TRMT11

tRNA methyltransferase 11 homolog, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 6:125986478-126203817

Previous symbols: [ "C6orf75" ]

Links

ENSG00000066651 ∙ NCBI:60487 ∙ ∙ HGNC:21080 ∙ Uniprot:Q7Z4G4 ∙ 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 TRMT11 gene.

• Inborn genetic diseases (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT11 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in TRMT11

This is a list of pathogenic ClinVar variants found in the TRMT11 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-125986554-G-T		not specified	Uncertain significance (Dec 01, 2022)
6-125986558-T-C		not specified	Likely benign (Dec 03, 2021)
6-125986563-T-A		not specified	Uncertain significance (Jan 23, 2024)
6-125986569-C-T		not specified	Uncertain significance (Nov 22, 2021)
6-125996024-C-T		not specified	Uncertain significance (Nov 10, 2022)
6-125998061-T-C		not specified	Uncertain significance (Jan 23, 2023)
6-125998103-G-A		not specified	Uncertain significance (Apr 10, 2023)
6-125998596-C-T		not specified	Uncertain significance (Dec 03, 2021)
6-125998638-C-G		not specified	Uncertain significance (Jul 07, 2022)
6-125998638-C-T		not specified	Uncertain significance (Mar 29, 2022)
6-125998668-T-C		not specified	Uncertain significance (Dec 07, 2021)
6-125999536-C-T		not specified	Uncertain significance (Nov 01, 2022)
6-125999572-T-C		not specified	Uncertain significance (Apr 17, 2023)
6-125999611-C-T		not specified	Uncertain significance (Jun 06, 2023)
6-126008425-C-T		not specified	Uncertain significance (Oct 14, 2021)
6-126008430-G-A		not specified	Uncertain significance (Dec 12, 2023)
6-126011258-G-C		not specified	Uncertain significance (Jan 26, 2023)
6-126011274-A-G		not specified	Uncertain significance (Sep 17, 2021)
6-126011310-A-G		not specified	Uncertain significance (Mar 07, 2023)
6-126011316-G-A		not specified	Uncertain significance (Apr 07, 2022)
6-126011346-A-G		not specified	Uncertain significance (May 25, 2022)
6-126011349-T-C		not specified	Uncertain significance (Nov 09, 2022)
6-126011358-C-T		not specified	Uncertain significance (Dec 02, 2021)
6-126011387-G-A		not specified	Uncertain significance (Jul 26, 2022)
6-126012818-G-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT11	protein_coding	protein_coding	ENST00000334379	13	52847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.91e-12	0.308	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0239	242	243	0.996	0.0000118	3041
Missense in Polyphen		51	55.229	0.92343		720
Synonymous	-0.889	97	86.5	1.12	0.00000429	834
Loss of Function	1.08	21	27.1	0.776	0.00000131	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00212	0.00187
Ashkenazi Jewish	0.000719	0.000695
East Asian	0.000329	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000329	0.000326
South Asian	0.000563	0.000555
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of an S-adenosyl-L-methionine- dependent tRNA methyltransferase complex that mediates the methylation of the guanosine nucleotide at position 10 (m2G10) in tRNAs. {ECO:0000250}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.907
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.0788
• hipred: N
• hipred_score: 0.237
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt11

Gene ontology

• Biological process: tRNA methylation
• Molecular function: tRNA binding;tRNA (guanine-N2-)-methyltransferase activity