QTRT1

queuine tRNA-ribosyltransferase catalytic subunit 1

Basic information

Region (hg38): 19:10701430-10713437

Links

ENSG00000213339 ∙ NCBI:81890 ∙ OMIM:609615 ∙ HGNC:23797 ∙ Uniprot:Q9BXR0 ∙ 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 QTRT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QTRT1 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					1	1
missense			46	3		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	46	3	2

Variants in QTRT1

This is a list of pathogenic ClinVar variants found in the QTRT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10701467-G-A		not specified	Uncertain significance (Nov 22, 2023)
19-10701512-C-T		not specified	Uncertain significance (Jun 16, 2023)
19-10701513-G-A		not specified	Uncertain significance (Oct 07, 2024)
19-10701638-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-10701645-T-G		not specified	Uncertain significance (Jul 20, 2021)
19-10701651-C-G		not specified	Uncertain significance (Aug 26, 2024)
19-10701663-G-C		not specified	Uncertain significance (Dec 13, 2023)
19-10701699-G-A		not specified	Uncertain significance (Jul 08, 2021)
19-10701975-A-G		not specified	Uncertain significance (Oct 13, 2023)
19-10702017-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-10702112-T-G			Benign (Dec 31, 2019)
19-10702123-G-T		not specified	Uncertain significance (Jan 24, 2024)
19-10702179-C-G		not specified	Uncertain significance (Oct 13, 2023)
19-10702186-G-C		not specified	Uncertain significance (Jan 10, 2022)
19-10702224-G-C		not specified	Uncertain significance (Jun 24, 2022)
19-10707331-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-10707350-C-A		not specified	Uncertain significance (Feb 05, 2024)
19-10707358-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-10707359-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-10707508-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-10707519-C-T		not specified	Uncertain significance (Nov 17, 2022)
19-10707520-G-A		not specified	Uncertain significance (Oct 26, 2024)
19-10707538-A-G		not specified	Likely benign (Jun 18, 2024)
19-10707541-G-A		not specified	Likely benign (Dec 16, 2022)
19-10707543-C-T		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QTRT1	protein_coding	protein_coding	ENST00000250237	10	12008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.59e-7	0.745	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.945	227	271	0.838	0.0000171	2594
Missense in Polyphen		83	114.62	0.72413		1057
Synonymous	0.299	114	118	0.965	0.00000809	845
Loss of Function	1.29	13	19.1	0.680	9.91e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000679	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the queuine tRNA-ribosyltransferase (TGT) that catalyzes the base-exchange of a guanine (G) residue with queuine (Q) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis- dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine) (PubMed:11255023, PubMed:20354154). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming queuine, allowing a nucleophilic attack on the C1' of the ribose to form the product (By similarity). {ECO:0000250|UniProtKB:P28720, ECO:0000255|HAMAP- Rule:MF_03218, ECO:0000269|PubMed:11255023, ECO:0000269|PubMed:20354154}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.235
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.351
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Qtrt1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: tRNA modification;tRNA-guanine transglycosylation
• Cellular component: nucleus;mitochondrial outer membrane;protein-containing complex
• Molecular function: queuine tRNA-ribosyltransferase activity;protein homodimerization activity;metal ion binding;protein heterodimerization activity