CPSF4L

Summary

CPSF4L (cleavage and polyadenylation specific factor 4 like, HGNC:33632) is a protein-coding gene on chromosome 17q25.1, encoding Putative cleavage and polyadenylation specificity factor subunit 4-like protein (A6NMK7).

Predicted to enable RNA binding activity and zinc ion binding activity. Predicted to be involved in mRNA 3’-end processing. Predicted to be located in nucleus. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex.

Source: NCBI Gene 642843 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001129885

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33632
Approved symbol	CPSF4L
Name	cleavage and polyadenylation specific factor 4 like
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187959
Ensembl biotype	protein_coding
Entrez	642843

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000344935, ENST00000397671

RefSeq mRNA: 1 — MANE Select: NM_001129885 NM_001129885

CCDS: CCDS45768

Canonical transcript exons

ENST00000344935 — 6 exons

Exon	Start	End
ENSE00001375429	73261716	73261880
ENSE00001600175	73252630	73252723
ENSE00001708260	73248449	73248536
ENSE00002463371	73253931	73254026
ENSE00003462738	73260933	73260983
ENSE00003624887	73257681	73257833

Expression profiles

Bgee: expression breadth ubiquitous, 110 present calls, max score 91.11.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.11	gold quality
right uterine tube	UBERON:0001302	54.05	gold quality
body of pancreas	UBERON:0001150	52.12	gold quality
left uterine tube	UBERON:0001303	49.35	gold quality
fallopian tube	UBERON:0003889	49.30	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	48.33	gold quality
omental fat pad	UBERON:0010414	47.52	gold quality
thoracic mammary gland	UBERON:0005200	46.82	gold quality
mucosa of stomach	UBERON:0001199	46.79	gold quality
hindlimb stylopod muscle	UBERON:0004252	46.02	gold quality
adipose tissue	UBERON:0001013	45.84	gold quality
cortical plate	UBERON:0005343	45.68	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	45.35	gold quality
tibial nerve	UBERON:0001323	45.25	gold quality
pancreas	UBERON:0001264	45.14	gold quality
left ovary	UBERON:0002119	45.02	gold quality
subcutaneous adipose tissue	UBERON:0002190	44.69	gold quality
ovary	UBERON:0000992	44.52	gold quality
saliva-secreting gland	UBERON:0001044	44.34	gold quality
right testis	UBERON:0004534	44.11	gold quality
minor salivary gland	UBERON:0001830	43.61	gold quality
body of stomach	UBERON:0001161	42.84	gold quality
testis	UBERON:0000473	42.72	gold quality
left testis	UBERON:0004533	42.66	gold quality
stomach	UBERON:0000945	42.44	gold quality
right lobe of liver	UBERON:0001114	41.96	silver quality
granulocyte	CL:0000094	41.74	silver quality
right coronary artery	UBERON:0001625	41.47	silver quality
skin of leg	UBERON:0001511	41.39	gold quality
adenohypophysis	UBERON:0002196	41.31	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.93

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cpsf4l	ENSMUSG00000018727
rattus_norvegicus	Cpsf4l	ENSRNOG00000056582
caenorhabditis_elegans		WBGENE00044329

Paralogs (2): ZC3H3 (ENSG00000014164), CPSF4 (ENSG00000160917)

Protein

Protein identifiers

Putative cleavage and polyadenylation specificity factor subunit 4-like protein — A6NMK7 (reviewed: A6NMK7)

All UniProt accessions (2): A6NMK7, H9KVA5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CPSF4/YTH1 family.

