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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	51095
Gene name Gene Name - the full gene name approved by the HGNC.	TRNA nucleotidyl transferase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TRNT1
Synonyms (NCBI Gene) Gene synonyms aliases	CCA1, CGI-47, MtCCA, RPEM, SIFD
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p26.2
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3` terminus of tR

Show/Hide all(11)

SNP ID	Visualize variation	Clinical significance	Consequence
rs370011798	T>C	Pathogenic	Missense variant, intron variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs606231287	G>C,T	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs606231289	T>C	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs606231290	C>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant, intron variant, genic downstream transcript variant
rs761516140	C>G,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant, genic downstream transcript variant, intron variant
rs769317780	TTAG>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, frameshift variant
rs776199133	CGGAACA>-	Pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, frameshift variant
rs876661297	AAG>-	Pathogenic	Inframe deletion, non coding transcript variant, coding sequence variant
rs876661299	T>C	Pathogenic	Genic downstream transcript variant, intron variant
rs1553554007	C>-	Likely-pathogenic	Non coding transcript variant, intron variant, genic downstream transcript variant, frameshift variant, coding sequence variant
rs1575066836	T>-	Pathogenic	Non coding transcript variant, genic downstream transcript variant, frameshift variant, coding sequence variant

Show/Hide all(195)

