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 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 57 (top 1% of genes corpus-wide)
• Clinical variants (ClinVar): 97 total
• GTEx eGene: eQTL in 10 tissues, sQTL in 2 (q < 0.05)
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.23 (highly constrained)
• MANE Select transcript: NM_022104
• Notable: 97 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 43 — 27 protein_coding, 15 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000372409

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 1

ENST00000372409, ENST00000479348, ENST00000616084, ENST00000904032, ENST00000904033, ENST00000904034, ENST00000904035, ENST00000904036, ENST00000904037, ENST00000904038, ENST00000904039, ENST00000904040, ENST00000920263, ENST00000920264, ENST00000920265, ENST00000920266, ENST00000944654, ENST00000944655, ENST00000944656, ENST00000944657, ENST00000944658, ENST00000944659, ENST00000944660, ENST00000944661, ENST00001003802, ENST00001003803, ENST00001003804, ENST00001003805, ENST00001055475, ENST00001055477, ENST00001055478, ENST00001055479, ENST00001055480, ENST00001055481, ENST00001055482, ENST00001055484, ENST00001055485, ENST00001063044, ENST00001120835, ENST00001122152, ENST00001122153, ENST00001122154, ENST00001132965

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.

Highest expression (Bgee): mucosa of stomach, body of uterus, uterine tube, apex of heart, popliteal artery.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PCIF1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 10 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

12 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Adrenal Gland	eqtl	2.1e-11	-0.38	20:45951111:C:T
Whole Blood	eqtl	6.1e-07	-0.08	20:45951111:C:T
Cells EBV-transformed lymphocytes	eqtl	7.9e-04	-0.53	20:46735174:G:A
Cells Cultured fibroblasts	sqtl	1.8e-03	-0.82	20:44940085:A:C
Brain Amygdala	eqtl	2.3e-03	+0.31	20:46716318:G:A
Testis	sqtl	4.9e-03	-0.43	20:45957397:G:A
Esophagus Gastroesophageal Junction	eqtl	6.2e-03	-0.16	20:45927136:GC:G
Colon Sigmoid	eqtl	1.1e-02	+0.37	20:45623586:C:A
Skin Sun Exposed Lower leg	eqtl	1.1e-02	-0.07	20:45951111:C:T
Muscle Skeletal	eqtl	3.3e-02	-0.10	20:45919331:C:T
Brain Hippocampus	eqtl	3.4e-02	-1.87	20:45833836:C:T
Brain Cerebellar Hemisphere	eqtl	3.9e-02	+0.62	20:46438878:A:G

