CSTF2T

gene
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Also known as DKFZp434C1013KIAA0689CstF-64TtauCstF-64

Summary

CSTF2T (cleavage stimulation factor subunit 2 tau variant, HGNC:17086) is a protein-coding gene on chromosome 10q21.1, encoding Cleavage stimulation factor subunit 2 tau variant (Q9H0L4). May play a significant role in AAUAAA-independent mRNA polyadenylation in germ cells.

Enables RNA binding activity. Predicted to be involved in mRNA 3’-end processing. Located in nucleoplasm.

Source: NCBI Gene 23283 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 93 total
  • MANE Select transcript: NM_015235

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17086
Approved symbolCSTF2T
Namecleavage stimulation factor subunit 2 tau variant
Location10q21.1
Locus typegene with protein product
StatusApproved
AliasesDKFZp434C1013, KIAA0689, CstF-64T, tauCstF-64
Ensembl geneENSG00000177613
Ensembl biotypeprotein_coding
OMIM611968
Entrez23283

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000331173

RefSeq mRNA: 1 — MANE Select: NM_015235 NM_015235

CCDS: CCDS7245

Canonical transcript exons

ENST00000331173 — 1 exons

ExonStartEnd
ENSE000013244395169548651699595

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 91.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.5406 / max 692.9407, expressed in 1815 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
10937227.37331815
1093710.167359

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011591.44gold quality
germinal epithelium of ovaryUBERON:000130490.87gold quality
choroid plexus epitheliumUBERON:000391190.77gold quality
parietal pleuraUBERON:000240087.53gold quality
ponsUBERON:000098887.36gold quality
islet of LangerhansUBERON:000000687.09gold quality
ganglionic eminenceUBERON:000402387.07gold quality
corpus callosumUBERON:000233686.76gold quality
descending thoracic aortaUBERON:000234586.68gold quality
subthalamic nucleusUBERON:000190686.57gold quality
cortical plateUBERON:000534386.57gold quality
cervix squamous epitheliumUBERON:000692286.57gold quality
skeletal muscle tissueUBERON:000113486.56gold quality
biceps brachiiUBERON:000150786.46gold quality
hair follicleUBERON:000207386.24silver quality
Brodmann (1909) area 23UBERON:001355486.15gold quality
hindlimb stylopod muscleUBERON:000425286.13gold quality
lymph nodeUBERON:000002986.07gold quality
inferior vagus X ganglionUBERON:000536385.80gold quality
C1 segment of cervical spinal cordUBERON:000646985.79gold quality
ventricular zoneUBERON:000305385.78gold quality
ventral tegmental areaUBERON:000269185.75gold quality
muscle of legUBERON:000138385.72gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450285.69gold quality
pleuraUBERON:000097785.64gold quality
muscle tissueUBERON:000238585.64gold quality
superficial temporal arteryUBERON:000161485.57gold quality
spinal cordUBERON:000224085.56gold quality
muscle organUBERON:000163085.55gold quality
heart right ventricleUBERON:000208085.55gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

128 targeting CSTF2T, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3646100.0073.565283
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548AW99.9972.573559
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-480399.9871.993117
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548N99.9871.944170
HSA-MIR-50799.9770.111915
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-55799.9670.011640
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-570-3P99.9672.414910
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426

Literature-anchored findings (GeneRIF, showing 7)

  • Radiation hybrid mapping places the human tauCstF-64 gene at 10q22-q23, which is the site of a translocation that has been associated with human neurological problems and male infertility. (PMID:12408968)
  • structure of the RNA-binding domain of CstF-64 containing an RNA recognition motif (RRM) augmented by N- and C-terminal helices (PMID:12773396)
  • upstream element in human papillomavirus type 16 interacted specifically with CstF-64, hnRNP C1/C2 & polypyrimidine tract binding protein, suggesting these factors were enhancing or regulating polyadenylation at the HPV-16 early polyadenylation signal (PMID:15767428)
  • Studied expression levels of CstF-64 in EV71-infected cells; showed reduction of CstF-64 during virus infection correlated with production of viral 3C(pro). CstF-64 was cleaved in vitro by 3C(pro) not by mutant 3C(pro) variants. (PMID:19779565)
  • CstF64 and CstF64tau modulate one another’s expression and play overlapping as well as distinct roles in regulating global alternative polyadenylation profiles. (PMID:24149845)
  • CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs with critical roles in tumorigenesis and cardiac function. (PMID:28334977)
  • CSTF2T up-regulates IGHG1 by binding to ZEB1 to promote melanoma cell proliferation, migration, and invasion. (PMID:36736099)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusCstf2tENSMUSG00000053536
rattus_norvegicusCstf2tENSRNOG00000070422
drosophila_melanogasterCstF64FBGN0027841
caenorhabditis_elegansWBGENE00000774
caenorhabditis_elegansR06C1.4WBGENE00011059

