TRDMT1

tRNA aspartic acid methyltransferase 1, the group of 7BS C5-cytosine DNA/RNA methyltransferases

Basic information

Region (hg38): 10:17137335-17202054

Previous symbols: [ "DNMT2" ]

Links

ENSG00000107614 ∙ NCBI:1787 ∙ OMIM:602478 ∙ HGNC:2977 ∙ Uniprot:O14717 ∙ 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 TRDMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRDMT1 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					1	1
missense			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	2

Variants in TRDMT1

This is a list of pathogenic ClinVar variants found in the TRDMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-17149081-C-G		not specified	Uncertain significance (Aug 08, 2023)
10-17149111-G-A		not specified	Uncertain significance (May 24, 2023)
10-17149114-G-C		not specified	Uncertain significance (Nov 07, 2023)
10-17149125-A-G		not specified	Uncertain significance (Feb 28, 2023)
10-17153570-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-17154691-C-T		not specified	Likely benign (Feb 07, 2023)
10-17157502-A-G		not specified	Uncertain significance (Jan 09, 2024)
10-17157553-C-T		not specified	Uncertain significance (May 12, 2024)
10-17157650-A-C			Benign (Feb 25, 2018)
10-17157754-C-G		not specified	Uncertain significance (Feb 03, 2022)
10-17157756-G-A		not specified	Uncertain significance (Feb 03, 2022)
10-17157758-T-A		not specified	Uncertain significance (Feb 03, 2022)
10-17157760-C-G		not specified	Uncertain significance (Jun 10, 2024)
10-17157774-T-C		not specified	Uncertain significance (Oct 25, 2022)
10-17157781-G-A			Benign (Dec 14, 2017)
10-17159229-G-T		not specified	Uncertain significance (Apr 25, 2022)
10-17160310-T-C		not specified	Uncertain significance (Jun 29, 2023)
10-17160355-T-C		not specified	Uncertain significance (Feb 02, 2022)
10-17161520-A-C		not specified	Uncertain significance (Oct 13, 2023)
10-17162202-G-A		not specified	Uncertain significance (Apr 25, 2023)
10-17162211-T-C		not specified	Uncertain significance (Jun 28, 2022)
10-17162229-C-T		not specified	Uncertain significance (Sep 22, 2022)
10-17168862-G-A		not specified	Uncertain significance (Sep 13, 2023)
10-17168905-C-G		not specified	Uncertain significance (May 27, 2022)
10-17174555-A-G		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRDMT1	protein_coding	protein_coding	ENST00000377799	11	59801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.56e-10	0.317	125689	0	45	125734	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.822	224	192	1.17	0.00000965	2527
Missense in Polyphen		61	72.279	0.84395		956
Synonymous	-1.16	83	70.6	1.18	0.00000363	717
Loss of Function	0.883	17	21.4	0.794	0.00000117	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000414	0.000414
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.0000546	0.0000544
Finnish	0.000329	0.000323
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.0000546	0.0000544
South Asian	0.000133	0.000131
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp). {ECO:0000269|PubMed:16424344}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA;Methionine and cysteine metabolism (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.438
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.0538
• hipred: N
• hipred_score: 0.174
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.864

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trdmt1
• Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: trdmt1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: response to amphetamine;tRNA modification;tRNA methylation
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: RNA binding;tRNA methyltransferase activity;tRNA (cytosine-5-)-methyltransferase activity