RefSeq proteins (1): NP_001123357* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR036855	Znf_CCCH_sf	Homologous_superfamily
IPR041686	Znf-CCCH_3	Domain
IPR045348	CPSF4/Yth1	Family

Pfam: PF14608, PF15663

UniProt features (6 total): zinc finger region 5, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NMK7-F1	84.79	0.46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): YAMAZAKI_TCEB3_TARGETS_DN, GOCC_MRNA_CLEAVAGE_FACTOR_COMPLEX, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, MIKKELSEN_ES_ICP_WITH_H3K4ME3, KOHOUTEK_CCNT2_TARGETS, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, DELACROIX_RAR_BOUND_ES, RAO_BOUND_BY_SALL4, GOCC_MRNA_CLEAVAGE_AND_POLYADENYLATION_SPECIFICITY_FACTOR_COMPLEX, NFKBIA_TARGET_GENES, GSE17721_CTRL_VS_LPS_1H_BMDC_DN, GSE17721_CTRL_VS_POLYIC_6H_BMDC_DN, GSE17721_PAM3CSK4_VS_CPG_4H_BMDC_DN, GSE17721_PAM3CSK4_VS_GADIQUIMOD_16H_BMDC_DN, DESCARTES_MAIN_FETAL_LENS_FIBRE_CELLS

GO Biological Process (2): mRNA processing (GO:0006397), mRNA 3’-end processing (GO:0031124)

GO Molecular Function (3): RNA binding (GO:0003723), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (2): mRNA cleavage and polyadenylation specificity factor complex (GO:0005847), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	1
mRNA metabolic process	1
mRNA processing	1
RNA 3’-end processing	1
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
mRNA cleavage factor complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

548 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CPSF4L	KRCC1	Q9NPI7	493
CPSF4L	CPSF3	Q9UKF6	473
CPSF4L	SLC25A35	Q3KQZ1	451
CPSF4L	PABPN1L	A6NDY0	440
CPSF4L	PIH1D2	Q8WWB5	419
CPSF4L	SEC14L4	Q9UDX3	404
CPSF4L	CCDC32	Q9BV29	391
CPSF4L	RBPMS2	Q6ZRY4	383
CPSF4L	DPH7	Q9BTV6	375
CPSF4L	NPM3	O75607	350
CPSF4L	SYMPK	Q92797	349
CPSF4L	PCF11	O94913	349
CPSF4L	CPSF2	Q9P2I0	349
CPSF4L	RBBP6	Q7Z6E9	349
CPSF4L	WDR33	Q9C0J8	349
CPSF4L	FIP1L1	Q6UN15	349
CPSF4L	CPSF1	Q10570	349

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CPSF4L	CCNH	psi-mi:“MI:0914”(association)	0.530
CPSF4L	AP2A2	psi-mi:“MI:0914”(association)	0.350

BioGRID (18): CCNG1 (Affinity Capture-MS), FIP1L1 (Affinity Capture-MS), WDR33 (Affinity Capture-MS), BANP (Affinity Capture-MS), CCNH (Affinity Capture-MS), CCNG1 (Affinity Capture-MS), WDR33 (Affinity Capture-MS), BANP (Affinity Capture-MS), CCNH (Affinity Capture-MS), FIP1L1 (Affinity Capture-MS), AP2A2 (Affinity Capture-MS), CPSF3 (Affinity Capture-MS), CCNG1 (Affinity Capture-MS), CCNH (Affinity Capture-MS), WDR33 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L1SUL6, A4QJJ7, A4QK16, A6H5F6, A6MM34, A6NH52, A6NMK7, A7M939, A8SEA1, A8W3M5, B0Z4S1, B0Z505, B0Z589, B0Z5H3, B1AR13, B1NWE8, B2LMJ1, O19048, O19137, O95639, P0C7P0, P0DI19, P46292, P60335, P83870, P83871, P98138, Q09G48, Q0G9M1, Q0WMV8, Q15365, Q1KXW1, Q332Y0, Q5E9A3, Q5FVR7, Q5R654, Q63789, Q66KE3, Q68S08, Q6DJP7

Diamond homologs: A6NMK7, A9LNK9, O19137, O95639, Q4P384, Q4WKD9, Q59T36, Q5BGN2, Q5FVR7, Q66KE3, Q6DJP7, Q8BQZ5, Q9VPT8, A0A9P4XWM4, B2RR83, E9Q5K9, P0CS64, P0CS65, Q06102, Q0DA50, Q2URI6, Q4IPA4, Q5R746, Q6BTT1, Q6C922, Q6CKU1, Q6FTL0, Q758T3, Q7SGR2, Q96MU7, Q9H6S0, Q9QY02, Q9UTD1, Q9VZQ1, Q9FE91

