TRMT10B

tRNA methyltransferase 10B, the group of SPOUT methyltransferase domain containing

Basic information

Region (hg38): 9:37753802-37778972

Previous symbols: [ "RG9MTD3" ]

Links

ENSG00000165275 ∙ NCBI:158234 ∙ ∙ HGNC:26454 ∙ Uniprot:Q6PF06 ∙ 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 TRMT10B gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT10B 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			15	2		17
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in TRMT10B

This is a list of pathogenic ClinVar variants found in the TRMT10B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-37761968-G-A		not specified	Uncertain significance (Apr 04, 2023)
9-37761975-C-T		not specified	Uncertain significance (May 23, 2023)
9-37762069-G-C		not specified	Uncertain significance (Aug 30, 2021)
9-37762586-C-G		not specified	Uncertain significance (Jul 05, 2022)
9-37762614-T-C		not specified	Uncertain significance (Feb 15, 2023)
9-37762634-A-G		not specified	Uncertain significance (Jun 22, 2021)
9-37762667-A-C		not specified	Uncertain significance (Aug 17, 2021)
9-37763635-G-A		not specified	Uncertain significance (May 16, 2023)
9-37763715-T-C		not specified	Uncertain significance (Feb 27, 2023)
9-37769942-T-C		not specified	Uncertain significance (Apr 26, 2023)
9-37769999-T-C		not specified	Uncertain significance (May 09, 2022)
9-37770710-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-37770723-A-T		not specified	Uncertain significance (Feb 22, 2023)
9-37770724-T-G		not specified	Uncertain significance (Feb 22, 2023)
9-37776373-A-C		not specified	Uncertain significance (Nov 14, 2023)
9-37777616-C-G		not specified	Uncertain significance (Jan 23, 2024)
9-37777622-A-T			Likely benign (Jan 01, 2023)
9-37777623-C-A			Likely benign (Jan 01, 2023)
9-37777666-T-C		not specified	Uncertain significance (Jan 10, 2022)
9-37777687-C-T		not specified	Uncertain significance (Nov 03, 2023)
9-37777691-G-A		not specified	Likely benign (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT10B	protein_coding	protein_coding	ENST00000297994	8	25166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000493	0.869	123667	18	1114	124799	0.00455

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.298	151	162	0.934	0.00000839	2045
Missense in Polyphen		32	31.116	1.0284		394
Synonymous	-0.225	61	58.8	1.04	0.00000307	569
Loss of Function	1.49	11	17.8	0.620	9.02e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0348	0.0342
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.000389	0.000389
Finnish	0.00895	0.00894
European (Non-Finnish)	0.00262	0.00261
Middle Eastern	0.000389	0.000389
South Asian	0.00188	0.00180
Other	0.00330	0.00330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent guanine N(1)- methyltransferase that catalyzes the formation of N(1)- methylguanine at position 9 (m1G9) in tRNAs (PubMed:23042678). Probably not able to catalyze formation of N(1)-methyladenine at position 9 (m1A9) in tRNAs (PubMed:23042678). {ECO:0000269|PubMed:23042678}.

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.0591
• hipred: N
• hipred_score: 0.197
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trmt10b

Gene ontology

• Biological process: tRNA methylation
• Cellular component: cytosol
• Molecular function: tRNA binding;tRNA (guanine-N1-)-methyltransferase activity;tRNA (guanine(9)-N(1))-methyltransferase activity