TRMT6

tRNA methyltransferase 6 non-catalytic subunit

Basic information

Region (hg38): 20:5937228-5950558

Links

ENSG00000089195 ∙ NCBI:51605 ∙ ∙ HGNC:20900 ∙ Uniprot:Q9UJA5 ∙ 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 TRMT6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT6 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						0
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	18	1	1

Variants in TRMT6

This is a list of pathogenic ClinVar variants found in the TRMT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-5938605-C-T		not specified	Uncertain significance (Mar 19, 2024)
20-5941263-C-G		not specified	Uncertain significance (May 20, 2024)
20-5941328-C-T		not specified	Uncertain significance (Apr 12, 2022)
20-5941329-G-A		not specified	Uncertain significance (Mar 16, 2024)
20-5941972-A-G		not specified	Uncertain significance (Oct 10, 2023)
20-5941979-C-T		not specified	Uncertain significance (May 25, 2022)
20-5942472-G-A		not specified	Uncertain significance (May 07, 2024)
20-5942556-G-C		not specified	Uncertain significance (Jun 10, 2024)
20-5942603-A-G		not specified	Likely benign (Jan 12, 2024)
20-5942685-A-C		not specified	Uncertain significance (Jul 30, 2023)
20-5942741-C-T		not specified	Uncertain significance (Jul 14, 2022)
20-5942778-A-T		not specified	Uncertain significance (Jun 28, 2022)
20-5943597-G-A		not specified	Uncertain significance (Aug 09, 2021)
20-5943603-G-A		not specified	Uncertain significance (Jul 25, 2023)
20-5943648-G-A		not specified	Uncertain significance (Mar 01, 2024)
20-5943679-T-C		not specified	Uncertain significance (May 03, 2023)
20-5943993-C-A		not specified	Uncertain significance (Feb 22, 2023)
20-5944037-G-A			Benign (Feb 26, 2018)
20-5944213-C-T		not specified	Uncertain significance (Apr 28, 2022)
20-5946418-C-T		not specified	Uncertain significance (Dec 03, 2021)
20-5946484-G-A		not specified	Uncertain significance (Nov 21, 2022)
20-5950269-C-G			Benign (May 25, 2018)
20-5950281-C-A		not specified	Uncertain significance (Apr 20, 2023)
20-5950342-C-T		not specified	Uncertain significance (Dec 01, 2022)
20-5950350-C-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT6	protein_coding	protein_coding	ENST00000203001	11	13302

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000240	0.996	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	224	272	0.824	0.0000139	3261
Missense in Polyphen		51	89.6	0.5692		1025
Synonymous	-0.691	107	98.3	1.09	0.00000540	933
Loss of Function	2.55	12	26.0	0.461	0.00000141	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000218	0.000217
South Asian	0.000168	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-binding subunit of tRNA (adenine-N(1)-)- methyltransferase, which catalyzes the formation of N(1)- methyladenine at position 58 (m1A58) in initiator methionyl-tRNA (PubMed:16043508). Together with the TRMT61A catalytic subunit, part of a mRNA N(1)-methyltransferase complex that mediates methylation of adenosine residues at the N(1) position of a small subset of mRNAs: N(1) methylation takes place in tRNA T-loop-like structures of mRNAs and is only present at low stoichiometries (PubMed:29107537, PubMed:29072297). {ECO:0000269|PubMed:16043508, ECO:0000269|PubMed:29072297, ECO:0000269|PubMed:29107537}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.644
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.554
• ghis: 0.593

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Trmt6

Gene ontology

• Biological process: tRNA methylation;mRNA methylation
• Cellular component: nucleus;nucleoplasm;tRNA (m1A) methyltransferase complex
• Molecular function: RNA binding;tRNA (adenine-N1-)-methyltransferase activity