miRTarBase ID	miRNA	Experiments	Reference
MIRT032454	hsa-let-7b-5p	Proteomics	18668040
MIRT447873	hsa-miR-3168	PAR-CLIP	22100165
MIRT447872	hsa-miR-148b-5p	PAR-CLIP	22100165
MIRT447871	hsa-miR-6874-3p	PAR-CLIP	22100165
MIRT447870	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT447869	hsa-miR-4635	PAR-CLIP	22100165
MIRT447868	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT447867	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT447873	hsa-miR-3168	PAR-CLIP	22100165
MIRT447872	hsa-miR-148b-5p	PAR-CLIP	22100165
MIRT447871	hsa-miR-6874-3p	PAR-CLIP	22100165
MIRT447870	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT447869	hsa-miR-4635	PAR-CLIP	22100165
MIRT447868	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT447867	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT447873	hsa-miR-3168	PAR-CLIP	22100165
MIRT447872	hsa-miR-148b-5p	PAR-CLIP	22100165
MIRT447871	hsa-miR-6874-3p	PAR-CLIP	22100165
MIRT447870	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT447869	hsa-miR-4635	PAR-CLIP	22100165
MIRT447868	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT447867	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT447873	hsa-miR-3168	PAR-CLIP	22100165
MIRT447872	hsa-miR-148b-5p	PAR-CLIP	22100165
MIRT447871	hsa-miR-6874-3p	PAR-CLIP	22100165
MIRT447870	hsa-miR-5584-3p	PAR-CLIP	22100165
MIRT447869	hsa-miR-4635	PAR-CLIP	22100165
MIRT447868	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT447867	hsa-miR-203a-3p	PAR-CLIP	22100165
MIRT1457078	hsa-miR-10a	CLIP-seq
MIRT1457079	hsa-miR-10b	CLIP-seq
MIRT1457080	hsa-miR-1202	CLIP-seq
MIRT1457081	hsa-miR-1278	CLIP-seq
MIRT1457082	hsa-miR-1321	CLIP-seq
MIRT1457083	hsa-miR-140-3p	CLIP-seq
MIRT1457084	hsa-miR-186	CLIP-seq
MIRT1457085	hsa-miR-2053	CLIP-seq
MIRT1457086	hsa-miR-2355-5p	CLIP-seq
MIRT1457087	hsa-miR-23a	CLIP-seq
MIRT1457088	hsa-miR-23b	CLIP-seq
MIRT1457089	hsa-miR-23c	CLIP-seq
MIRT1457090	hsa-miR-3133	CLIP-seq
MIRT1457091	hsa-miR-3140-3p	CLIP-seq
MIRT1457092	hsa-miR-3155	CLIP-seq
MIRT1457093	hsa-miR-3155b	CLIP-seq
MIRT1457094	hsa-miR-3175	CLIP-seq
MIRT1457095	hsa-miR-3194-3p	CLIP-seq
MIRT1457096	hsa-miR-3194-5p	CLIP-seq
MIRT1457097	hsa-miR-323b-3p	CLIP-seq
MIRT1457098	hsa-miR-376a	CLIP-seq
MIRT1457099	hsa-miR-376b	CLIP-seq
MIRT1457100	hsa-miR-3972	CLIP-seq
MIRT1457101	hsa-miR-4275	CLIP-seq
MIRT1457102	hsa-miR-4289	CLIP-seq
MIRT1457103	hsa-miR-4293	CLIP-seq
MIRT1457104	hsa-miR-4328	CLIP-seq
MIRT1457105	hsa-miR-4419a	CLIP-seq
MIRT1457106	hsa-miR-4474-5p	CLIP-seq
MIRT1457107	hsa-miR-4504	CLIP-seq
MIRT1457108	hsa-miR-4510	CLIP-seq
MIRT1457109	hsa-miR-4511	CLIP-seq
MIRT1457110	hsa-miR-4662a-3p	CLIP-seq
MIRT1457111	hsa-miR-4728-5p	CLIP-seq
MIRT1457112	hsa-miR-4739	CLIP-seq
MIRT1457113	hsa-miR-4756-5p	CLIP-seq
MIRT1457114	hsa-miR-4773	CLIP-seq
MIRT1457115	hsa-miR-484	CLIP-seq
MIRT1457116	hsa-miR-486-5p	CLIP-seq
MIRT1457117	hsa-miR-491-3p	CLIP-seq
MIRT1457118	hsa-miR-542-3p	CLIP-seq
MIRT1457119	hsa-miR-548ag	CLIP-seq
MIRT1457120	hsa-miR-548ai	CLIP-seq
MIRT1457121	hsa-miR-548b-3p	CLIP-seq
MIRT1457122	hsa-miR-616	CLIP-seq
MIRT1457123	hsa-miR-642b	CLIP-seq
MIRT1457124	hsa-miR-758	CLIP-seq
MIRT1457125	hsa-miR-760	CLIP-seq
MIRT1457126	hsa-miR-890	CLIP-seq
MIRT1457127	hsa-miR-944	CLIP-seq
MIRT1457078	hsa-miR-10a	CLIP-seq
MIRT1457079	hsa-miR-10b	CLIP-seq
MIRT1457085	hsa-miR-2053	CLIP-seq
MIRT1457097	hsa-miR-323b-3p	CLIP-seq
MIRT2137064	hsa-miR-3689a-5p	CLIP-seq
MIRT2137065	hsa-miR-3689b	CLIP-seq
MIRT2137066	hsa-miR-3689e	CLIP-seq
MIRT2137067	hsa-miR-3689f	CLIP-seq
MIRT1457098	hsa-miR-376a	CLIP-seq
MIRT1457099	hsa-miR-376b	CLIP-seq
MIRT2137068	hsa-miR-4276	CLIP-seq
