TRMT61A

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

Basic information

Region (hg38): 14:103529196-103537073

Previous symbols: [ "C14orf172" ]

Links

ENSG00000166166 ∙ NCBI:115708 ∙ ∙ HGNC:23790 ∙ Uniprot:Q96FX7 ∙ 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 TRMT61A gene.

• not_specified (39 variants)
• De_Lange_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT61A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152307.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	37	2		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	37	2	0

Highest pathogenic variant AF is 0.00020854344

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT61A	protein_coding	protein_coding	ENST00000389749	3	7890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0244	0.921	124960	0	22	124982	0.0000880

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	160	212	0.753	0.0000155	1818
Missense in Polyphen		36	71.476	0.50366		624
Synonymous	0.253	92	95.1	0.967	0.00000730	641
Loss of Function	1.65	4	9.48	0.422	4.91e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000112	0.000106
Middle Eastern	0.000111	0.000111
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of tRNA (adenine-N(1)-)- methyltransferase, which catalyzes the formation of N(1)- methyladenine at position 58 (m1A58) in initiator methionyl-tRNA (PubMed:16043508). Catalytic subunit of mRNA N(1)- methyltransferase complex, which mediates methylation of adenosine residues at the N(1) position of a small subset of mRNAs: N(1) methylation takes place in tRNA T-loop-like structures of mRNAs and is only present at low stoichiometries (PubMed:29107537, PubMed:29072297). {ECO:0000269|PubMed:16043508, ECO:0000269|PubMed:29072297, ECO:0000269|PubMed:29107537}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.487
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.422
• ghis: 0.668

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt61a

Gene ontology

• Biological process: tRNA methylation;mRNA methylation
• Cellular component: nucleus;nucleoplasm;tRNA (m1A) methyltransferase complex
• Molecular function: tRNA (adenine-N1-)-methyltransferase activity;mRNA (adenine-N1-)-methyltransferase activity