Paralogs (5): U2AF2 (ENSG00000063244), CSTF2 (ENSG00000101811), RBMX2 (ENSG00000134597), ZCRB1 (ENSG00000139168), UHMK1 (ENSG00000152332)

Protein

Protein identifiers

Cleavage stimulation factor subunit 2 tau variantQ9H0L4 (reviewed: Q9H0L4)

Alternative names: CF-1 64 kDa subunit tau variant, Cleavage stimulation factor 64 kDa subunit tau variant, TauCstF-64

All UniProt accessions (1): Q9H0L4

UniProt curated annotations — full annotation on UniProt →

Function. May play a significant role in AAUAAA-independent mRNA polyadenylation in germ cells. Directly involved in the binding to pre-mRNAs.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_056050* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR025742CSTF2_hingeDomain
IPR026896CSTF_CDomain
IPR035979RBD_domain_sfHomologous_superfamily
IPR038192CSTF_C_sfHomologous_superfamily

Pfam: PF00076, PF14304, PF14327

UniProt features (33 total): repeat 18, region of interest 5, compositionally biased region 4, modified residue 2, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H0L4-F160.270.14

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 (2): 320, 563

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-72187mRNA 3’-end processing
R-HSA-73856RNA Polymerase II Transcription Termination
R-HSA-77595Processing of Intronless Pre-mRNAs
R-HSA-9770562mRNA Polyadenylation
R-HSA-9918481Dengue Virus-Host Interactions
R-HSA-72203Processing of Capped Intron-Containing Pre-mRNA

MSigDB gene sets: 139 (showing top): BROWNE_HCMV_INFECTION_6HR_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, MATTIOLI_MGUS_VS_PCL, chr10q21, BOYLAN_MULTIPLE_MYELOMA_D_DN, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, GOBP_REGULATION_OF_MRNA_3_END_PROCESSING, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_MRNA_3_END_PROCESSING, GARY_CD5_TARGETS_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, REACTOME_METABOLISM_OF_RNA, OSMAN_BLADDER_CANCER_DN

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

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

GO Cellular Component (3): nucleoplasm (GO:0005654), mRNA cleavage and polyadenylation specificity factor complex (GO:0005847), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Processing of Capped Intron-Containing Pre-mRNA1
RNA Polymerase II Transcription1
Processing of Capped Intronless Pre-mRNA1
mRNA 3’-end processing1
Dengue Virus Infection1
Metabolism of RNA1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
mRNA processing1
RNA 3’-end processing1
RNA processing1
mRNA metabolic process1
nucleic acid binding1
RNA binding1
nuclear lumen1
cellular anatomical structure1
mRNA cleavage factor complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2608 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CSTF2TLMOD1P29536760
CSTF2TCSTF3Q12996742
CSTF2TCSTF1Q05048715
CSTF2TCPSF1Q10570665
CSTF2TNUDT21O43809664
CSTF2TCPSF3Q9UKF6646
CSTF2TPCF11O94913615
CSTF2TCPSF2Q9P2I0613
CSTF2TSYMPKQ92797605
CSTF2TWDR33Q9C0J8601
CSTF2TCPSF4O95639563
CSTF2TCPSF6Q16630549
CSTF2TNONOP30807532
CSTF2TFIP1L1Q6UN15525
CSTF2TPAPOLGQ9BWT3487

IntAct

128 interactions, top by confidence:

