TRPT1

protein-coding

tRNA phosphotransferase 1

Gene summary

Predicted to enable tRNA 2'-phosphotransferase activity. Predicted to be involved in tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to act upstream of or within regulation of protein kinase activity. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001033678.4

Inheritance

—

ClinVar variants

U:48B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr11:64,223,799-64,226,254

External References & Databases

Ensembl (ENSG00000149743)

Transcript & Mutation Effects

hg38 • Region Span ~2.5 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 TRPT1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001033678.4. 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				1 clinvar		1
missense			42 clinvar	3 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	48	4	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 93 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001033678.4	RefSeq	NP_001028850.2	7	MANE Select
ENST00000317459.11	Ensembl	ENSP00000314073.6	7	MANE Select
NM_001160389.2	RefSeq	NP_001153861.1	7	Standard
NM_001160390.2	RefSeq	NP_001153862.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

tRNA splicing

Biological Process

tRNA splicing, via endonucleolytic cleavage and ligation
biological_process
regulation of protein kinase activity

Molecular Function

tRNA 2'-phosphotransferase activity
molecular_function

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394546
Coding exons: 7
Length: 2456
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125729
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.551	129	148	0.872	0.00000840	1612
Missense (PolyPhen)		38	38.428	0.98887		412
Synonymous	0.489	58	62.9	0.922	0.00000349	545
Loss of Function	1.58	6	11.9	0.505	6.95e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00042	0.00040	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00030	0.00029	rare
South Asian	0.00018	0.00016	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the last step of tRNA splicing, the transfer of the splice junction 2'-phosphate from ligated tRNA to NAD to produce ADP-ribose 1''-2'' cyclic phosphate. {ECO:0000305|PubMed:14504659}.;

Recessive Scores

pRec: 0.0955

Intolerance Scores

LoFtool: 0.940
RVIS EVS: 0.39
RVIS percentile EVS: 76.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.697

Gene Damage Prediction

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