TRMT44

tRNA methyltransferase 44 homolog, the group of 7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 4:8436140-8493531

Previous symbols: [ "C4orf23", "METTL19" ]

Links

ENSG00000155275 ∙ NCBI:152992 ∙ OMIM:614309 ∙ HGNC:26653 ∙ Uniprot:Q8IYL2 ∙ 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 TRMT44 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT44 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			65	3		68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	65	3	0

Variants in TRMT44

This is a list of pathogenic ClinVar variants found in the TRMT44 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-8440826-G-C		not specified	Uncertain significance (Dec 20, 2023)
4-8440863-C-A		not specified	Uncertain significance (Aug 12, 2021)
4-8440938-G-C		not specified	Uncertain significance (Jun 11, 2021)
4-8440966-C-G		not specified	Uncertain significance (Jun 22, 2021)
4-8441016-C-T		not specified	Uncertain significance (Nov 03, 2023)
4-8441031-G-A		not specified	Uncertain significance (Mar 13, 2023)
4-8441043-C-T		not specified	Uncertain significance (Sep 13, 2023)
4-8441063-G-C		not specified	Uncertain significance (Oct 06, 2021)
4-8441080-G-C		not specified	Uncertain significance (Aug 26, 2022)
4-8441108-G-T		not specified	Uncertain significance (Dec 30, 2023)
4-8441121-T-C		not specified	Uncertain significance (May 18, 2023)
4-8441181-C-T		not specified	Uncertain significance (Apr 06, 2024)
4-8441217-G-T		not specified	Uncertain significance (Jun 29, 2023)
4-8441234-C-A		not specified	Uncertain significance (Jan 22, 2024)
4-8441289-G-C		not specified	Uncertain significance (Dec 19, 2022)
4-8441307-C-A		not specified	Uncertain significance (Jul 06, 2021)
4-8441363-G-A		not specified	Uncertain significance (Apr 20, 2023)
4-8441411-A-G		not specified	Uncertain significance (May 20, 2024)
4-8441430-T-C		not specified	Uncertain significance (Feb 15, 2023)
4-8446485-A-G		not specified	Uncertain significance (Jun 04, 2024)
4-8446547-A-T		not specified	Uncertain significance (Apr 19, 2023)
4-8446571-A-G		not specified	Uncertain significance (Aug 09, 2021)
4-8449673-A-G		not specified	Uncertain significance (Dec 20, 2023)
4-8449721-G-A		not specified	Uncertain significance (Feb 27, 2023)
4-8449805-A-G		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRMT44	protein_coding	protein_coding	ENST00000389737	11	57392

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.03e-22	0.000812	125450	1	297	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.855	454	406	1.12	0.0000225	4880
Missense in Polyphen		111	99.435	1.1163		1241
Synonymous	-0.139	166	164	1.01	0.00000937	1521
Loss of Function	-0.0754	33	32.5	1.01	0.00000164	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000985	0.000977
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000217
Finnish	0.00590	0.00584
European (Non-Finnish)	0.000996	0.000976
Middle Eastern	0.000226	0.000217
South Asian	0.000935	0.000915
Other	0.00184	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable adenosyl-L-methionine (AdoMet)-dependent tRNA (uracil-O(2)-)-methyltransferase. {ECO:0000250}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.0799

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.144
• ghis: 0.520

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: Trmt44

Gene ontology

• Biological process: tRNA methylation
• Cellular component: cytoplasm
• Molecular function: tRNA (uracil) methyltransferase activity;metal ion binding