MIRT1457102	hsa-miR-4289	CLIP-seq
MIRT2137069	hsa-miR-4453	CLIP-seq
MIRT2137070	hsa-miR-4477a	CLIP-seq
MIRT2137071	hsa-miR-4538	CLIP-seq
MIRT1457114	hsa-miR-4773	CLIP-seq
MIRT1457116	hsa-miR-486-5p	CLIP-seq
MIRT2137072	hsa-miR-495	CLIP-seq
MIRT2137073	hsa-miR-518a-5p	CLIP-seq
MIRT2137074	hsa-miR-527	CLIP-seq
MIRT1457119	hsa-miR-548ag	CLIP-seq
MIRT1457120	hsa-miR-548ai	CLIP-seq
MIRT1457122	hsa-miR-616	CLIP-seq
MIRT1457123	hsa-miR-642b	CLIP-seq
MIRT1457078	hsa-miR-10a	CLIP-seq
MIRT1457079	hsa-miR-10b	CLIP-seq
MIRT1457080	hsa-miR-1202	CLIP-seq
MIRT1457083	hsa-miR-140-3p	CLIP-seq
MIRT1457085	hsa-miR-2053	CLIP-seq
MIRT1457086	hsa-miR-2355-5p	CLIP-seq
MIRT1457090	hsa-miR-3133	CLIP-seq
MIRT1457092	hsa-miR-3155	CLIP-seq
MIRT1457093	hsa-miR-3155b	CLIP-seq
MIRT1457096	hsa-miR-3194-5p	CLIP-seq
MIRT1457097	hsa-miR-323b-3p	CLIP-seq
MIRT2357789	hsa-miR-3667-5p	CLIP-seq
MIRT2357790	hsa-miR-374c	CLIP-seq
MIRT1457098	hsa-miR-376a	CLIP-seq
MIRT1457099	hsa-miR-376b	CLIP-seq
MIRT1457100	hsa-miR-3972	CLIP-seq
MIRT2357791	hsa-miR-4273	CLIP-seq
MIRT1457102	hsa-miR-4289	CLIP-seq
MIRT2357792	hsa-miR-4643	CLIP-seq
MIRT2357793	hsa-miR-466	CLIP-seq
MIRT2357794	hsa-miR-4677-5p	CLIP-seq
MIRT2357795	hsa-miR-4719	CLIP-seq
MIRT2357796	hsa-miR-4738-3p	CLIP-seq
MIRT2357797	hsa-miR-4789-3p	CLIP-seq
MIRT1457115	hsa-miR-484	CLIP-seq
MIRT1457116	hsa-miR-486-5p	CLIP-seq
MIRT2137072	hsa-miR-495	CLIP-seq
MIRT2357798	hsa-miR-513b	CLIP-seq
MIRT2137073	hsa-miR-518a-5p	CLIP-seq
MIRT2137074	hsa-miR-527	CLIP-seq
MIRT1457119	hsa-miR-548ag	CLIP-seq
MIRT1457120	hsa-miR-548ai	CLIP-seq
MIRT1457122	hsa-miR-616	CLIP-seq
MIRT2357799	hsa-miR-617	CLIP-seq
MIRT1457123	hsa-miR-642b	CLIP-seq
MIRT2357800	hsa-miR-655	CLIP-seq
MIRT1457078	hsa-miR-10a	CLIP-seq
MIRT1457079	hsa-miR-10b	CLIP-seq
MIRT1457085	hsa-miR-2053	CLIP-seq
MIRT1457098	hsa-miR-376a	CLIP-seq
MIRT1457099	hsa-miR-376b	CLIP-seq
MIRT1457102	hsa-miR-4289	CLIP-seq
MIRT1457119	hsa-miR-548ag	CLIP-seq
MIRT1457120	hsa-miR-548ai	CLIP-seq
MIRT1457122	hsa-miR-616	CLIP-seq
MIRT1457123	hsa-miR-642b	CLIP-seq
MIRT1457078	hsa-miR-10a	CLIP-seq
MIRT1457079	hsa-miR-10b	CLIP-seq
MIRT1457081	hsa-miR-1278	CLIP-seq
MIRT1457085	hsa-miR-2053	CLIP-seq
MIRT1457090	hsa-miR-3133	CLIP-seq
MIRT2651382	hsa-miR-3156-5p	CLIP-seq
MIRT2651383	hsa-miR-3658	CLIP-seq
MIRT2137064	hsa-miR-3689a-5p	CLIP-seq
MIRT2137065	hsa-miR-3689b	CLIP-seq
MIRT2137066	hsa-miR-3689e	CLIP-seq
MIRT2137067	hsa-miR-3689f	CLIP-seq
MIRT1457098	hsa-miR-376a	CLIP-seq
MIRT1457099	hsa-miR-376b	CLIP-seq
MIRT2137068	hsa-miR-4276	CLIP-seq
MIRT1457102	hsa-miR-4289	CLIP-seq
MIRT1457109	hsa-miR-4511	CLIP-seq
MIRT2651384	hsa-miR-4659a-3p	CLIP-seq
MIRT2651385	hsa-miR-4659b-3p	CLIP-seq
MIRT2357796	hsa-miR-4738-3p	CLIP-seq
MIRT2137072	hsa-miR-495	CLIP-seq
MIRT2137073	hsa-miR-518a-5p	CLIP-seq
MIRT2137074	hsa-miR-527	CLIP-seq
MIRT1457119	hsa-miR-548ag	CLIP-seq
MIRT1457120	hsa-miR-548ai	CLIP-seq
MIRT1457122	hsa-miR-616	CLIP-seq
MIRT1457123	hsa-miR-642b	CLIP-seq
MIRT2651386	hsa-miR-935	CLIP-seq
MIRT1457078	hsa-miR-10a	CLIP-seq
MIRT1457079	hsa-miR-10b	CLIP-seq
MIRT1457085	hsa-miR-2053	CLIP-seq
MIRT1457090	hsa-miR-3133	CLIP-seq
MIRT1457098	hsa-miR-376a	CLIP-seq
MIRT1457099	hsa-miR-376b	CLIP-seq
MIRT2137068	hsa-miR-4276	CLIP-seq
MIRT1457102	hsa-miR-4289	CLIP-seq
MIRT1457109	hsa-miR-4511	CLIP-seq
MIRT2651384	hsa-miR-4659a-3p	CLIP-seq
MIRT2651385	hsa-miR-4659b-3p	CLIP-seq
MIRT2357796	hsa-miR-4738-3p	CLIP-seq
MIRT2137072	hsa-miR-495	CLIP-seq
MIRT2137073	hsa-miR-518a-5p	CLIP-seq
MIRT2137074	hsa-miR-527	CLIP-seq
MIRT1457119	hsa-miR-548ag	CLIP-seq
MIRT1457120	hsa-miR-548ai	CLIP-seq
MIRT1457122	hsa-miR-616	CLIP-seq
MIRT1457123	hsa-miR-642b	CLIP-seq

