TRMT12

tRNA methyltransferase 12 homolog, the group of Seven-beta-strand methyltransferase motif containing

Basic information

Region (hg38): 8:124450820-124462150

Links

ENSG00000183665 ∙ NCBI:55039 ∙ OMIM:611244 ∙ HGNC:26091 ∙ Uniprot:Q53H54 ∙ 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 TRMT12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT12 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in TRMT12

This is a list of pathogenic ClinVar variants found in the TRMT12 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-124450992-C-T		not specified	Uncertain significance (Apr 07, 2022)
8-124451010-G-C		not specified	Uncertain significance (Feb 28, 2024)
8-124451171-A-T		not specified	Uncertain significance (Apr 22, 2024)
8-124451196-C-T		not specified	Likely benign (Apr 28, 2022)
8-124451208-C-T		not specified	Uncertain significance (May 14, 2024)
8-124451229-G-T		not specified	Uncertain significance (Jan 27, 2022)
8-124451322-G-T		not specified	Uncertain significance (May 09, 2022)
8-124451340-G-A		not specified	Uncertain significance (Mar 07, 2024)
8-124451394-T-C		not specified	Uncertain significance (Aug 15, 2023)
8-124451429-C-T		not specified	Uncertain significance (Jul 13, 2022)
8-124451468-C-T		not specified	Uncertain significance (Dec 13, 2021)
8-124451498-C-G		not specified	Uncertain significance (Jul 13, 2021)
8-124451547-G-A		not specified	Uncertain significance (Jun 12, 2023)
8-124451729-C-A		not specified	Uncertain significance (Sep 29, 2022)
8-124451751-G-C		not specified	Uncertain significance (Jan 03, 2022)
8-124451783-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-124451972-G-A		not specified	Uncertain significance (Mar 01, 2023)
8-124451975-C-T		not specified	Uncertain significance (Mar 16, 2022)
8-124452092-A-G		not specified	Uncertain significance (Jan 04, 2024)
8-124452110-T-C		not specified	Uncertain significance (Jul 14, 2022)
8-124452146-C-G		not specified	Uncertain significance (Aug 10, 2021)
8-124452167-C-T		not specified	Uncertain significance (Jan 05, 2022)
8-124452198-C-T		not specified	Uncertain significance (Mar 29, 2022)
8-124452210-A-G		not specified	Uncertain significance (Jan 23, 2023)
8-124452219-A-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT12	protein_coding	protein_coding	ENST00000328599	1	11344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.326	0.673	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.153	230	237	0.972	0.0000112	2888
Missense in Polyphen		51	65.381	0.78004		828
Synonymous	-0.114	96	94.6	1.01	0.00000448	937
Loss of Function	2.96	4	17.2	0.232	8.74e-7	175

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent transferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the transfer of the alpha-amino-alpha- carboxypropyl (acp) group from S-adenosyl-L-methionine to the C-7 position of 4-demethylwyosine (imG-14) to produce wybutosine-86. {ECO:0000269|PubMed:22761755}.
• Pathway: Synthesis of wybutosine at G37 of tRNA(Phe);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.629
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0891
• hipred: N
• hipred_score: 0.469
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt12

Gene ontology

• Biological process: tRNA methylation;wybutosine biosynthetic process
• Cellular component: cytoplasm
• Molecular function: protein binding;tRNA methyltransferase activity;tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity