPAM (cap-specific adenosine methyltransferase) is a cap-specific N (6)-methyladenosine writer for mRNAs (PMID:30467178)
• The authors identified, characterized biochemical property and substrate preference of PCIF1 as “stand-alone” RNA methyltransferase and proposed a model for mammalian mRNA m6Am modification mediated by PCIF1. (PMID:30487554)
• We find that depleting PCIF1 does not substantially affect mRNA translation but is associated with reduced stability of a subset of m(6)Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m(6)Am’s function. (PMID:31279658)
• we identify the only human mRNA m6Am methyltransferase and demonstrate a mechanism of gene expression regulation through PCIF1-mediated m6Am mRNA methylation. (PMID:31279659)
• PCIF1 depletion leads to loss of m6Am RNA modification from the transcriptional-start-sites of mRNAs (PMID:31822664)
• Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. (PMID:33428944)
• Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-beta. (PMID:34266951)
• HIV reprograms host m(6)Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1. (PMID:34545078)
• The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features. (PMID:34634806)
• Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. (PMID:35189146)
• Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas. (PMID:35868483)
• Role of PCIF1-mediated 5’-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy. (PMID:36514940)
• The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma. (PMID:37643007)
• m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression. (PMID:38526325)
• LncRNA PCIF1 promotes aerobic glycolysis in A549/DDP cells by competitively binding miR-326 to regulate PKM expression. (PMID:39074568)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pcif1	ENSDARG00000099084
mus_musculus	Pcif1	ENSMUSG00000039849
rattus_norvegicus	Pcif1	ENSRNOG00000016870
drosophila_melanogaster	Pcif1	FBGN0037021

Protein

Protein identifiers

mRNA (2’-O-methyladenosine-N(6)-)-methyltransferase — Q9H4Z3 (reviewed: Q9H4Z3)

Alternative names: Cap-specific adenosine methyltransferase, Phosphorylated CTD-interacting factor 1, Protein phosphatase 1 regulatory subunit 121

All UniProt accessions (2): Q9H4Z3, A0A087WWZ2

UniProt curated annotations — full annotation on UniProt →

Function. Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2’-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs. Recruited to the early elongation complex of RNA polymerase II (RNAPII) via interaction with POLR2A and mediates formation of m6A(m) co-transcriptionally.

Subunit / interactions. Interacts with POLR2A; interacts with the phosphorylated C-terminal domain (CTD) of POLR2A.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

Activity regulation. Cap-specific adenosine methyltransferase activity is inhibited by zinc.

Domain organisation. The WW domain is sufficient for direct and specific interaction with the phosphorylated CTD of RNAPII largest subunit.

Similarity. Belongs to the CAPAM family.

RefSeq proteins (1): NP_071387* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001202	WW_dom	Domain
IPR022035	PCIF1_WW	Domain
IPR029048	HSP70_C_sf	Homologous_superfamily
IPR036020	WW_dom_sf	Homologous_superfamily
IPR039881	PCIF1-like	Family

Pfam: PF00397, PF12237

Catalyzed reactions (Rhea), 1 shown:

• a 5’-end (N(7)-methyl 5’-triphosphoguanosine)-(2’-O-methyladenosine) in mRNA + S-adenosyl-L-methionine = a 5’-end (N(7)-methyl 5’-triphosphoguanosine)-(N(6),2’-O-dimethyladenosine) in mRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:22744)

UniProt features (67 total): helix 20, strand 20, binding site 6, compositionally biased region 4, turn 4, modified residue 3, region of interest 3, mutagenesis site 3, short sequence motif 2, chain 1, domain 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
6IRV	X-RAY DIFFRACTION	2.7
6IRW	X-RAY DIFFRACTION	2.9
2JX8	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H4Z3-F1	81.22	0.63

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (6): 235; 265; 553–556; 558; 588–592; 614–616

Post-translational modifications (3): 30, 116, 152

Mutagenesis-validated functional residues (3):

Position	Phenotype
553–556	abolishes formation of n(6),2’-o-dimethyladenosine cap (m6a(m)).
553	strongly reduced formation of n(6),2’-o-dimethyladenosine cap (m6a(m)).
556	strongly reduced formation of n(6),2’-o-dimethyladenosine cap (m6a(m)).

