TRMT1L

tRNA methyltransferase 1 like, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 1:185118101-185157072

Previous symbols: [ "C1orf25" ]

Links

ENSG00000121486 ∙ NCBI:81627 ∙ OMIM:611673 ∙ HGNC:16782 ∙ Uniprot:Q7Z2T5 ∙ 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 TRMT1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT1L 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			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	2	0

Variants in TRMT1L

This is a list of pathogenic ClinVar variants found in the TRMT1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-185120054-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-185120141-G-T		not specified	Uncertain significance (Apr 14, 2022)
1-185120251-T-C		not specified	Uncertain significance (Jun 29, 2022)
1-185123881-T-C		not specified	Uncertain significance (May 23, 2024)
1-185124952-T-C		not specified	Uncertain significance (May 11, 2022)
1-185124973-A-G		not specified	Uncertain significance (Oct 27, 2022)
1-185137684-C-T		not specified	Uncertain significance (Nov 12, 2021)
1-185137687-T-C		not specified	Uncertain significance (Dec 27, 2022)
1-185137723-C-G		not specified	Uncertain significance (Dec 12, 2023)
1-185137734-A-C		not specified	Uncertain significance (Dec 31, 2023)
1-185137789-C-T		not specified	Uncertain significance (Dec 31, 2023)
1-185139523-A-G		not specified	Uncertain significance (Dec 22, 2023)
1-185139524-T-C		not specified	Uncertain significance (Mar 01, 2023)
1-185140033-T-G		not specified	Uncertain significance (Dec 19, 2023)
1-185140063-A-G		not specified	Uncertain significance (Dec 06, 2022)
1-185140076-T-C		not specified	Likely benign (Oct 26, 2022)
1-185140138-A-G		not specified	Uncertain significance (Dec 16, 2023)
1-185140195-T-A		not specified	Uncertain significance (Feb 21, 2024)
1-185143391-T-G		not specified	Uncertain significance (Nov 02, 2023)
1-185143405-C-A		not specified	Uncertain significance (Mar 25, 2024)
1-185143907-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-185143988-C-G		not specified	Uncertain significance (Aug 04, 2023)
1-185144020-G-A			Likely benign (Feb 01, 2023)
1-185145519-G-T		not specified	Uncertain significance (Jan 16, 2024)
1-185147201-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT1L	protein_coding	protein_coding	ENST00000367506	15	38985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.797	0.203	125726	0	20	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	275	377	0.730	0.0000179	4790
Missense in Polyphen		48	126.39	0.37978		1544
Synonymous	1.09	115	131	0.879	0.00000600	1381
Loss of Function	4.48	7	36.1	0.194	0.00000201	457

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000147	0.000141
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in motor coordination and exploratory behavior. {ECO:0000250}.

Recessive Scores

• pRec: 0.207

Intolerance Scores

• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.606
• hipred: Y
• hipred_score: 0.540
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt1l
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: tRNA N2-guanine methylation;behavior
• Cellular component: nucleus
• Molecular function: tRNA binding;RNA binding;tRNA (guanine-N2-)-methyltransferase activity;metal ion binding