Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	9150
Gene name	CTD phosphatase subunit 1
Gene symbol	CTDP1
Synonyms (NCBI Gene)	CCFDNFCP1
Chromosome	18
Chromosome location	18q23
Summary	This gene encodes a protein which interacts with the carboxy-terminus of the RAP74 subunit of transcription initiation factor TFIIF, and functions as a phosphatase that processively dephosphorylates the C-terminus of POLR2A (a subunit of RNA polymerase II

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113994102	C>T	Pathogenic	Intron variant
rs146831211	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs1403055370	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant

Show/Hide all (49)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017032	hsa-miR-335-5p	Microarray	18185580
MIRT052631	hsa-let-7a-5p	CLASH	23622248
MIRT051717	hsa-let-7d-5p	CLASH	23622248
MIRT041328	hsa-miR-193b-3p	CLASH	23622248
MIRT914073	hsa-miR-1287	CLIP-seq
MIRT914074	hsa-miR-3135b	CLIP-seq
MIRT914075	hsa-miR-3155	CLIP-seq
MIRT914076	hsa-miR-3155b	CLIP-seq
MIRT914077	hsa-miR-3191	CLIP-seq
MIRT914078	hsa-miR-3616-3p	CLIP-seq
MIRT914079	hsa-miR-3689d	CLIP-seq
MIRT914080	hsa-miR-4446-3p	CLIP-seq
MIRT914081	hsa-miR-4492	CLIP-seq
MIRT914082	hsa-miR-4498	CLIP-seq
MIRT914083	hsa-miR-4499	CLIP-seq
MIRT914084	hsa-miR-4523	CLIP-seq
MIRT914085	hsa-miR-4721	CLIP-seq
MIRT914086	hsa-miR-4800-5p	CLIP-seq
MIRT914087	hsa-miR-484	CLIP-seq
MIRT914088	hsa-miR-486-5p	CLIP-seq
MIRT914089	hsa-miR-548a-3p	CLIP-seq
MIRT914090	hsa-miR-548ac	CLIP-seq
MIRT914091	hsa-miR-548ae	CLIP-seq
MIRT914092	hsa-miR-548aj	CLIP-seq
MIRT914093	hsa-miR-548am	CLIP-seq
MIRT914094	hsa-miR-548d-3p	CLIP-seq
MIRT914095	hsa-miR-548e	CLIP-seq
MIRT914096	hsa-miR-548f	CLIP-seq
MIRT914097	hsa-miR-548x	CLIP-seq
MIRT914098	hsa-miR-548z	CLIP-seq
MIRT914099	hsa-miR-762	CLIP-seq
MIRT914100	hsa-miR-3670	CLIP-seq
MIRT914101	hsa-miR-4663	CLIP-seq
MIRT914102	hsa-miR-9	CLIP-seq
MIRT2206788	hsa-miR-125a-3p	CLIP-seq
MIRT2206789	hsa-miR-3934	CLIP-seq
MIRT2206790	hsa-miR-4645-5p	CLIP-seq
MIRT2206791	hsa-miR-4673	CLIP-seq
MIRT2206792	hsa-miR-499-3p	CLIP-seq
MIRT2206793	hsa-miR-499a-3p	CLIP-seq
MIRT2206794	hsa-miR-654-3p	CLIP-seq
MIRT2206795	hsa-miR-764	CLIP-seq
MIRT2510110	hsa-miR-4266	CLIP-seq
MIRT2510111	hsa-miR-4419a	CLIP-seq
MIRT2510112	hsa-miR-4506	CLIP-seq
MIRT2510113	hsa-miR-4510	CLIP-seq
MIRT2510114	hsa-miR-4695-5p	CLIP-seq
MIRT2510115	hsa-miR-4707-5p	CLIP-seq
MIRT2510116	hsa-miR-4779	CLIP-seq

Show/Hide all (33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000922	Component	Spindle pole	IDA	22692537
GO:0000922	Component	Spindle pole	IEA
GO:0001096	Function	TFIIF-class transcription factor complex binding	IPI	12732728, 15723517
GO:0004721	Function	Phosphoprotein phosphatase activity	IEA
GO:0004721	Function	Phosphoprotein phosphatase activity	TAS
GO:0004722	Function	Protein serine/threonine phosphatase activity	IEA
GO:0005515	Function	Protein binding	IPI	9765293, 12732728, 31240132
GO:0005634	Component	Nucleus	IDA	15723517
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	22692537
GO:0005813	Component	Centrosome	IEA
GO:0005819	Component	Spindle	IDA	22692537
GO:0005856	Component	Cytoskeleton	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0006368	Process	Transcription elongation by RNA polymerase II	TAS
GO:0006470	Process	Protein dephosphorylation	IDA	9765293, 22692537
GO:0008420	Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	IBA
GO:0008420	Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	IDA	9765293, 12721286
GO:0008420	Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	IEA
GO:0010458	Process	Exit from mitosis	IMP	22692537
GO:0016787	Function	Hydrolase activity	IEA
GO:0030496	Component	Midbody	IDA	22692537
GO:0030496	Component	Midbody	IEA
GO:0030957	Function	Tat protein binding	IPI	15723517
GO:0032991	Component	Protein-containing complex	IMP	12732728
GO:0043923	Process	Host-mediated activation of viral transcription	IDA	15723517
GO:0051233	Component	Spindle midzone	IDA	22692537
GO:0051301	Process	Cell division	IEA
GO:0061052	Process	Negative regulation of cell growth involved in cardiac muscle cell development	IEA

MIM	HGNC	e!Ensembl
604927	2498	ENSG00000060069

Q9Y5B0

Protein name

RNA polymerase II subunit A C-terminal domain phosphatase (EC 3.1.3.16) (TFIIF-associating CTD phosphatase)

Protein function

Processively dephosphorylates 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. This promotes the activity of RNA polymerase II. Plays a role in the exit from mitosis by dephosph

PDB

1J2X , 1ONV , 2K7L

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03031	NIF	183 → 331	NLI interacting factor-like phosphatase	Family
PF09309	FCP1_C	716 → 961	FCP1, C-terminal	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:9765293}.

