TRMT9B

tRNA methyltransferase 9B (putative), the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 8:12945642-13031503

Previous symbols: [ "C8orf79", "KIAA1456" ]

Links

ENSG00000250305 ∙ NCBI:57604 ∙ OMIM:615666 ∙ HGNC:26725 ∙ Uniprot:Q9P272 ∙ 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 TRMT9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT9B 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			55	4		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	4	0

Variants in TRMT9B

This is a list of pathogenic ClinVar variants found in the TRMT9B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-13006245-A-G		not specified	Likely benign (Jun 29, 2023)
8-13006246-A-G		not specified	Uncertain significance (Jun 28, 2022)
8-13006247-T-A		not specified	Uncertain significance (Mar 21, 2023)
8-13006254-G-C		not specified	Uncertain significance (Jul 26, 2022)
8-13006257-A-G		not specified	Uncertain significance (May 17, 2023)
8-13006261-C-T		not specified	Uncertain significance (Mar 28, 2024)
8-13006288-G-A		not specified	Uncertain significance (Jan 26, 2023)
8-13006294-C-A		not specified	Uncertain significance (Feb 14, 2023)
8-13006309-G-C		not specified	Uncertain significance (Jan 03, 2024)
8-13006313-G-C		not specified	Uncertain significance (Oct 06, 2022)
8-13006317-C-G		not specified	Uncertain significance (Dec 15, 2022)
8-13006318-T-G		not specified	Uncertain significance (Jul 19, 2023)
8-13012714-A-C		not specified	Uncertain significance (Sep 17, 2021)
8-13012720-A-G		not specified	Uncertain significance (Jan 24, 2023)
8-13012731-G-A		not specified	Uncertain significance (Sep 16, 2021)
8-13012774-A-G		not specified	Likely benign (May 18, 2022)
8-13012783-G-A		not specified	Uncertain significance (Jun 29, 2023)
8-13012822-G-A		not specified	Uncertain significance (Jan 24, 2024)
8-13012836-G-A		not specified	Uncertain significance (Jun 29, 2023)
8-13012849-C-T		not specified	Uncertain significance (May 31, 2023)
8-13021032-A-G		not specified	Uncertain significance (Jul 25, 2023)
8-13021068-T-C		not specified	Uncertain significance (Apr 05, 2023)
8-13021079-G-A		not specified	Uncertain significance (Aug 13, 2021)
8-13021088-C-A		not specified	Uncertain significance (Jun 16, 2024)
8-13021109-A-G		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT9B	protein_coding	protein_coding	ENST00000524591	3	85862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-9	0.0180	124511	10	120	124641	0.000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.44	445	248	1.79	0.0000131	2996
Missense in Polyphen		133	92.259	1.4416		1067
Synonymous	-4.85	149	90.4	1.65	0.00000496	835
Loss of Function	-1.49	11	6.80	1.62	2.88e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00297	0.00245
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000279	0.000278
Finnish	0.000233	0.000186
European (Non-Finnish)	0.000455	0.000442
Middle Eastern	0.000279	0.000278
South Asian	0.000558	0.000556
Other	0.000501	0.000496

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modifie wobble uridines in specific arginine and glutamic acid tRNAs. Acts as a tumor suppressor by promoting the expression of LIN9. {ECO:0000269|PubMed:23381944}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.0881

Intolerance Scores

• rvis_EVS: 0.43
• rvis_percentile_EVS: 77.31

Haploinsufficiency Scores

• pHI: 0.0869
• ghis: 0.534

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Trmt9b

Gene ontology

• Biological process: tRNA wobble uridine modification;tRNA modification;tRNA methylation;oxidation-reduction process
• Cellular component: nucleus;cytoplasm
• Molecular function: tRNA binding;tRNA methyltransferase activity;tRNA (uracil) methyltransferase activity;2-oxoglutarate-dependent dioxygenase activity