TRMT13

tRNA methyltransferase 13 homolog, the group of 7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 1:100133150-100150496

Previous symbols: [ "CCDC76" ]

Links

ENSG00000122435 ∙ NCBI:54482 ∙ ∙ HGNC:25502 ∙ Uniprot:Q9NUP7 ∙ 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 TRMT13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT13 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		2	24
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	0	2

Variants in TRMT13

This is a list of pathogenic ClinVar variants found in the TRMT13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-100133173-C-A		not specified	Uncertain significance (Jun 27, 2022)
1-100133223-T-C		not specified	Uncertain significance (Jan 26, 2023)
1-100133232-T-A		not specified	Uncertain significance (Apr 29, 2024)
1-100133239-A-G		not specified	Uncertain significance (Dec 14, 2023)
1-100133284-G-C		not specified	Uncertain significance (May 04, 2022)
1-100133310-G-A			Benign (Jun 19, 2021)
1-100133311-C-T			Benign (Jun 19, 2021)
1-100136902-A-C		not specified	Uncertain significance (Jan 31, 2023)
1-100140185-C-T		not specified	Uncertain significance (Oct 14, 2023)
1-100140460-T-G		not specified	Uncertain significance (May 18, 2023)
1-100140467-A-G		not specified	Uncertain significance (Sep 01, 2021)
1-100140935-A-T		not specified	Uncertain significance (Jun 30, 2023)
1-100140939-T-G		not specified	Uncertain significance (Mar 06, 2023)
1-100140963-A-G		not specified	Uncertain significance (Mar 26, 2024)
1-100147894-A-G		not specified	Uncertain significance (Jul 06, 2021)
1-100147944-A-G		not specified	Uncertain significance (Apr 08, 2024)
1-100147963-C-G		not specified	Uncertain significance (Mar 22, 2023)
1-100147987-C-T		not specified	Uncertain significance (May 10, 2024)
1-100148011-C-A		not specified	Uncertain significance (Dec 14, 2023)
1-100148045-G-T		not specified	Uncertain significance (Sep 01, 2021)
1-100148053-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-100148089-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-100148136-C-G		not specified	Uncertain significance (May 26, 2022)
1-100148173-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-100148227-A-T		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT13	protein_coding	protein_coding	ENST00000370141	11	17348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-7	0.933	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.410	227	245	0.926	0.0000114	3146
Missense in Polyphen		65	87.21	0.74533		1106
Synonymous	0.413	84	89.0	0.944	0.00000425	877
Loss of Function	1.84	15	24.9	0.603	0.00000129	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000371	0.000363
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000334	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000214	0.000211
Middle Eastern	0.000334	0.000326
South Asian	0.000524	0.000523
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His). {ECO:0000250|UniProtKB:Q12383}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Intolerance Scores

• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.333
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt13

Gene ontology

• Biological process: tRNA methylation
• Molecular function: tRNA methyltransferase activity;metal ion binding;tRNA 2'-O-methyltransferase activity