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

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Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 54931
• Gene name: TRNA methyltransferase 10C, mitochondrial RNase P subunit
• Gene symbol: TRMT10C
• Synonyms (NCBI Gene): COXPD30, HNYA, MRPP1, RG9MTD1
• 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

SNPs

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

miRNA 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

Gene ontology (GO) 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

Other IDs

• MIM: 615423
• HGNC: 26022
• e!Ensembl: ENSG00000174173

Protein

• UniProt ID: 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

Pathways

Reactome Pathway

tRNA processing in the mitochondrion

tRNA modification in the mitochondrion

rRNA processing in the mitochondrion

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
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)

Unknown / Other Associations Show/Hide Unknown Diseases (7)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
ASTHMA	—	GWAS catalog	29083406, 31361310, 36777996	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATOPIC ECZEMA	—	GWAS catalog	38663478	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BASAL CELL CARCINOMA	—	GWAS catalog	38182794	★★☆☆☆ 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	34924174, 38177345	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASES	—	Disgenet, ClinGen	ClinGen report	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRMT10C-related disorder	Likely benign; Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (17)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
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	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 Diseases	Mitochondrial Diseases	BEFREE	27132592		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Respiratory Chain Deficiencies	Mitochondrial Respiratory Chain Deficiencies	BEFREE	27132592		★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

