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	10978
Gene name	Cleavage factor polyribonucleotide kinase subunit 1
Gene symbol	CLP1
Synonyms (NCBI Gene)	HEABhClp1
Chromosome	11
Chromosome location	11q12.1
Summary	This gene encodes a member of the Clp1 family. The encoded protein is a multifunctional kinase which is a component of the tRNA splicing endonuclease complex and a component of the pre-mRNA cleavage complex II. This protein is implicated in tRNA, mRNA, an

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SNP ID	Visualize variation	Clinical significance	Consequence
rs587777616	G>A	Likely-pathogenic, pathogenic-likely-pathogenic	Intron variant, coding sequence variant, missense variant

Show/Hide all (86)

miRTarBase ID	miRNA	Experiments	Reference
MIRT027594	hsa-miR-98-5p	Microarray	19088304
MIRT897635	hsa-miR-128	CLIP-seq
MIRT897636	hsa-let-7a	CLIP-seq
MIRT897637	hsa-let-7b	CLIP-seq
MIRT897638	hsa-let-7c	CLIP-seq
MIRT897639	hsa-let-7d	CLIP-seq
MIRT897640	hsa-let-7e	CLIP-seq
MIRT897641	hsa-let-7f	CLIP-seq
MIRT897642	hsa-let-7g	CLIP-seq
MIRT897643	hsa-let-7i	CLIP-seq
MIRT897644	hsa-miR-1303	CLIP-seq
MIRT897645	hsa-miR-3927	CLIP-seq
MIRT897646	hsa-miR-4458	CLIP-seq
MIRT897647	hsa-miR-4500	CLIP-seq
MIRT897648	hsa-miR-4506	CLIP-seq
MIRT897649	hsa-miR-4511	CLIP-seq
MIRT897650	hsa-miR-4517	CLIP-seq
MIRT897651	hsa-miR-4650-3p	CLIP-seq
MIRT897652	hsa-miR-4694-3p	CLIP-seq
MIRT897653	hsa-miR-522	CLIP-seq
MIRT897654	hsa-miR-548b-3p	CLIP-seq
MIRT897655	hsa-miR-555	CLIP-seq
MIRT897656	hsa-miR-577	CLIP-seq
MIRT897657	hsa-miR-659	CLIP-seq
MIRT897658	hsa-miR-877	CLIP-seq
MIRT897659	hsa-miR-98	CLIP-seq
MIRT897636	hsa-let-7a	CLIP-seq
MIRT897637	hsa-let-7b	CLIP-seq
MIRT897638	hsa-let-7c	CLIP-seq
MIRT897639	hsa-let-7d	CLIP-seq
MIRT897640	hsa-let-7e	CLIP-seq
MIRT897641	hsa-let-7f	CLIP-seq
MIRT897642	hsa-let-7g	CLIP-seq
MIRT897643	hsa-let-7i	CLIP-seq
MIRT897644	hsa-miR-1303	CLIP-seq
MIRT1966195	hsa-miR-142-5p	CLIP-seq
MIRT1966196	hsa-miR-340	CLIP-seq
MIRT1966197	hsa-miR-3688-3p	CLIP-seq
MIRT1966198	hsa-miR-3923	CLIP-seq
MIRT897645	hsa-miR-3927	CLIP-seq
MIRT1966199	hsa-miR-409-5p	CLIP-seq
MIRT1966200	hsa-miR-4422	CLIP-seq
MIRT897646	hsa-miR-4458	CLIP-seq
MIRT897647	hsa-miR-4500	CLIP-seq
MIRT897649	hsa-miR-4511	CLIP-seq
MIRT897650	hsa-miR-4517	CLIP-seq
MIRT897651	hsa-miR-4650-3p	CLIP-seq
MIRT897654	hsa-miR-548b-3p	CLIP-seq
MIRT897658	hsa-miR-877	CLIP-seq
MIRT897659	hsa-miR-98	CLIP-seq
MIRT897636	hsa-let-7a	CLIP-seq
MIRT897637	hsa-let-7b	CLIP-seq
MIRT897638	hsa-let-7c	CLIP-seq
MIRT897639	hsa-let-7d	CLIP-seq
MIRT897640	hsa-let-7e	CLIP-seq
MIRT897641	hsa-let-7f	CLIP-seq
MIRT897642	hsa-let-7g	CLIP-seq
MIRT897643	hsa-let-7i	CLIP-seq
MIRT2201967	hsa-miR-125a-3p	CLIP-seq
MIRT2201968	hsa-miR-1289	CLIP-seq
MIRT897644	hsa-miR-1303	CLIP-seq
MIRT2201969	hsa-miR-132	CLIP-seq
MIRT2201970	hsa-miR-2114	CLIP-seq
MIRT2201971	hsa-miR-212	CLIP-seq
MIRT1966198	hsa-miR-3923	CLIP-seq
MIRT897645	hsa-miR-3927	CLIP-seq
MIRT2201972	hsa-miR-3934	CLIP-seq
MIRT1966199	hsa-miR-409-5p	CLIP-seq
MIRT897646	hsa-miR-4458	CLIP-seq
MIRT897647	hsa-miR-4500	CLIP-seq
MIRT897650	hsa-miR-4517	CLIP-seq
MIRT897651	hsa-miR-4650-3p	CLIP-seq
MIRT2201973	hsa-miR-4709-5p	CLIP-seq
MIRT2201974	hsa-miR-554	CLIP-seq
MIRT2201975	hsa-miR-582-5p	CLIP-seq
MIRT897657	hsa-miR-659	CLIP-seq
MIRT2201976	hsa-miR-663b	CLIP-seq
MIRT2201977	hsa-miR-764	CLIP-seq
MIRT897658	hsa-miR-877	CLIP-seq
MIRT897659	hsa-miR-98	CLIP-seq
MIRT1966195	hsa-miR-142-5p	CLIP-seq
MIRT1966196	hsa-miR-340	CLIP-seq
MIRT1966197	hsa-miR-3688-3p	CLIP-seq
MIRT1966200	hsa-miR-4422	CLIP-seq
MIRT897649	hsa-miR-4511	CLIP-seq
MIRT897654	hsa-miR-548b-3p	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000214	Component	TRNA-intron endonuclease complex	IDA	17495927
GO:0000214	Component	TRNA-intron endonuclease complex	IEA
GO:0005515	Function	Protein binding	IPI	32296183, 33961781, 35177536
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	TAS	8896421
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	24766810
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005829	Component	Cytosol	IDA
GO:0005849	Component	MRNA cleavage factor complex	IEA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IBA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IDA	17495927
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IEA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IMP	24766809, 24766810
GO:0006396	Process	RNA processing	IEA
GO:0006397	Process	MRNA processing	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0021695	Process	Cerebellar cortex development	IEA
GO:0021695	Process	Cerebellar cortex development	IMP	24766809, 24766810
GO:0031124	Process	MRNA 3'-end processing	IEA
GO:0031124	Process	MRNA 3'-end processing	TAS	17495927
GO:0046404	Function	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IDA	17495927
GO:0046404	Function	ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity	IEA
GO:0051731	Function	Polynucleotide 5'-hydroxyl-kinase activity	IBA
GO:0051731	Function	Polynucleotide 5'-hydroxyl-kinase activity	IEA
GO:0051734	Function	ATP-dependent polynucleotide 5'-hydroxyl-kinase activity	IEA
GO:0051736	Function	ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	IDA	17495927
GO:0051736	Function	ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	IEA
GO:0051736	Function	ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity	IMP	24766809, 24766810
GO:0070922	Process	RISC complex assembly	IDA	17495927
GO:0070922	Process	RISC complex assembly	IEA
GO:0098795	Process	Global gene silencing by mRNA cleavage	IMP	17495927