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
184971	27.9423	1814

Top tissues by expression

showing 100 of 269 tissues 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
right lobe of thyroid gland	UBERON:0001119	91.48	gold quality
right uterine tube	UBERON:0001302	91.38	gold quality
thoracic aorta	UBERON:0001515	91.37	gold quality
left coronary artery	UBERON:0001626	91.37	gold quality
ascending aorta	UBERON:0001496	91.35	gold quality
cerebellum	UBERON:0002037	91.35	gold quality
thyroid gland	UBERON:0002046	91.17	gold quality
right coronary artery	UBERON:0001625	90.97	gold quality
descending thoracic aorta	UBERON:0002345	90.92	gold quality
adenohypophysis	UBERON:0002196	90.85	gold quality
leukocyte	CL:0000738	90.84	gold quality
monocyte	CL:0000576	90.75	gold quality
mononuclear cell	CL:0000842	90.73	gold quality
left adrenal gland cortex	UBERON:0035825	90.60	gold quality
right adrenal gland	UBERON:0001233	90.59	gold quality
coronary artery	UBERON:0001621	90.55	gold quality
right atrium auricular region	UBERON:0006631	90.55	gold quality
spleen	UBERON:0002106	90.51	gold quality
left adrenal gland	UBERON:0001234	90.48	gold quality
cortical plate	UBERON:0005343	90.26	gold quality
upper lobe of lung	UBERON:0008948	90.17	gold quality
right adrenal gland cortex	UBERON:0035827	90.11	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.03	gold quality
metanephros cortex	UBERON:0010533	90.00	gold quality
heart left ventricle	UBERON:0002084	89.98	gold quality
lower esophagus mucosa	UBERON:0035834	89.96	gold quality
body of stomach	UBERON:0001161	89.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.83	gold quality
esophagus	UBERON:0001043	89.77	gold quality
pituitary gland	UBERON:0000007	89.76	gold quality
cardiac atrium	UBERON:0002081	89.73	gold quality
zone of skin	UBERON:0000014	89.66	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.63	gold quality
cardiac ventricle	UBERON:0002082	89.54	gold quality
transverse colon	UBERON:0001157	89.51	gold quality
omental fat pad	UBERON:0010414	89.37	gold quality
adrenal cortex	UBERON:0001235	89.35	gold quality
muscle organ	UBERON:0001630	89.30	gold quality
peritoneum	UBERON:0002358	89.30	gold quality
ovary	UBERON:0000992	89.29	gold quality
body of pancreas	UBERON:0001150	89.24	gold quality
minor salivary gland	UBERON:0001830	88.99	gold quality
smooth muscle tissue	UBERON:0001135	88.90	gold quality
olfactory bulb	UBERON:0002264	88.90	gold quality
heart	UBERON:0000948	88.87	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.85	gold quality
prefrontal cortex	UBERON:0000451	88.82	gold quality
right frontal lobe	UBERON:0002810	88.82	gold quality
mucosa of transverse colon	UBERON:0004991	88.56	gold quality
blood	UBERON:0000178	88.53	gold quality
adipose tissue of abdominal region	UBERON:0007808	88.50	gold quality
adrenal gland	UBERON:0002369	88.40	gold quality
lymph node	UBERON:0000029	88.26	gold quality
saliva-secreting gland	UBERON:0001044	88.17	gold quality
spinal cord	UBERON:0002240	88.09	gold quality
small intestine	UBERON:0002108	87.98	gold quality
esophagus mucosa	UBERON:0002469	87.87	gold quality
stomach	UBERON:0000945	87.79	gold quality
gall bladder	UBERON:0002110	87.67	gold quality
vagina	UBERON:0000996	87.57	gold quality
pancreas	UBERON:0001264	87.57	gold quality
embryo	UBERON:0000922	87.52	gold quality
cingulate cortex	UBERON:0003027	87.44	gold quality
anterior cingulate cortex	UBERON:0009835	87.43	gold quality
type B pancreatic cell	CL:0000169	87.38	gold quality
stromal cell of endometrium	CL:0002255	87.38	gold quality
islet of Langerhans	UBERON:0000006	87.33	gold quality
anatomical system	UBERON:0000467	86.88	gold quality
mouth mucosa	UBERON:0003729	86.77	gold quality
amygdala	UBERON:0001876	86.71	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Ovary	tissue	34.2	medium
Thymus	tissue	32.1
Bone marrow	tissue	32.0	low
Skeletal muscle	tissue	31.6	medium
Fallopian tube	tissue	29.1	medium
Vagina	tissue	28.5	medium
Corpus callosum	tissue	28.1
Cerebellum	tissue	27.7	high
Nucleus accumbens	tissue	26.2
Pituitary gland	tissue	26.1
Skin 1	tissue	25.8	high
Tongue	tissue	25.8
Lymph node	tissue	25.6	medium
Heart muscle	tissue	25.5	medium
Thyroid gland	tissue	25.5	high
Pancreas	tissue	24.8	medium
Spleen	tissue	24.2	low
Spinal cord	tissue	24.2
Hippocampus	tissue	24.2	high
Endometrium 1	tissue	24.1	medium
Superior colliculi	tissue	23.6
Locus coeruleus	tissue	23.3
Medulla oblongata	tissue	23.0
Midbrain	tissue	22.8
Choroid plexus	tissue	22.6
Thalamus	tissue	22.4
Salivary gland	tissue	22.2	medium
Substantia nigra	tissue	21.7
Olfactory bulb	tissue	21.6
Parathyroid gland	tissue	21.5
Postcentral gyrus	tissue	21.4
Hypothalamus	tissue	21.2
Periaqueductal gray	tissue	20.8
Pons	tissue	20.5
Seminal vesicle	tissue	20.1	medium
Esophagus	tissue	19.9	medium
Smooth muscle	tissue	19.9	medium
Lung	tissue	19.9	medium
Cervix	tissue	19.3	medium
Caudate putamen	tissue	19.2
Putamen	tissue	18.9
Hippocampal formation	tissue	18.8
Septum	tissue	18.7
Ventral forebrain	tissue	18.5
Tonsil	tissue	18.3	medium
Cerebral cortex	tissue	18.0	medium
Somatosensory cortex	tissue	18.0
Appendix	tissue	17.5	medium
Frontal cortex	tissue	17.3
Basal ganglia	tissue	16.8
Occipital cortex	tissue	16.8
Motor cortex	tissue	16.4
Prefrontal cortex	tissue	16.2
Amygdala	tissue	16.0
Placenta	tissue	16.0	high
Small intestine	tissue	16.0	medium
Entorhinal cortex	tissue	15.8
Retrosplenial cortex	tissue	15.8
Insular cortex	tissue	15.6
Adipose tissue	tissue	15.5	medium