Show/Hide all(38)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IBA
GO:0000049	Function	TRNA binding	IDA	11504732
GO:0000166	Function	Nucleotide binding	IEA
GO:0001680	Process	TRNA 3'-terminal CCA addition	IBA
GO:0001680	Process	TRNA 3'-terminal CCA addition	IDA	25193871, 25652405, 29454993, 30959222, 31011209, 32075755, 34023389
GO:0001680	Process	TRNA 3'-terminal CCA addition	IEA
GO:0003723	Function	RNA binding	IEA
GO:0004810	Function	CCA tRNA nucleotidyltransferase activity	IDA	11504732, 25652405, 29454993, 30959222, 31011209, 32075755, 34023389
GO:0004810	Function	CCA tRNA nucleotidyltransferase activity	IEA
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	TAS	11504732
GO:0005634	Component	Nucleus	IDA	27317422
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	27317422
GO:0005739	Component	Mitochondrion	IDA	11504732
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0005829	Component	Cytosol	IDA	27317422
GO:0006396	Process	RNA processing	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0034062	Function	5'-3' RNA polymerase activity	TAS
GO:0042780	Process	TRNA 3'-end processing	TAS
GO:0042803	Function	Protein homodimerization activity	IDA	30959222
GO:0046872	Function	Metal ion binding	IEA
GO:0072344	Process	Rescue of stalled ribosome	IDA	32075755
GO:0106354	Process	TRNA surveillance	IDA	22076379, 25640237
GO:0160016	Function	CCACCA tRNA nucleotidyltransferase activity	IDA	22076379, 25640237
GO:0160016	Function	CCACCA tRNA nucleotidyltransferase activity	IEA
GO:1990180	Process	Mitochondrial tRNA 3'-end processing	IBA
GO:1990180	Process	Mitochondrial tRNA 3'-end processing	IDA	11504732
GO:1990180	Process	Mitochondrial tRNA 3'-end processing	TAS

