TRPT1

tRNA phosphotransferase 1

Basic information

Region (hg38): 11:64223799-64226254

Links

ENSG00000149743 ∙ NCBI:83707 ∙ OMIM:610470 ∙ HGNC:20316 ∙ Uniprot:Q86TN4 ∙ 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 TRPT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPT1 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	21	2	0

Variants in TRPT1

This is a list of pathogenic ClinVar variants found in the TRPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64223912-C-A		not specified	Uncertain significance (Dec 20, 2023)
11-64223931-T-A		not specified	Uncertain significance (Jan 09, 2024)
11-64223934-G-C		not specified	Uncertain significance (Sep 04, 2024)
11-64223946-C-T		not specified	Uncertain significance (Feb 06, 2023)
11-64224184-T-C		not specified	Uncertain significance (Jun 17, 2022)
11-64224192-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-64224300-G-A		not specified	Uncertain significance (May 06, 2024)
11-64224332-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-64224338-A-G		not specified	Uncertain significance (Aug 22, 2023)
11-64224555-C-T		not specified	Likely benign (Sep 06, 2024)
11-64224623-A-G		not specified	Uncertain significance (Jan 19, 2024)
11-64224653-C-T		not specified	Uncertain significance (Feb 12, 2024)
11-64224668-G-A		not specified	Likely benign (Jun 30, 2022)
11-64224797-C-T		not specified	Likely benign (May 23, 2023)
11-64224836-G-A		not specified	Uncertain significance (Nov 15, 2024)
11-64224871-C-T		not specified	Uncertain significance (May 27, 2022)
11-64224917-A-G		not specified	Uncertain significance (Jun 16, 2024)
11-64224927-G-T		not specified	Uncertain significance (Sep 27, 2024)
11-64225559-T-G		not specified	Uncertain significance (Jan 24, 2024)
11-64225561-G-A		not specified	Uncertain significance (Oct 12, 2024)
11-64225580-C-T		not specified	Uncertain significance (Sep 14, 2023)
11-64225815-C-G		not specified	Uncertain significance (Nov 16, 2021)
11-64225833-C-T		not specified	Uncertain significance (May 26, 2024)
11-64225847-C-T		not specified	Uncertain significance (Sep 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRPT1	protein_coding	protein_coding	ENST00000394546	7	2456

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00222	0.927	125672	0	57	125729	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.551	129	148	0.872	0.00000840	1612
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000243
Ashkenazi Jewish	0.000423	0.000397
East Asian	0.000221	0.000217
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000298	0.000290
Middle Eastern	0.000221	0.000217
South Asian	0.000178	0.000163
Other	0.000167	0.000163

dbNSFP

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}.
• Pathway: tRNA splicing (Consensus)

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.940
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.0716
• hipred: N
• hipred_score: 0.196
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.697

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trpt1

Gene ontology

• Biological process: tRNA splicing, via endonucleolytic cleavage and ligation;biological_process;regulation of protein kinase activity
• Molecular function: tRNA 2'-phosphotransferase activity;molecular_function