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Flocculonodular lobe (48.3), Cerebellar cortex (47.2), Vermis (45.4), Blood vessel (37.8), Temporal white matter (37.2).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PDX1

miRNA regulators (miRDB)

Targeting PCIF1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 33 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.229, missense Z 3.19 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000372409 splits into 7 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
20:45,939,000–45,939,227	60 / 58.6	1.02	no
20:45,939,228–45,940,502	31 / 62.8	0.49	no
20:45,940,503–45,941,112	125 / 126.8	0.99	no
20:45,941,113–45,944,979	129 / 245.9	0.52	no
20:45,944,980–45,946,093	121 / 131.7	0.92	no
20:45,946,094–45,947,128	61 / 118.5	0.51	no
20:45,947,129–45,947,752	174 / 206.9	0.84	no

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

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2443858) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 12 distinct phenotype terms.

Mouse phenotype (MP)	Records
decreased body length	1
decreased body weight	1
abnormal retina morphology	1
hyperactivity	1
abnormal retina outer nuclear layer morphology	1
abnormal retina inner nuclear layer morphology	1
abnormal bone structure	1
increased lean body mass	1
abnormal optic disk morphology	1
decreased total body fat amount	1
preweaning lethality, incomplete penetrance	1
decreased thigmotaxis	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Macaca fascicularis	Q4R383	99.4%	Diamond
Bos taurus	Q5BIN5	98.2%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SPATA25	protein-coding	128497
NEURL2	protein-coding	140825
PLTP	protein-coding	5360
CTSA	protein-coding	5476
ZNF335	protein-coding	63925
ZSWIM3	protein-coding	140831
ZSWIM1	protein-coding	90204
SLC12A5-AS1	ncRNA	109729184
MMP9	protein-coding	4318
SLC12A5	protein-coding	57468

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): A0A087WWZ2, Q9H4Z3

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)

• 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 (71 total): helix 25, strand 19, 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 by resolution:

PDB	Title	Method	Resolution (Å)
6IRV	Crystal structure of the human cap-specific adenosine methyltransferase	X-RAY DIFFRACTION	2.7
6IRW	Crystal structure of the human cap-specific adenosine methyltransferase bound to SAH	X-RAY DIFFRACTION	2.9
2JX8	Solution structure of hPCIF1 WW domain	SOLUTION NMR

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Transferases, Predicted intracellular proteins, Plasma proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; cytokinetic bridge; microtubules

Antibody reliability (HPA): IH enhanced · IF supported

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)

Position	Role
235	substrate
265	substrate
553–556	S-adenosyl-L-methionine
558	substrate
588–592	substrate
614–616	S-adenosyl-L-methionine

Post-translational modifications (3)

Type	Positions
Phosphoserine	30, 116
Phosphothreonine	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 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

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

22 GO namespaces:

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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 11 of 15 annotations. The rest are phylogenetic / computational / electronic (IEA).

11 experimentally-supported GO terms:

GO term	NS	Evidence
mRNA processing	BP	direct assay
negative regulation of translation	BP	direct assay
positive regulation of translation	BP	mutant phenotype
intercellular bridge	CC	direct assay
microtubule cytoskeleton	CC	direct assay
nucleoplasm	CC	direct assay
nucleus	CC	direct assay
RNA polymerase II C-terminal domain binding	MF	direct assay
RNA polymerase II C-terminal domain phosphoserine binding	MF	direct assay
S-adenosyl-L-methionine binding	MF	direct assay
mRNA (2’-O-methyladenosine-N6-)-methyltransferase activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 472 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCIF1	METTL4	Q8N3J2	689
PCIF1	ZCCHC4	Q9H5U6	655
PCIF1	METTL16	Q86W50	619
PCIF1	FTO	Q9C0B1	596
PCIF1	METTL14	Q9HCE5	596
PCIF1	TRMT112	Q9UI30	591
PCIF1	WTAP	Q15007	578
PCIF1	METTL3	Q86U44	577
PCIF1	VIRMA	Q69YN4	573
PCIF1	METTL5	Q9NRN9	570
PCIF1	ALKBH5	Q6P6C2	558
PCIF1	ZNF335	Q9H4Z2	549
PCIF1	CBLL1	Q75N03	540
PCIF1	ZC3H13	Q5T200	538
PCIF1	YTHDC1	Q96MU7	508

IntAct

Human interaction partners of PCIF1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

4 partners by confidence:

