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

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
Combined oxidative phosphorylation defect type 30	Pathogenic	rs875989831	RCV000225275	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Mitochondrial disease	Pathogenic	rs875989831	RCV000754101	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (7)

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.
ASTHMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATOPIC ECZEMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BASAL CELL CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 30	—	CTD, HPO CTD, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRMT10C-related disorder	Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (17)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acidosis Lactic	Lactic acidosis	Pubtator	27132592	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	35833147, 37170222	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37542141	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	26884257		★★★★★ ★☆☆☆☆ Found in Text Mining only
Combined oxidative phosphorylation defect type 30	Combined Oxidative Phosphorylation Deficiency	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 30	Combined Oxidative Phosphorylation Deficiency	ORPHANET_DG	27132592		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 30	Combined Oxidative Phosphorylation Deficiency	GENOMICS_ENGLAND_DG	27132592		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 30	Combined Oxidative Phosphorylation Deficiency	UNIPROT_DG	27132592		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 30	Combined Oxidative Phosphorylation Deficiency	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 30	Combined Oxidative Phosphorylation Deficiency	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Abnormalities	Congenital abnormalities	Pubtator	27132592	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	27132592	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial Diseases	BEFREE	27132592		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial Diseases	CLINVAR_DG	27132592		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial disease	Pubtator	27132592	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Respiratory Chain Deficiencies	Mitochondrial Respiratory Chain Deficiencies	BEFREE	27132592		★★★★★ ★☆☆☆☆ Found in Text Mining only

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