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	54931
Gene name	TRNA methyltransferase 10C, mitochondrial RNase P subunit
Gene symbol	TRMT10C
Synonyms (NCBI Gene)	COXPD30HNYAMRPP1RG9MTD1
Chromosome	3
Chromosome location	3q12.3
Summary	This gene encodes the precursor of a subunit of the mitochondrial ribonuclease P, which is involved in 5` processing of mitochondrial tRNAs. The encoded protein may confer RNA-binding capacity to mitochondrial ribonuclease P and may be essential for trans

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs199730889	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs875989831	A>G	Pathogenic	Missense variant, coding sequence variant

Show/Hide all (37)

miRTarBase ID	miRNA	Experiments	Reference
MIRT031383	hsa-miR-16-5p	Proteomics	18668040
MIRT648065	hsa-miR-6782-3p	HITS-CLIP	23824327
MIRT648064	hsa-miR-4781-3p	HITS-CLIP	23824327
MIRT648063	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT648062	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT648061	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT648060	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT648059	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT648058	hsa-miR-3663-5p	HITS-CLIP	23824327
MIRT648057	hsa-miR-6759-3p	HITS-CLIP	23824327
MIRT648056	hsa-miR-4755-3p	HITS-CLIP	23824327
MIRT648055	hsa-miR-6131	HITS-CLIP	23824327
MIRT648054	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT648053	hsa-miR-548s	HITS-CLIP	23824327
MIRT648052	hsa-miR-588	HITS-CLIP	23824327
MIRT648051	hsa-miR-4435	HITS-CLIP	23824327
MIRT648050	hsa-miR-3187-3p	HITS-CLIP	23824327
MIRT648049	hsa-miR-6843-3p	HITS-CLIP	23824327
MIRT648048	hsa-miR-6848-3p	HITS-CLIP	23824327
MIRT648065	hsa-miR-6782-3p	HITS-CLIP	23824327
MIRT648064	hsa-miR-4781-3p	HITS-CLIP	23824327
MIRT648063	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT648062	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT648061	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT648060	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT648059	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT648058	hsa-miR-3663-5p	HITS-CLIP	23824327
MIRT648057	hsa-miR-6759-3p	HITS-CLIP	23824327
MIRT648056	hsa-miR-4755-3p	HITS-CLIP	23824327
MIRT648055	hsa-miR-6131	HITS-CLIP	23824327
MIRT648054	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT648053	hsa-miR-548s	HITS-CLIP	23824327
MIRT648052	hsa-miR-588	HITS-CLIP	23824327
MIRT648051	hsa-miR-4435	HITS-CLIP	23824327
MIRT648050	hsa-miR-3187-3p	HITS-CLIP	23824327
MIRT648049	hsa-miR-6843-3p	HITS-CLIP	23824327
MIRT648048	hsa-miR-6848-3p	HITS-CLIP	23824327

Show/Hide all (36)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IBA
GO:0000049	Function	TRNA binding	IDA	29040705
GO:0000964	Process	Mitochondrial RNA 5'-end processing	IMP	21593607
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0005515	Function	Protein binding	IPI	18984158, 23042678, 28514442, 29040705, 29880640, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005654	Component	Nucleoplasm	IBA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	23042678, 29880640
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	IMP	27132592
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006397	Process	MRNA processing	IDA	29072297
GO:0008033	Process	TRNA processing	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030678	Component	Mitochondrial ribonuclease P complex	IPI	29880640
GO:0030678	Component	Mitochondrial ribonuclease P complex	TAS	23042678
GO:0032259	Process	Methylation	IEA
GO:0042645	Component	Mitochondrial nucleoid	IDA	24703694
GO:0042645	Component	Mitochondrial nucleoid	IEA
GO:0042802	Function	Identical protein binding	IPI	29880640
GO:0043527	Component	TRNA methyltransferase complex	IPI	23042678
GO:0052905	Function	TRNA (guanosine(9)-N1)-methyltransferase activity	IDA	23042678
GO:0052905	Function	TRNA (guanosine(9)-N1)-methyltransferase activity	IEA
GO:0070131	Process	Positive regulation of mitochondrial translation	IBA
GO:0070131	Process	Positive regulation of mitochondrial translation	IMP	27132592
GO:0070901	Process	Mitochondrial tRNA methylation	IDA	23042678
GO:0090646	Process	Mitochondrial tRNA processing	IMP	27132592
GO:0097745	Process	Mitochondrial tRNA 5'-end processing	IBA
GO:0097745	Process	Mitochondrial tRNA 5'-end processing	IDA	29040705, 29880640
GO:0160106	Function	TRNA (adenine(9)-N1)-methyltransferase activity	IDA	23042678
GO:0160106	Function	TRNA (adenine(9)-N1)-methyltransferase activity	IEA
GO:1990180	Process	Mitochondrial tRNA 3'-end processing	IDA	29040705