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 155 (showing top): RNGTGGGC_UNKNOWN, TGCGCANK_UNKNOWN, SP3_Q3, MODULE_511, AP2_Q3, YY1_Q6, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, E2F1DP1_01, E2F1DP2_01, YY1_02, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, RYTTCCTG_ETS2_B, EGR1_01

GO Biological Process (4): mRNA processing (GO:0006397), negative regulation of translation (GO:0017148), methylation (GO:0032259), positive regulation of translation (GO:0045727)

GO Molecular Function (7): mRNA (2’-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422), RNA polymerase II C-terminal domain binding (GO:0099122), S-adenosyl-L-methionine binding (GO:1904047), RNA polymerase II C-terminal domain phosphoserine binding (GO:1990269), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), microtubule cytoskeleton (GO:0015630), intercellular bridge (GO:0045171)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
translation	2
regulation of translation	2
cellular anatomical structure	2
RNA processing	1
mRNA metabolic process	1
negative regulation of gene expression	1
negative regulation of protein metabolic process	1
metabolic process	1
positive regulation of gene expression	1
positive regulation of protein metabolic process	1
mRNA methyltransferase activity	1
RNA polymerase II complex binding	1
cation binding	1
sulfur compound binding	1
phosphoserine residue binding	1
RNA polymerase II C-terminal domain binding	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoskeleton	1

Protein interactions and networks

STRING

520 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCIF1	METTL4	Q8N3J2	624
PCIF1	METTL16	Q86W50	623
PCIF1	METTL3	Q86U44	609
PCIF1	METTL14	Q9HCE5	590
PCIF1	ZNF335	Q9H4Z2	584
PCIF1	ZCCHC4	Q9H5U6	577
PCIF1	FTO	Q9C0B1	571
PCIF1	METTL5	Q9NRN9	565
PCIF1	TRMT112	Q9UI30	546
PCIF1	WTAP	Q15007	523
PCIF1	ALKBH5	Q6P6C2	522
PCIF1	ZC3H13	Q5T200	494
PCIF1	VIRMA	Q69YN4	481
PCIF1	YTHDF2	Q9Y5A9	474
PCIF1	YTHDC1	Q96MU7	471

IntAct

9 interactions, top by confidence:

A	B	Type	Score
PPP1CA	PCIF1	psi-mi:“MI:0407”(direct interaction)	0.440
PCIF1	PKM	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
PCIF1	HDAC3	psi-mi:“MI:0915”(physical association)	0.400
PCIF1	POLR2A	psi-mi:“MI:0914”(association)	0.350
	MYO9A	psi-mi:“MI:0914”(association)	0.350
S100A2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
S100P	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MAGEA10	KANSL1L	psi-mi:“MI:0914”(association)	0.350

BioGRID (33): MNAT1 (Affinity Capture-MS), POLR2A (Affinity Capture-MS), POLR2I (Affinity Capture-MS), HNRNPUL1 (Affinity Capture-MS), CAMSAP2 (Affinity Capture-MS), PARP16 (Affinity Capture-MS), FANCM (Affinity Capture-MS), C19orf43 (Affinity Capture-MS), ZCCHC6 (Affinity Capture-MS), PCIF1 (Affinity Capture-Western), PCIF1 (Co-localization), PCIF1 (Reconstituted Complex), PCIF1 (Affinity Capture-MS), PCIF1 (Proximity Label-MS), PCIF1 (Reconstituted Complex)

ESM2 similar proteins: A0A0R4IKJ1, A0A364LXP7, A5PF44, B0XPE7, D3ZKV9, F4IAE9, G0RYC6, G2WWH6, I1RQE2, J9VG42, O13719, O14302, O60291, P0CP02, P0CP03, P22015, P22016, P22017, P22018, P22019, P22020, P22021, P59114, P87233, Q09750, Q11076, Q14693, Q1DU03, Q2H1Q1, Q2UTN6, Q4IB50, Q4PBL3, Q4WJI7, Q4WTT2, Q5ASA5, Q6C229, Q6C519, Q6E3D2, Q75BF1, Q7XZU0

