TRMT61B

tRNA methyltransferase 61B, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 2:28849820-28870309

Links

ENSG00000171103 ∙ NCBI:55006 ∙ OMIM:619404 ∙ HGNC:26070 ∙ Uniprot:Q9BVS5 ∙ 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 TRMT61B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT61B 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			44			44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	45	0	0

Variants in TRMT61B

This is a list of pathogenic ClinVar variants found in the TRMT61B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-28849861-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-28850230-T-G		not specified	Uncertain significance (Mar 07, 2024)
2-28850233-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-28850337-C-G		not specified	Uncertain significance (Dec 13, 2023)
2-28850356-T-G		not specified	Uncertain significance (May 11, 2022)
2-28851219-T-C		not specified	Uncertain significance (Jul 13, 2021)
2-28851255-C-T		not specified	Uncertain significance (Nov 17, 2022)
2-28851264-G-A		not specified	Uncertain significance (Aug 17, 2021)
2-28851278-A-G		not specified	Uncertain significance (Oct 17, 2023)
2-28852421-C-T		not specified	Uncertain significance (Dec 20, 2021)
2-28852445-G-C		not specified	Uncertain significance (Oct 29, 2021)
2-28852484-A-T		not specified	Uncertain significance (Aug 22, 2023)
2-28861144-C-G		not specified	Uncertain significance (Jul 13, 2021)
2-28861147-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-28861149-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-28861156-C-T		not specified	Uncertain significance (Jun 03, 2024)
2-28861208-A-T		not specified	Uncertain significance (Apr 07, 2022)
2-28861240-A-C		not specified	Uncertain significance (Dec 19, 2023)
2-28861293-C-T		not specified	Uncertain significance (Jan 04, 2022)
2-28865049-G-A		not specified	Uncertain significance (Aug 17, 2022)
2-28865079-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-28865098-T-C		not specified	Uncertain significance (Oct 26, 2021)
2-28865107-T-C		not specified	Uncertain significance (Oct 13, 2023)
2-28865109-A-G		not specified	Uncertain significance (Mar 08, 2024)
2-28869581-T-C		not specified	Uncertain significance (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT61B	protein_coding	protein_coding	ENST00000306108	7	20481

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.11e-8	0.817	125686	0	31	125717	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.644	282	253	1.11	0.0000117	3081
Missense in Polyphen		59	63.055	0.93569		815
Synonymous	-0.451	106	100	1.06	0.00000479	945
Loss of Function	1.51	15	22.8	0.659	0.00000115	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.000757	0.000752
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methyltransferase that catalyzes the formation of N(1)- methyladenine at position 58 (m1A58) in various tRNAs in mitochondrion, including tRNA(Leu) (deciphering codons UUA or UUG), tRNA(Lys) and tRNA(Ser) (deciphering codons UCA, UCU, UCG or UCC) (PubMed:23097428). Catalyzes the formation of 1- methyladenosine at position 947 of mitochondrial 16S ribosomal RNA and this modification is most likely important for mitoribosomal structure and function (PubMed:27631568). In addition to tRNA N(1)-methyltransferase activity, also acts as a mRNA N(1)- methyltransferase by mediating methylation of adenosine residues at the N(1) position of MT-ND5 mRNA, leading to interfere with mitochondrial translation (PubMed:29107537). {ECO:0000269|PubMed:23097428, ECO:0000269|PubMed:27631568, ECO:0000269|PubMed:29107537}.
• Pathway: tRNA processing;tRNA modification in the mitochondrion;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.0722

Intolerance Scores

• loftool: 0.904
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.36

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

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

Gene ontology

• Biological process: tRNA methylation;rRNA methylation;protein homooligomerization;mitochondrial tRNA methylation;mRNA methylation
• Cellular component: mitochondrion;mitochondrial matrix;tRNA (m1A) methyltransferase complex
• Molecular function: protein binding;tRNA (adenine-N1-)-methyltransferase activity;rRNA (adenine) methyltransferase activity;mRNA (adenine-N1-)-methyltransferase activity