Sequence

MEVPAAGRVPAEGAPTAAVAEVRCPGPAPLRLLEWRVAAGAAVRIGSVLAVFEAAASAQS
SGASQSRVASGGCVRPARPERRLRSERAGVVRELCAQPGQVVAPGAVLVRLEGCSHPVVM
KGLCAECGQDLTQLQSKNGKQQVPLSTATVSMVHSVPELMVSSEQAEQLGREDQQRLHRN
RKLVLMVDLDQTLIHTTEQHCQQMSNKGIFHFQLGRGEPMLHTRLRPHCKDFLEKIAKLY
ELHVFTFGSRLYAHTIAGFLDPEKKLFSHRILSRDECIDPFSKTGNLRNLFPCGDSMVCI
IDDREDVWKFAPNLITVKKYVYFQGTGDMNAPPGSRESQTRKKVNHSRGTEVSEPSPPVR
DPEGVTQAPGVEPSNGLEKPARELNGSEAATPRDSPRPGKPDERDIWPPAQAPTSSQELA
GAPEPQGSCAQGGRVAPGQRPAQGATGTDLDFDLSSDSESSSESEGTKSSSSASDGESEG
KRGRQKPKAAPEGAGALAQGSSLEPGRPAAPSLPGEAEPGAHAPDKEPELGGQEEGERDG
LCGLGNGCADRKEAETESQNSELSGVTAGESLDQSMEEEEEEDTDEDDHLIYLEEILVRV
HTDYYAKYDRYLNKEIEEAPDIRKIVPELKSKVLADVAIIFSGLHPTNFPIEKTREHYHA
TALGAKILTRLVLSPDAPDRATHLIAARAGTEKVLQAQECGHLHVVNPDWLWSCLERWDK
VEEQLFPLRDDHTKAQRENSPAAFPDREGVPPTALFHPMPVLPKAQPGPEVRIYDSNTGK
LIRTGARGPPAPSSSLPIRQEPSSFRAVPPPQPQMFGEELPDAQDGEQPGPSRRKRQPSM
SETMPLYTLCKEDLESMDKEVDDILGEGSDDSDSEKRRPEEQEEEPQPRKPGTRRERTLG
APASSERSAAGGRGPRGHKRKLNEEDAASESSRESSNEDEGSSSEADEMAKALEAELNDL
M

Sequence length

961

Interactions

View interactions

	Reactome
			Formation of RNA Pol II elongation complex Formation of the Early Elongation Complex Formation of HIV-1 elongation complex containing HIV-1 Tat RNA Polymerase II Pre-transcription Events TP53 Regulates Transcription of DNA Repair Genes RNA Polymerase II Transcription Elongation

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Charcot-Marie-Tooth disease	Pathogenic	rs113994102	RCV000789083
Congenital cataracts-facial dysmorphism-neuropathy syndrome	Pathogenic	rs113994102	RCV000005622

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Likely benign	rs637103	RCV005914859
Cholangiocarcinoma	Likely benign	rs112743048, rs637103	RCV005914622 RCV005914864
CTDP1-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity; Benign	rs372171375, rs748190220, rs377764231, rs775966859, rs112476862, rs202180742, rs770864397, rs978655653, rs146831211, rs746730170, rs372238734, rs1470313122, rs762372815, rs2511986604, rs573314400 View all (19 more)	RCV003898767 RCV003936576 RCV003919015 RCV004756417 RCV004756428 RCV003898591 RCV003943600 RCV003961220 RCV003939996 RCV003420851 RCV003408787 RCV003946567 RCV003939077 RCV003981531 RCV003981543 RCV003899814 RCV003941862 RCV003949288 RCV003934678 RCV003944297 RCV003934651 RCV003959463 RCV003963815 RCV003918523 RCV003916154 RCV003895409 RCV003930832 RCV003957938 RCV003910817 RCV003950555 RCV003960411 RCV003913021 RCV003953330 RCV003936232
Gastric cancer	Benign; Likely benign	rs145726709	RCV005905184
Hepatocellular carcinoma	Likely benign	rs370568072	RCV005931121
Lung cancer	Benign; Likely benign	rs140538707	RCV005928068
Malignant lymphoma, large B-cell, diffuse	Likely benign; Benign	rs637103, rs599554	RCV005914861 RCV005900069
Malignant tumor of esophagus	Likely benign	rs637103	RCV005914860
Ovarian serous cystadenocarcinoma	Likely benign	rs637103	RCV005914862
See cases	Uncertain significance	rs769147755	RCV002252907
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	rs145726709	RCV005905185
Uterine carcinosarcoma	Likely benign; Benign	rs637103, rs599554	RCV005914863 RCV005900070
Uterine corpus endometrial carcinoma	Likely benign	rs112743048, rs637103	RCV005914623 RCV005914865

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Behcet Syndrome	Associate	27777341
Cataract	Associate	24690360
Congenital Cataracts Facial Dysmorphism And Neuropathy	Associate	24690360
Demyelinating Diseases	Associate	24690360
Depressive Disorder	Associate	34585950
Disease	Associate	34585950
Microphthalmos	Associate	24690360
Uterine Cervical Neoplasms	Associate	16004614

CTDP1 (CTD phosphatase subunit 1)