Diamond homologs: A0A0R4IKJ1, P59114, Q9H4Z3, A2A5Z6, A9JRZ0, O15428, O55148, O60045, O60861, P0C1J8, P46934, P46935, P54353, Q13526, Q2TAS2, Q4R383, Q5BIN5, Q5F389, Q60780, Q62940, Q7XZU0, Q803A8, Q9HAU4, Q9N2Z7, Q9QUR7, Q9V853, Q9Y0H4, A4IKU2, A6QI23, A6QPY8, A6U2U4, A7X3U8, A8YY10, B5KFL3, C5D6L9, O00308, O74448, P0A265, P0A266, P0A9L5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2740 predictions. Top by Δscore:

Variant	Effect	Δscore
20:45934801:GCAG:G	donor_gain	1.0000
20:45934803:AGGT:A	donor_loss	1.0000
20:45934804:GGTA:G	donor_loss	1.0000
20:45934805:G:GG	donor_gain	1.0000
20:45934805:GTAAG:G	donor_loss	1.0000
20:45934806:T:A	donor_loss	1.0000
20:45938979:AGGTC:A	acceptor_loss	1.0000
20:45938980:G:A	acceptor_loss	1.0000
20:45939206:T:A	acceptor_gain	1.0000
20:45939213:A:AG	acceptor_gain	1.0000
20:45939213:AGAG:A	acceptor_gain	1.0000
20:45939214:G:GA	acceptor_gain	1.0000
20:45939214:GA:G	acceptor_gain	1.0000
20:45939214:GAGG:G	acceptor_gain	1.0000
20:45939214:GAGGA:G	acceptor_gain	1.0000
20:45939336:GATT:G	donor_gain	1.0000
20:45939337:ATTGT:A	donor_loss	1.0000
20:45939338:TT:T	donor_gain	1.0000
20:45939338:TTG:T	donor_loss	1.0000
20:45939339:TG:T	donor_loss	1.0000
20:45939340:G:GG	donor_gain	1.0000
20:45939340:GT:G	donor_loss	1.0000
20:45940458:T:TA	acceptor_gain	1.0000
20:45940471:C:G	acceptor_gain	1.0000
20:45940473:A:AG	acceptor_gain	1.0000
20:45940473:AGTC:A	acceptor_gain	1.0000
20:45940473:AGTCG:A	acceptor_gain	1.0000
20:45940474:G:GA	acceptor_gain	1.0000
20:45940474:GT:G	acceptor_gain	1.0000
20:45940474:GTC:G	acceptor_gain	1.0000

AlphaMissense

4602 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:45939233:G:A	G48D	1.000
20:45939235:T:A	W49R	1.000
20:45939235:T:C	W49R	1.000
20:45939236:G:C	W49S	1.000
20:45939237:G:C	W49C	1.000
20:45939237:G:T	W49C	1.000
20:45939266:G:C	R59P	1.000
20:45939271:T:G	Y61D	1.000
20:45939274:T:G	Y62D	1.000
20:45939277:T:C	F63L	1.000
20:45939279:C:A	F63L	1.000
20:45939279:C:G	F63L	1.000
20:45939282:C:A	N64K	1.000
20:45939282:C:G	N64K	1.000
20:45939302:T:C	L71P	1.000
20:45939304:T:A	W72R	1.000
20:45939304:T:C	W72R	1.000
20:45939305:G:C	W72S	1.000
20:45939306:G:C	W72C	1.000
20:45939306:G:T	W72C	1.000
20:45941060:T:A	W176R	1.000
20:45941060:T:C	W176R	1.000
20:45941169:T:C	L212P	1.000
20:45941190:T:C	L219P	1.000
20:45941192:T:C	C220R	1.000
20:45941194:C:G	C220W	1.000
20:45943118:C:T	S232F	1.000
20:45943129:T:A	W236R	1.000
20:45943129:T:C	W236R	1.000
20:45943131:G:C	W236C	1.000

dbSNP variants (sampled 300 via entrez): RS1000389174 (20:45944235 T>C), RS1000518165 (20:45935640 T>C), RS1000987793 (20:45934384 C>T), RS1001096743 (20:45938341 C>G,T), RS1001133934 (20:45946290 G>A), RS1001220131 (20:45936598 A>G), RS1001315080 (20:45936319 C>G,T), RS1001321744 (20:45938794 G>A), RS1001352155 (20:45944801 T>G), RS1001382213 (20:45941979 A>C,T), RS1001720701 (20:45941620 A>G), RS1001850382 (20:45946772 A>T), RS1001865705 (20:45944502 A>G), RS1002020021 (20:45940116 T>A), RS1002086390 (20:45941442 A>G)