MIM	HGNC	e!Ensembl
608757	16999	ENSG00000172409

Q92989

Protein name

Polyribonucleotide 5'-hydroxyl-kinase Clp1 (EC 2.7.1.78) (Polyadenylation factor Clp1) (Polynucleotide kinase Clp1) (Pre-mRNA cleavage complex II protein Clp1)

Protein function

Polynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA

PDB

8HMY , 8HMZ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF16573	CLP1_N	16 → 107	N-terminal beta-sandwich domain of polyadenylation factor	Family
PF16575	CLP1_P	121 → 307	mRNA cleavage and polyadenylation factor CLP1 P-loop	Domain
PF06807	Clp1	312 → 423	Pre-mRNA cleavage complex II protein Clp1	Family

Sequence

MGEEANDDKKPTTKFELERETELRFEVEASQSVQLELLTGMAEIFGTELTRNKKFTFDAG
AKVAVFTWHGCSVQLSGRTEVAYVSKDTPMLLYLNTHTALEQMRRQAEKEEERGPRVMVV
GPTDVGKSTVCRLLLNYAVRLGRRPTYVELDVGQGSVSIPGTMGALYIERPADVEEGFSI
QAPLVYHFGSTTPGTNIKLYNKITSRLADVFNQRCEVNRRASVSGCVINTCGWVKGSGYQ
ALVHAASAFEVDVVVVLDQERLYNELKRDLPHFVRTVLLPKSGGVVERSKDFRRECRDER
IREYFYGFRGCFYPHAFNVKFSDVKIYKVGAPTIPDSCLPLGMSQEDNQLKLVPVTPGRD
MVHHLLSVSTAEGTEENLSETSVAGFIVVTSVDLEHQVFTVLSPAPRPLPKNFLLIMDIR
FMDLK

Sequence length

425

Interactions

View interactions

	KEGG		Reactome
	mRNA surveillance pathway		tRNA processing in the nucleus mRNA Splicing - Major Pathway mRNA 3'-end processing RNA Polymerase II Transcription Termination Processing of Intronless Pre-mRNAs

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Pontocerebellar hypoplasia type 10	Likely pathogenic; Pathogenic	rs587777616	RCV000133463
Pontoneocerebellar hypoplasia	Likely pathogenic; Pathogenic	rs587777616	RCV005431485

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
CLP1-related disorder	Likely benign; Benign	rs140965892, rs184720631, rs111754731, rs17152015, rs148451233	RCV003958692 RCV003939173 RCV003922818 RCV003922817 RCV003928534
Thyroid cancer, nonmedullary, 1	Likely benign	rs149223879	RCV005925536

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	28630030
Diabetes Mellitus	Stimulate	30894181
Glioma	Associate	24532499
Myocardial Ischemia	Stimulate	30894181
Neoplasms	Associate	24532499
Neurodegenerative Diseases	Associate	32476018, 35139363
Pontocerebellar Hypoplasia	Associate	36076253
Thrombosis	Associate	34668383

CLP1 (cleavage factor polyribonucleotide kinase subunit 1)