MIM	HGNC	e!Ensembl
612907	17341	ENSG00000072756

Protein

UniProt ID

Q96Q11

Protein name

CCA tRNA nucleotidyltransferase 1, mitochondrial (EC 2.7.7.72) (Mitochondrial tRNA nucleotidyl transferase, CCA-adding) (mt CCA-adding enzyme) (mt tRNA CCA-diphosphorylase) (mt tRNA CCA-pyrophosphorylase) (mt tRNA adenylyltransferase)

Protein function

Nucleotidyltransferase that catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs, which is necessary for the attachment of amino acids to the 3' terminus of tRNA molecules, using CTP and ATP as substrates (PubMed:

PDB

1OU5 , 4X4W , 8CBM

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01743	PolyA_pol	59 → 182	Poly A polymerase head domain	Domain
PF12627	PolyA_pol_RNAbd	215 → 272	Probable RNA and SrmB- binding site of polymerase A	Domain

Sequence

MLRCLYHWHRPVLNRRWSRLCLPKQYLFTMKLQSPEFQSLFTEGLKSLTELFVKENHELR
IAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENF
EITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKK
VRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWV
ELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLF
KVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATT
RVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGY
QMEKDELLSYIKKT

Sequence length

434

Interactions

View interactions

	Reactome
			tRNA processing in the nucleus tRNA processing in the mitochondrion

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
retinal dystrophy	Retinal dystrophy	rs876661298, rs769317780	N/A
Retinitis Pigmentosa And Erythrocytic Microcytosis	retinitis pigmentosa and erythrocytic microcytosis	rs876661298, rs876661299	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
Sideroblastic Anemia	congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome	N/A	N/A	GenCC

Show/Hide Text Mining Associations (37)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acidosis Lactic	Associate	25652405
Anemia Hemolytic	Associate	31338833
Anemia Sideroblastic	Associate	25193871, 25652405, 27317422, 33936027, 36729249, 37239403
Atrophy	Associate	25652405
Breast Neoplasms	Associate	31512554
Cardiomyopathies	Associate	33484326
Colorectal Neoplasms	Associate	22276153
Common Variable Immunodeficiency	Associate	33859323
Death	Associate	29358286
Developmental Disabilities	Associate	25652405, 27317422, 29055896, 37239403
Diabetes Mellitus	Associate	33484326
Epilepsy	Associate	33484326
Fanconi Syndrome	Associate	25652405
Fever	Associate	25193871, 27370603, 29055896, 29358286, 33936027
Gait Ataxia	Associate	25652405
Hearing Loss Sensorineural	Associate	25652405, 33484326
Hereditary Autoinflammatory Diseases	Associate	27317422, 29358286, 36729249, 37239403
Hyperbilirubinemia	Associate	31619706
Hypoalbuminemia	Associate	31619706
Immune System Diseases	Associate	33936027
Immunologic Deficiency Syndromes	Associate	27317422, 29055896, 29358286
Iron Overload	Associate	31338833
Leukemia B Cell	Associate	31338833
Metabolic Diseases	Associate	27370603
Mitochondrial Diseases	Associate	33484326
Mitochondrial encephalopathy	Associate	33484326
Multiple Myeloma	Associate	31619706
Multiple Organ Failure	Associate	36729249
Muscle Hypotonia	Associate	25652405
Psychomotor Disorders	Associate	31338833
Retinitis Pigmentosa	Associate	27370603, 28390992
Seizures	Associate	25652405, 33484326
Syndrome	Associate	33936027
Systemic Inflammatory Response Syndrome	Associate	31338833
T cell immunodeficiency primary	Associate	32652938
Thrombocytosis	Associate	31338833
X linked sideroblastic anemia	Associate	29055896, 29358286, 31338833

TRNT1 (tRNA nucleotidyl transferase 1)