Partner	Interaction type	MIscore	Records
PKM	phosphorylation reaction	0.440	1
PPP1CA	direct interaction	0.440	1
HDAC3	physical association	0.400	1
POLR2A	association	0.350	1

BioGRID (34 interactions; top human partners by supporting records): PDX1 (Affinity Capture-Western; 5 records), POLR2A (Affinity Capture-MS; 3 records), AGO2 (Affinity Capture-RNA), APP (Reconstituted Complex), BTRC (Proximity Label-MS), C19orf43 (Affinity Capture-MS), CAMSAP2 (Affinity Capture-MS), DDA1 (Proximity Label-MS), FANCM (Affinity Capture-MS), HNRNPUL1 (Affinity Capture-MS), MNAT1 (Affinity Capture-MS), NCBP2 (Proximity Label-MS), NELFE (Affinity Capture-MS), NUDT21 (Affinity Capture-RNA), PARP16 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for PCIF1: 97 ClinVar records (0 pathogenic / likely pathogenic); 57 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	11
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 21 predictions of 1,490):

Position(s)	Effect	Δscore	Sites
20:45934805–45934806	donor_loss	1.0000	3
20:45938979–45938980	acceptor_loss	1.0000	6
20:45939206	acceptor_gain	1.0000
20:45939340	donor_loss	1.0000	2
20:45940458	acceptor_gain	1.0000
20:45940471	acceptor_gain	1.0000
20:45940613–45940614	donor_loss	1.0000	3
20:45940803	acceptor_gain	1.0000
20:45940806	acceptor_gain	1.0000
20:45940807–45940808	acceptor_loss	1.0000	2

AlphaMissense

2,231 missense substitutions predicted likely pathogenic (of 4,602 scored), across 485 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M561	9	0.894	0.993
D85	8	0.995	0.999
D531	8	0.995	0.999
S54	8	0.991	0.999
F534	8	0.991	0.999
D81	8	0.986	0.995
F512	8	0.985	0.999
D270	8	0.983	0.997
N64	8	0.980	1.000
H616	8	0.980	0.996
D244	8	0.978	0.995
F550	8	0.978	0.999
D529	8	0.977	0.995
F581	8	0.974	0.999
D248	8	0.973	0.992
D458	8	0.973	0.994
F505	8	0.973	0.997
F556	8	0.965	0.999
F643	8	0.961	0.999
N517	8	0.958	0.999

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Bladder Urothelial Carcinoma (TCGA)	favorable	0.000169

Disease associations

OMIM: gene MIM:618626 | disease phenotypes:

GWAS associations

showing 30 of 57 associations:

Study	Trait	p-value
GCST008084_144	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	1e-69
GCST008084_9	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	6e-57
GCST008075_72	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	8e-56
GCST90002396_459	Mean reticulocyte volume	1e-48
GCST008075_214	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2e-45
GCST008083_38	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	8e-44
GCST008074_32	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	1e-43
GCST008074_101	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	5e-27
GCST008085_173	HDL cholesterol levels in current drinkers	9e-27
GCST008083_10	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2e-26
GCST011348_39	High density lipoprotein cholesterol levels	2e-25
GCST011345_37	Triglyceride levels	3e-24
GCST008087_65	Triglyceride levels in current drinkers	3e-22
GCST90002390_35	Mean corpuscular hemoglobin	4e-21
GCST008070_62	HDL cholesterol levels	8e-20
GCST008076_63	Triglyceride levels	2e-19
GCST003877_9	Abdominal aortic aneurysm	2e-17
GCST009602_26	Metabolic syndrome	6e-17
GCST90002403_47	Red blood cell count	3e-16
GCST90011900_34	Serum alkaline phosphatase levels	9e-16
GCST008085_44	HDL cholesterol levels in current drinkers	1e-15
GCST90002404_580	Red cell distribution width	7e-15
GCST006003_26	Triglyceride levels	1e-14
GCST009240_194	Serum metabolite levels (CMS)	3e-14
GCST006005_34	High density lipoprotein cholesterol levels	4e-14
GCST004602_108	Mean corpuscular volume	2e-13
GCST004630_198	Mean corpuscular hemoglobin	6e-13
GCST009240_122	Serum metabolite levels (CMS)	4e-12
GCST008084_98	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2e-11
GCST009240_108	Serum metabolite levels (CMS)	4e-11

EFO canonical traits (from GWAS)

12 canonical traits:

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 (CPIC guideline: no)

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	decreases expression, increases abundance, affects expression, affects cotreatment	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	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	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)

Via MONDO — disease-level, not drug-specific.