MRPL3 2 shared diseasesCombined oxidative phosphorylation deficiency, Mitochondrial disease 9 shared evidence sourcesCTD (Combined oxidative phosphorylation deficiency), ClinVar (Combined oxidative phosphorylation deficiency), Disgenet (Combined oxidative phosphorylation deficiency), Orphanet (Combined oxidative phosphorylation deficiency), GWAS catalog (Combined oxidative phosphorylation deficiency), HPO (Combined oxidative phosphorylation deficiency), ClinGen (Mitochondrial disease), CTD (Mitochondrial disease), Disgenet (Mitochondrial disease) Related via 2 shared diseases including Combined oxidative phosphorylation deficiency, Mitochondrial disease — evidence mostly CTD. ELAC2 2 shared diseasesCombined oxidative phosphorylation deficiency, Mitochondrial disease 2 shared pathwaystRNA processing in the mitochondrion, rRNA processing in the mitochondrion 7 shared evidence sourcesCTD (Combined oxidative phosphorylation deficiency), ClinVar (Combined oxidative phosphorylation deficiency), Disgenet (Combined oxidative phosphorylation deficiency), Orphanet (Combined oxidative phosphorylation deficiency), HPO (Combined oxidative phosphorylation deficiency), ClinGen (Mitochondrial disease), Disgenet (Mitochondrial disease) Related via 2 shared diseases including Combined oxidative phosphorylation deficiency, Mitochondrial disease — evidence mostly Disgenet. MRPS16 2 shared diseasesCombined oxidative phosphorylation deficiency, Mitochondrial disease 8 shared evidence sourcesCTD (Combined oxidative phosphorylation deficiency), ClinVar (Combined oxidative phosphorylation deficiency), Disgenet (Combined oxidative phosphorylation deficiency), Orphanet (Combined oxidative phosphorylation deficiency), GWAS catalog (Combined oxidative phosphorylation deficiency), HPO (Combined oxidative phosphorylation deficiency), ClinGen (Mitochondrial disease), Disgenet (Mitochondrial disease) Related via 2 shared diseases including Combined oxidative phosphorylation deficiency, Mitochondrial disease — evidence mostly Disgenet. VARS2 2 shared diseasesCombined oxidative phosphorylation deficiency, Mitochondrial disease 8 shared evidence sourcesCTD (Combined oxidative phosphorylation deficiency), ClinVar (Combined oxidative phosphorylation deficiency), Disgenet (Combined oxidative phosphorylation deficiency), Orphanet (Combined oxidative phosphorylation deficiency), GWAS catalog (Combined oxidative phosphorylation deficiency), HPO (Combined oxidative phosphorylation deficiency), ClinGen (Mitochondrial disease), Disgenet (Mitochondrial disease) Related via 2 shared diseases including Combined oxidative phosphorylation deficiency, Mitochondrial disease — evidence mostly Disgenet. SFXN4 2 shared diseasesCombined oxidative phosphorylation deficiency, Mitochondrial disease 6 shared evidence sourcesCTD (Combined oxidative phosphorylation deficiency), Disgenet (Combined oxidative phosphorylation deficiency), HPO (Combined oxidative phosphorylation deficiency), ClinGen (Mitochondrial disease), CTD (Mitochondrial disease), Disgenet (Mitochondrial disease) Related via 2 shared diseases including Combined oxidative phosphorylation deficiency, Mitochondrial disease — evidence mostly CTD.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
MRPL3	2	["Combined oxidative phosphorylation deficiency","Mitochondrial disease"]	0	[]	9	["CTD (Combined oxidative phosphorylation deficiency)","ClinVar (Combined oxidative phosphorylation deficiency)","Disgenet (Combined oxidative phosphorylation deficiency)","Orphanet (Combined oxidative phosphorylation deficiency)","GWAS catalog (Combined oxidative phosphorylation deficiency)","HPO (Combined oxidative phosphorylation deficiency)","ClinGen (Mitochondrial disease)","CTD (Mitochondrial disease)","Disgenet (Mitochondrial disease)"]
ELAC2	2	["Combined oxidative phosphorylation deficiency","Mitochondrial disease"]	2	["tRNA processing in the mitochondrion","rRNA processing in the mitochondrion"]	7	["CTD (Combined oxidative phosphorylation deficiency)","ClinVar (Combined oxidative phosphorylation deficiency)","Disgenet (Combined oxidative phosphorylation deficiency)","Orphanet (Combined oxidative phosphorylation deficiency)","HPO (Combined oxidative phosphorylation deficiency)","ClinGen (Mitochondrial disease)","Disgenet (Mitochondrial disease)"]
MRPS16	2	["Combined oxidative phosphorylation deficiency","Mitochondrial disease"]	0	[]	8	["CTD (Combined oxidative phosphorylation deficiency)","ClinVar (Combined oxidative phosphorylation deficiency)","Disgenet (Combined oxidative phosphorylation deficiency)","Orphanet (Combined oxidative phosphorylation deficiency)","GWAS catalog (Combined oxidative phosphorylation deficiency)","HPO (Combined oxidative phosphorylation deficiency)","ClinGen (Mitochondrial disease)","Disgenet (Mitochondrial disease)"]
VARS2	2	["Combined oxidative phosphorylation deficiency","Mitochondrial disease"]	0	[]	8	["CTD (Combined oxidative phosphorylation deficiency)","ClinVar (Combined oxidative phosphorylation deficiency)","Disgenet (Combined oxidative phosphorylation deficiency)","Orphanet (Combined oxidative phosphorylation deficiency)","GWAS catalog (Combined oxidative phosphorylation deficiency)","HPO (Combined oxidative phosphorylation deficiency)","ClinGen (Mitochondrial disease)","Disgenet (Mitochondrial disease)"]
SFXN4	2	["Combined oxidative phosphorylation deficiency","Mitochondrial disease"]	0	[]	6	["CTD (Combined oxidative phosphorylation deficiency)","Disgenet (Combined oxidative phosphorylation deficiency)","HPO (Combined oxidative phosphorylation deficiency)","ClinGen (Mitochondrial disease)","CTD (Mitochondrial disease)","Disgenet (Mitochondrial disease)"]

Diseases Linked via Similar Genes

Squamous cell carcinoma Linked via 2 of 5 related genesELAC2, VARS2 Color vision deficiency Linked via 1 of 5 related genesELAC2 Prostate cancer Linked via 1 of 5 related genesELAC2 Prostatic neoplasms Linked via 1 of 5 related genesELAC2 Schizophrenia Linked via 1 of 5 related genesELAC2

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Squamous cell carcinoma	2	["ELAC2","VARS2"]
Color vision deficiency	1	["ELAC2"]
Prostate cancer	1	["ELAC2"]
Prostatic neoplasms	1	["ELAC2"]
Schizophrenia	1	["ELAC2"]