TRMO

tRNA methyltransferase O, the group of Methyltransferase families

Basic information

Region (hg38): 9:97904488-97922500

Previous symbols: [ "C9orf156" ]

Links

ENSG00000136932 ∙ NCBI:51531 ∙ ∙ HGNC:30967 ∙ Uniprot:Q9BU70 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRMO gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMO gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in TRMO

This is a list of pathogenic ClinVar variants found in the TRMO region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-97904794-G-A		not specified	Uncertain significance (Dec 17, 2021)
9-97904853-G-C		not specified	Uncertain significance (Aug 02, 2021)
9-97904881-T-C		not specified	Uncertain significance (Oct 02, 2023)
9-97904896-C-A		not specified	Uncertain significance (Sep 15, 2021)
9-97904896-C-T		not specified	Uncertain significance (Jul 12, 2022)
9-97904917-G-A		not specified	Uncertain significance (Mar 22, 2023)
9-97904941-C-T		not specified	Likely benign (May 23, 2023)
9-97910131-G-T		not specified	Uncertain significance (Dec 27, 2023)
9-97910226-G-A		not specified	Uncertain significance (Jun 29, 2023)
9-97910230-C-T		not specified	Likely benign (Aug 13, 2021)
9-97910241-T-G		not specified	Uncertain significance (Dec 19, 2023)
9-97910254-A-C		not specified	Uncertain significance (Feb 27, 2023)
9-97910350-T-C		not specified	Uncertain significance (Oct 03, 2023)
9-97910527-G-C		not specified	Uncertain significance (Dec 12, 2023)
9-97910548-T-C		not specified	Uncertain significance (Mar 02, 2023)
9-97910569-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-97910580-T-C		not specified	Uncertain significance (Dec 19, 2023)
9-97913442-T-C		not specified	Uncertain significance (Feb 06, 2023)
9-97913487-C-T		not specified	Uncertain significance (Sep 29, 2023)
9-97913495-C-T			Benign (Mar 30, 2018)
9-97913535-T-C		not specified	Uncertain significance (Oct 27, 2022)
9-97916192-T-C		not specified	Uncertain significance (Oct 26, 2022)
9-97916206-G-A		not specified	Uncertain significance (Dec 17, 2023)
9-97916275-G-C		not specified	Uncertain significance (Dec 20, 2023)
9-97922439-C-A		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMO	protein_coding	protein_coding	ENST00000375119	5	18082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.47e-8	0.451	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0514	240	242	0.991	0.0000131	2855
Missense in Polyphen		69	78.4	0.8801		877
Synonymous	-0.983	102	90.1	1.13	0.00000490	882
Loss of Function	0.847	13	16.7	0.777	8.66e-7	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.000163	0.000163
Other	0.000327	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase responsible for the addition of the methyl group in the formation of N6-methyl-N6-threonylcarbamoyladenosine at position 37 (m(6)t(6)A37) of the tRNA anticodon loop of tRNA(Ser)(GCU) (PubMed:25063302). The methyl group of m(6)t(6)A37 may improve the efficiency of the tRNA decoding ability. May bind to tRNA (By similarity). {ECO:0000250|UniProtKB:P28634, ECO:0000269|PubMed:25063302}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.123
• ghis: 0.500

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Trmo
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: tRNA methylation
• Molecular function: tRNA (adenine-N6-)-methyltransferase activity