MIM	HGNC	e!Ensembl
615423	26022	ENSG00000174173

Q7L0Y3

Protein name

tRNA methyltransferase 10 homolog C (HBV pre-S2 trans-regulated protein 2) (Mitochondrial ribonuclease P protein 1) (Mitochondrial RNase P protein 1) (RNA (guanine-9-)-methyltransferase domain-containing protein 1) (Renal carcinoma antigen NY-REN-49) (mRN

Protein function

Mitochondrial tRNA N(1)-methyltransferase involved in mitochondrial tRNA maturation (PubMed:18984158, PubMed:21593607, PubMed:23042678, PubMed:27132592). Component of mitochondrial ribonuclease P, a complex composed of TRMT10C/MRPP1, HSD17B10/MR

PDB

5NFJ , 7ONU , 8CBK , 8CBL , 8CBM , 8CBO , 8RR1 , 8RR3 , 8RR4 , 9EY0 , 9EY1 , 9EY2 , 9GCH

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01746	tRNA_m1G_MT	212 → 380	tRNA (Guanine-1)-methyltransferase	Family

Sequence

MAAFLKMSVSVNFFRPFTRFLVPFTLHRKRNNLTILQRYMSSKIPAVTYPKNESTPPSEE
LELDKWKTTMKSSVQEECVSTISSSKDEDPLAATREFIEMWRLLGREVPEHITEEELKTL
MECVSNTAKKKYLKYLYTKEKVKKARQIKKEMKAAAREEAKNIKLLETTEEDKQKNFLFL
RLWDRNMDIAMGWKGAQAMQFGQPLVFDMAYENYMKRKELQNTVSQLLESEGWNRRNVDP
FHIYFCNLKIDGALHRELVKRYQEKWDKLLLTSTEKSHVDLFPKDSIIYLTADSPNVMTT
FRHDKVYVIGSFVDKSMQPGTSLAKAKRLNLATECLPLDKYLQWEIGNKNLTLDQMIRIL
LCLKNNGNWQEALQFVPKRKHTGFLEISQHSQEFINRLKKAKT

Sequence length

403

Interactions

View interactions

	Reactome
			tRNA processing in the mitochondrion tRNA modification in the mitochondrion rRNA processing in the mitochondrion

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Combined oxidative phosphorylation defect type 30	Pathogenic	rs875989831	RCV000225275
Mitochondrial disease	Pathogenic	rs875989831	RCV000754101

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
See cases	Conflicting classifications of pathogenicity	rs199730889	RCV002252056
TRMT10C-related disorder	Likely benign; Conflicting classifications of pathogenicity	rs373862967, rs199730889, rs754546905, rs756982289	RCV003931323 RCV004758673 RCV003946798 RCV003969066

Show/Hide Text Mining Associations (10)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acidosis Lactic	Associate	27132592
Carcinoma Hepatocellular	Associate	35833147, 37170222
Carcinoma Renal Cell	Associate	37542141
Congenital Abnormalities	Associate	27132592
Deafness	Associate	27132592
Feeding and Eating Disorders	Associate	27132592
Mitochondrial Diseases	Associate	27132592
Muscle Hypotonia	Associate	27132592
Respiratory Insufficiency	Associate	27132592
RNA Virus Infections	Associate	27132592

TRMT10C (tRNA methyltransferase 10C, mitochondrial RNase P subunit)