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

808 predictions. Top by Δscore:

Variant	Effect	Δscore
17:73261711:CTCA:C	donor_gain	1.0000
17:73261714:A:AC	donor_gain	1.0000
17:73261714:ACTGT:A	donor_gain	1.0000
17:73261715:C:CA	donor_gain	1.0000
17:73261715:CTGTC:C	donor_gain	1.0000
17:73261766:T:TA	donor_gain	1.0000
17:73261710:A:AC	donor_gain	0.9900
17:73261711:C:CC	donor_gain	0.9900
17:73261715:CT:C	donor_gain	0.9900
17:73261715:CTGT:C	donor_gain	0.9900
17:73257811:A:C	acceptor_gain	0.9800
17:73261709:CACT:C	donor_loss	0.9800
17:73261712:T:TG	donor_loss	0.9800
17:73261713:CACT:C	donor_loss	0.9800
17:73261714:A:T	donor_loss	0.9800
17:73261715:CTG:C	donor_gain	0.9800
17:73260982:CT:C	acceptor_gain	0.9700
17:73261710:ACT:A	donor_loss	0.9700
17:73261744:AGTGC:A	donor_gain	0.9700
17:73252194:C:CC	acceptor_gain	0.9600
17:73260928:CTCA:C	donor_loss	0.9600
17:73260929:TCA:T	donor_loss	0.9600
17:73260930:CACC:C	donor_loss	0.9600
17:73260931:A:C	donor_loss	0.9600
17:73260932:C:CT	donor_loss	0.9600
17:73260984:C:CC	acceptor_gain	0.9600
17:73261723:G:A	donor_gain	0.9600
17:73261724:C:CA	donor_gain	0.9600
17:73260932:CCTTT:C	donor_gain	0.9500
17:73261711:CT:C	donor_gain	0.9500

AlphaMissense

1197 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:73257736:G:C	F84L	0.976
17:73257736:G:T	F84L	0.976
17:73257738:A:G	F84L	0.976
17:73253998:G:C	F112L	0.954
17:73253998:G:T	F112L	0.954
17:73254000:A:G	F112L	0.954
17:73257781:C:A	K69N	0.951
17:73257781:C:G	K69N	0.951
17:73253941:G:C	F131L	0.948
17:73253941:G:T	F131L	0.948
17:73253943:A:G	F131L	0.948
17:73257732:G:C	H86D	0.947
17:73257694:G:C	F98L	0.935
17:73257694:G:T	F98L	0.935
17:73257696:A:G	F98L	0.935
17:73257785:C:G	C68S	0.933
17:73257786:A:T	C68S	0.933
17:73261729:G:C	F30L	0.917
17:73261729:G:T	F30L	0.917
17:73261731:A:G	F30L	0.917
17:73257785:C:T	C68Y	0.916
17:73252662:G:C	F155L	0.915
17:73252662:G:T	F155L	0.915
17:73252664:A:G	F155L	0.915
17:73257786:A:G	C68R	0.912
17:73257730:G:C	H86Q	0.910
17:73257730:G:T	H86Q	0.910
17:73257732:G:T	H86N	0.908
17:73257775:C:A	W71C	0.905
17:73257775:C:G	W71C	0.905

dbSNP variants (sampled 300 via entrez): RS1000087812 (17:73244762 C>T), RS1000147716 (17:73245599 G>A), RS1000321260 (17:73250731 C>T), RS1000413759 (17:73251225 C>A,T), RS1000483653 (17:73256475 G>A), RS1000524839 (17:73244982 G>A), RS1000852689 (17:73256088 G>A), RS1001129809 (17:73246467 C>T), RS1001245747 (17:73262144 C>A,T), RS1001312504 (17:73244179 A>G), RS1001327995 (17:73257019 G>A,T), RS1001417712 (17:73250000 T>C), RS1001497537 (17:73246263 G>A), RS1001510650 (17:73262686 T>C), RS1001612274 (17:73255696 A>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
diethyl maleate	increases expression	1
butyraldehyde	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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