ABTypeScore
FANCGFANCApsi-mi:“MI:0914”(association)0.960
RFX5RFXAPpsi-mi:“MI:0914”(association)0.880
UBQLN1CSTF2Tpsi-mi:“MI:0915”(physical association)0.780
CSTF2TUBQLN1psi-mi:“MI:0915”(physical association)0.780
BIRC2HTRA2psi-mi:“MI:0914”(association)0.650
CSTF2THGSpsi-mi:“MI:0915”(physical association)0.560
UBQLN1CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
HGSCSTF2Tpsi-mi:“MI:0915”(physical association)0.560
CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
FOXJ2CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
CSTF2TUBQLN2psi-mi:“MI:0915”(physical association)0.560
CTAG1ACSTF2Tpsi-mi:“MI:0915”(physical association)0.560
PKNOX2CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
CSTF2TCOL17A1psi-mi:“MI:0915”(physical association)0.560
TLE5CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
FAM168BCSTF2Tpsi-mi:“MI:0915”(physical association)0.560
LASP1CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
CSTF2TAKAP8Lpsi-mi:“MI:0915”(physical association)0.560
CSTF2TSMYD3psi-mi:“MI:0915”(physical association)0.560
CTDSP1CSTF2Tpsi-mi:“MI:0915”(physical association)0.560
FOXI1CSTF2Tpsi-mi:“MI:0915”(physical association)0.560

BioGRID (132): CSTF2T (Two-hybrid), UBQLN1 (Two-hybrid), CSTF2T (Affinity Capture-MS), UBQLN1 (Two-hybrid), CSTF1 (Co-fractionation), CSTF2T (Co-fractionation), CSTF2T (Co-fractionation), CSTF2T (Co-fractionation), CSTF2T (Co-fractionation), CSTF2T (Affinity Capture-Western), CSTF2T (Proximity Label-MS), GOLGA2 (Two-hybrid), CSTF2T (Affinity Capture-MS), CSTF2T (Affinity Capture-MS), CSTF2T (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q7JC00, A0JM64, A0JNC2, A2VE44, A4IHD9, B2C6R6, B5DE09, B8BCZ8, E7F1H9, F4JT98, O09000, O57539, P78364, Q0WVM7, Q15596, Q17BA4, Q2NLB0, Q3TCX3, Q5RDA3, Q5TP13, Q5ZL54, Q61026, Q64028, Q6GP15, Q6K271, Q6NS15, Q6PEH8, Q71SY5, Q7XYY2, Q7ZVN7, Q80TM6, Q8C7E9, Q8CHY6, Q8HXM1, Q8IZL2, Q8VCB2, Q8W234, Q90WJ3, Q924H2, Q940A7

Diamond homologs: A0A0F6MY85, O02008, P19018, P33240, Q05AT9, Q16560, Q1LZH0, Q4KMD3, Q5RDA3, Q5U1W5, Q8BIQ5, Q8C7E9, Q8HXM1, Q8LPQ9, Q9D384, Q9H0L4, Q9SHZ6, A0A8M1NHK4, A0AV96, A0JM51, A4FV72, A4QUF0, A8WLV5, O01671, O04425, O43040, O43390, O60506, P28659, P86049, Q08BH5, Q08E07, Q0P4R6, Q0V9L3, Q10B98, Q14498, Q28HE9, Q2HJG2, Q2UK72, Q3UEB3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 89 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:

PathwayPartnersFoldFDR
Processing of Intronless Pre-mRNAs657.1×2e-07
mRNA 3’-end processing723.0×2e-06
RNA Polymerase II Transcription Termination622.0×2e-05
mRNA Polyadenylation1014.6×2e-07
Dengue Virus-Host Interactions118.4×5e-06

GO biological processes:

GO termPartnersFoldFDR
mRNA processing98.8×5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance89
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

93 predictions. Top by Δscore:

