TRMT2A

tRNA methyltransferase 2 homolog A, the group of 7BS DNA/RNA methyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 22:20111874-20117392

Links

ENSG00000099899 ∙ NCBI:27037 ∙ OMIM:611151 ∙ HGNC:24974 ∙ Uniprot:Q8IZ69 ∙ 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 TRMT2A gene.

• Inborn genetic diseases (32 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT2A 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				2		2
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in TRMT2A

This is a list of pathogenic ClinVar variants found in the TRMT2A region.

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

Position	Type	Phenotype	Significance	ClinVar
22-20112579-G-A		not specified	Uncertain significance (Feb 11, 2022)
22-20112622-G-T		not specified	Uncertain significance (Nov 18, 2023)
22-20112702-C-T		not specified	Uncertain significance (Feb 14, 2023)
22-20112717-G-A		not specified	Uncertain significance (Apr 25, 2022)
22-20112924-C-T		not specified	Uncertain significance (Nov 07, 2023)
22-20112936-G-A		not specified	Uncertain significance (Apr 07, 2023)
22-20112943-G-C		not specified	Uncertain significance (Nov 16, 2022)
22-20112984-G-A		not specified	Uncertain significance (Jun 30, 2022)
22-20113473-G-A		not specified	Uncertain significance (Mar 11, 2024)
22-20113483-C-T		not specified	Uncertain significance (Nov 17, 2023)
22-20113491-A-G		not specified	Uncertain significance (Sep 26, 2023)
22-20113705-A-C		not specified	Uncertain significance (Sep 12, 2023)
22-20113760-C-T		not specified	Uncertain significance (Dec 27, 2023)
22-20113802-T-C		not specified	Uncertain significance (Jul 09, 2021)
22-20114599-C-T		not specified	Likely benign (May 11, 2022)
22-20114647-A-G		not specified	Uncertain significance (May 18, 2022)
22-20114682-C-A		not specified	Uncertain significance (Jun 10, 2022)
22-20114860-T-A		not specified	Uncertain significance (May 27, 2022)
22-20114987-G-A		not specified	Uncertain significance (Sep 25, 2023)
22-20115006-G-A		not specified	Uncertain significance (Aug 04, 2023)
22-20115015-G-A		not specified	Uncertain significance (Dec 03, 2021)
22-20115018-C-T		not specified	Uncertain significance (Nov 09, 2023)
22-20115267-G-A		not specified	Uncertain significance (Oct 03, 2022)
22-20115321-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-20115359-T-C		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT2A	protein_coding	protein_coding	ENST00000252136	12	5527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-8	0.930	125675	1	69	125745	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.132	405	398	1.02	0.0000254	4008
Missense in Polyphen		95	95.756	0.99211		940
Synonymous	-2.01	208	174	1.19	0.0000117	1315
Loss of Function	1.88	17	27.7	0.614	0.00000152	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00106
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000487	0.0000462
European (Non-Finnish)	0.000229	0.000220
Middle Eastern	0.000163	0.000163
South Asian	0.000471	0.000425
Other	0.000178	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in nucleic acid metabolism and/or modifications.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.907
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.32

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.229
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt2a
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: RNA methylation;RNA processing
• Molecular function: RNA binding;RNA methyltransferase activity