TRMT44

protein-coding

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

Gene summary

The protein encoded by this gene is a putative tRNA methyltransferase found in the cytoplasm. Defects in this gene may be a cause of partial epilepsy with pericentral spikes (PEPS), but that has not been proven definitively. [provided by RefSeq, May 2012]

Previous symbols:

C4orf23
METTL19

MANE transcript

NM_152544.3

Inheritance

—

ClinVar variants

U:156B:13

Top phenotype

Variant of unknown significance

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr4:8,436,140-8,493,531

External References & Databases

Ensembl (ENSG00000155275)

Transcript & Mutation Effects

hg38 • Region Span ~57.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRMT44 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 158

Variant of unknown significanceTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152544.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			150 clinvar	12 clinvar		162
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	156	13	0	169

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152544.3	RefSeq	NP_689757.2	11	MANE Select
ENST00000389737.5	Ensembl	ENSP00000374387.4	11	MANE Select
NM_001350233.2	RefSeq	NP_001337162.1	10	Standard
ENST00000504134.1	Ensembl	ENSP00000434207.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

tRNA modification in the nucleus and cytosol
tRNA processing
Metabolism of RNA

Biological Process

tRNA methylation

Molecular Function

tRNA (uracil) methyltransferase activity
metal ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389737
Coding exons: 11
Length: 57392
Individuals with no LoFs: 125450
Homozygous LoFs: 1
Heterozygous LoFs: 297
Defined: 125748
p: 0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.855	454	406	1.12	0.0000225	4880
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00087	0.00086	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00023	0.00022	rare
Finnish	0.0059	0.0058	notable
European (Non-Finnish)	0.0010	0.00098	rare
South Asian	0.00093	0.00091	rare
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable adenosyl-L-methionine (AdoMet)-dependent tRNA (uracil-O(2)-)-methyltransferase. {ECO:0000250}.;

Recessive Scores

pRec: 0.0799

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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