VariantEffectΔscore
10:51698941:G:Adonor_gain0.9400
10:51699080:T:TAdonor_gain0.9300
10:51695633:GAATT:Gdonor_gain0.8900
10:51695634:AATTA:Adonor_gain0.8900
10:51699437:T:TAdonor_gain0.7700
10:51699456:A:Cdonor_gain0.7300
10:51698970:T:TAdonor_gain0.6800
10:51696106:CA:Cacceptor_gain0.6300
10:51699466:AGTTG:Adonor_gain0.6200
10:51699449:T:TAdonor_gain0.6100
10:51698938:T:Cdonor_gain0.5700
10:51699018:C:CTdonor_gain0.5300
10:51699019:T:TTdonor_gain0.5300
10:51696977:TAGAA:Tacceptor_gain0.4700
10:51698931:A:ACdonor_gain0.4700
10:51698932:C:CCdonor_gain0.4700
10:51698967:T:Cdonor_gain0.4600
10:51699529:T:TAdonor_gain0.4400
10:51699433:A:Tdonor_gain0.4300
10:51696606:CT:Cacceptor_gain0.3900
10:51696625:T:Aacceptor_gain0.3900
10:51699254:T:TAdonor_gain0.3800
10:51699470:G:Adonor_gain0.3800
10:51696107:A:Cacceptor_gain0.3600
10:51699309:C:CAdonor_gain0.3600
10:51699431:CCAA:Cdonor_loss0.3600
10:51699432:CAACC:Cdonor_loss0.3600
10:51699433:AAC:Adonor_loss0.3600
10:51699434:A:ACdonor_loss0.3600
10:51699435:C:Adonor_loss0.3600

AlphaMissense

3970 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:51697724:A:CI609S1.000
10:51697724:A:GI609T1.000
10:51697724:A:TI609N1.000
10:51697727:T:GQ608P1.000
10:51697732:C:AK606N1.000
10:51697732:C:GK606N1.000
10:51697736:A:GL605S1.000
10:51697742:A:GL603P1.000
10:51697745:A:CI602S1.000
10:51697745:A:GI602T1.000
10:51697745:A:TI602N1.000
10:51697769:A:GL594P1.000
10:51697769:A:TL594Q1.000
10:51697793:A:GL586P1.000
10:51697799:A:GL584P1.000
10:51697802:A:TV583D1.000
10:51697805:T:GQ582P1.000
10:51697811:A:CI580S1.000
10:51697811:A:GI580T1.000
10:51697811:A:TI580N1.000
10:51697814:A:CL579W1.000
10:51697814:A:GL579S1.000
10:51698978:A:GL191P1.000
10:51698990:G:TA187D1.000
10:51699027:C:GA175P1.000
10:51699029:T:GQ174P1.000
10:51699032:A:GL173S1.000
10:51699035:A:GL172P1.000
10:51699035:A:TL172Q1.000
10:51699038:G:TA171E1.000

dbSNP variants (sampled 300 via entrez): RS1000903918 (10:51697454 T>C,G), RS1000988670 (10:51700404 T>A), RS1001221354 (10:51695443 T>C), RS1001714948 (10:51695199 C>A,T), RS1003268596 (10:51698358 G>A), RS1004894485 (10:51696166 A>G), RS1004954611 (10:51699820 G>A), RS1005690901 (10:51695977 G>A), RS1006369170 (10:51701285 CTT>C), RS1006883167 (10:51699830 G>A), RS1007229921 (10:51700868 A>G), RS1007245838 (10:51695342 CTAAG>C), RS1007275470 (10:51695619 C>T), RS1007400733 (10:51696998 A>C), RS1007624675 (10:51701170 T>C)

Disease associations

OMIM: gene MIM:611968 | disease phenotypes: MIM:615436

GenCC curated gene-disease

Mondo (1): aortic aneurysm, familial thoracic 8 (MONDO:0014187)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST002666_2Interferon alpha levels in systemic lupus erythematosus3.000000e-08
GCST002668_5Mammographic density (non-dense area)3.000000e-06
GCST007006_8Logical memory (delayed recall) in normal cognition2.000000e-08

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0006517interferon alpha measurement
EFO:0005941mammographic density measurement
EFO:0006504non-dense area measurement
EFO:0004874memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression6
trichostatin Aaffects cotreatment, decreases expression3
Air Pollutantsaffects expression, increases abundance, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
GSK-J4decreases expression1
FR900359increases phosphorylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
manganese chlorideincreases abundance, increases expression1
cyclic 3’,5’-uridine monophosphateaffects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Cadmiumdecreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Irondecreases expression1
Ivermectindecreases expression1
Manganeseincreases abundance, increases expression1
Ozoneaffects expression, increases abundance1
Ribonucleotidesaffects binding1
Silicon Dioxidedecreases expression1
Thiramdecreases expression1
Tretinoindecreases expression1
Urethanedecreases expression1
Vitamin Daffects expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): aortic aneurysm, familial thoracic 8