Disease associations

OMIM: gene MIM:618626 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

57 associations (top):

Study	Trait	p-value
GCST003122_8	Hemoglobin levels	7.000000e-06
GCST003854_19	Gut microbiota (functional units)	2.000000e-06
GCST003854_54	Gut microbiota (functional units)	4.000000e-06
GCST003877_9	Abdominal aortic aneurysm	2.000000e-17
GCST004602_233	Mean corpuscular volume	2.000000e-13
GCST004630_73	Mean corpuscular hemoglobin	6.000000e-13
GCST005195_86	Coronary artery disease	4.000000e-09
GCST005196_246	Coronary artery disease	3.000000e-09
GCST006003_26	Triglyceride levels	1.000000e-14
GCST006005_52	High density lipoprotein cholesterol levels	4.000000e-14
GCST008070_112	HDL cholesterol levels	1.000000e-07
GCST008070_135	HDL cholesterol levels	2.000000e-06
GCST008070_53	HDL cholesterol levels	8.000000e-20
GCST008070_87	HDL cholesterol levels	5.000000e-09
GCST008074_100	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	5.000000e-27
GCST008074_32	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	1.000000e-43
GCST008074_6	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	5.000000e-11
GCST008074_65	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	9.000000e-08
GCST008075_11	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2.000000e-45
GCST008075_145	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	8.000000e-56
GCST008075_225	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	1.000000e-06
GCST008075_95	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	9.000000e-10
GCST008076_24	Triglyceride levels	2.000000e-19
GCST008076_3	Triglyceride levels	6.000000e-09
GCST008076_71	Triglyceride levels	2.000000e-06
GCST008076_80	Triglyceride levels	7.000000e-06
GCST008083_105	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	8.000000e-44
GCST008083_145	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2.000000e-26
GCST008083_58	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	4.000000e-09
GCST008083_73	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	1.000000e-10

EFO canonical traits (12, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement
EFO:0005845	hemoglobin A2 measurement
EFO:0007874	gut microbiome measurement
EFO:0004527	mean corpuscular hemoglobin
EFO:0004530	triglyceride measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004329	alcohol drinking
EFO:0000195	metabolic syndrome
EFO:0010701	mean reticulocyte volume
EFO:0004305	erythrocyte count
EFO:0009188	Red cell distribution width
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5465357 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	7
sodium arsenite	decreases expression, affects cotreatment, increases abundance	3
cobaltous chloride	affects expression, decreases expression	2
Arsenic	affects cotreatment, decreases expression, increases abundance, affects expression	2
FR900359	affects phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
coumarin	increases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
jinfukang	increases expression, affects cotreatment	1
Atrazine	increases expression	1
Caffeine	affects phosphorylation	1
Cisplatin	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	decreases expression	1
Lead	decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Methyl Methanesulfonate	decreases expression	1
Smoke	decreases expression	1
Dronabinol	increases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases 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
CHEMBL5317816	Binding	Inhibition of human PCIF1 using m7GpppAmG as substrate and SAM as cosubstrate at 10 uM incubated for 15 mins	Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile-Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. — J Med Chem

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E2GD	HAP1 PCIF1 (-) 1	Cancer cell line	Male
CVCL_E2GE	HAP1 PCIF1 (-) 2	Cancer cell line	Male
CVCL_E2GF	HAP1 PCIF1 (-) 3	Cancer cell line	Male
CVCL_E2GG	HAP1 PCIF1 (-) 4	Cancer cell line	Male
CVCL_E2GH	HAP1 PCIF1 (-) 5	Cancer cell line	Male

Clinical trials (associated diseases)

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