TRMT2B

tRNA methyltransferase 2 homolog B, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): X:101009346-101052116

Previous symbols: [ "CXorf34" ]

Links

ENSG00000188917 ∙ NCBI:79979 ∙ ∙ HGNC:25748 ∙ Uniprot:Q96GJ1 ∙ 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 TRMT2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT2B 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in TRMT2B

This is a list of pathogenic ClinVar variants found in the TRMT2B region.

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

Position	Type	Phenotype	Significance	ClinVar
X-101019320-T-C		not specified	Likely benign (Feb 12, 2024)
X-101021223-C-A		not specified	Uncertain significance (Oct 12, 2022)
X-101021250-A-G		not specified	Uncertain significance (Mar 19, 2024)
X-101021291-C-A		not specified	Uncertain significance (Aug 26, 2022)
X-101021305-G-A		not specified	Uncertain significance (Jul 19, 2023)
X-101022037-A-G		not specified	Likely benign (Aug 10, 2023)
X-101023501-A-G		not specified	Uncertain significance (Nov 21, 2022)
X-101023532-G-A		not specified	Uncertain significance (Feb 28, 2024)
X-101037001-C-G		not specified	Uncertain significance (Dec 12, 2023)
X-101037028-G-C		not specified	Uncertain significance (Jun 02, 2024)
X-101037063-T-C		not specified	Uncertain significance (Jul 31, 2023)
X-101037990-T-C		not specified	Uncertain significance (Jun 30, 2022)
X-101038014-A-C		not specified	Uncertain significance (Oct 12, 2022)
X-101041342-C-T		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT2B	protein_coding	protein_coding	ENST00000372936	12	42771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.59e-7	0.847	125665	11	42	125718	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	151	191	0.790	0.0000142	3273
Missense in Polyphen		34	38.811	0.87605		735
Synonymous	-0.188	71	69.0	1.03	0.00000491	1016
Loss of Function	1.50	13	20.3	0.641	0.00000163	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00243	0.00199
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000163
Finnish	0.000250	0.000185
European (Non-Finnish)	0.000123	0.0000879
Middle Eastern	0.000217	0.000163
South Asian	0.0000524	0.0000327
Other	0.000222	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.925
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.0828
• hipred: N
• hipred_score: 0.218
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt2b

Gene ontology

• Biological process: RNA methylation;tRNA processing
• Molecular function: protein binding;S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity