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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Charcot-Marie-Tooth disease	Pathogenic	rs113994102	RCV000789083	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital cataracts-facial dysmorphism-neuropathy syndrome	Pathogenic	rs113994102	RCV000005622	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL CATARACTS, FACIAL DYSMORPHISM, AND NEUROPATHY	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CTDP1-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (46)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acquired Kyphoscoliosis	Acquired Kyphoscoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet Syndrome	BEFREE	27777341		★★★★★ ★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet disease	Pubtator	27777341	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	26590573		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	LHGDN	14517542		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	Pubtator	24690360	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Charcot-Marie-Tooth Disease	Charcot-Marie-Tooth Disease	CLINVAR_DG	16194727		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Clumsiness - motor delay	Motor delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Cataracts Facial Dysmorphism And Neuropathy	Congenital cataract facial dysmorphism neuropathy syndrome	Pubtator	24690360	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Cataracts, Facial Dysmorphism, And Neuropathy	Congenital Cataracts, Facial Dysmorphism, And Neuropathy	GENOMICS_ENGLAND_DG	14517542		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Cataracts, Facial Dysmorphism, And Neuropathy	Congenital Cataracts, Facial Dysmorphism, And Neuropathy	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Cataracts, Facial Dysmorphism, And Neuropathy	Congenital Cataracts, Facial Dysmorphism, And Neuropathy	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital cataracts-facial dysmorphism-neuropathy syndrome	Congenital Cataracts, Facial Dysmorphism, And Neuropathy	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital genu recurvatum	Congenital genu recurvatum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital kyphoscoliosis	Congenital kyphoscoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Demyelinating Diseases	Demyelinating diseases	Pubtator	24690360	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	34585950	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	23771925	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	23771925		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemochromatosis	Hemochromatosis	Pubtator	1379090	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	26590573		★★★★★ ★☆☆☆☆ Found in Text Mining only
Marinesco-Sjogren syndrome	Marinesco-Sjogren Syndrome	BEFREE	11805249		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	Pubtator	24690360	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26590573, 28729428		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Peripheral demyelinating neuropathy	Demyelinating neuropathy	BEFREE	11805249		★★★★★ ★☆☆☆☆ Found in Text Mining only
Polyneuropathy, Motor	Polyneuropathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary hypogonadism	Hypogonadism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	16004614	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

CTDP1 (CTD phosphatase subunit 1)