QTRT2

queuine tRNA-ribosyltransferase accessory subunit 2

Basic information

Region (hg38): 3:114005833-114088422

Previous symbols: [ "QTRTD1" ]

Links

ENSG00000151576 ∙ NCBI:79691 ∙ ∙ HGNC:25771 ∙ Uniprot:Q9H974 ∙ 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 QTRT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QTRT2 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in QTRT2

This is a list of pathogenic ClinVar variants found in the QTRT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-114005901-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-114010890-T-A		not specified	Uncertain significance (Apr 24, 2024)
3-114010897-T-C		not specified	Uncertain significance (Sep 26, 2023)
3-114010942-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-114010999-A-G		not specified	Likely benign (Jul 25, 2023)
3-114018680-G-C		not specified	Uncertain significance (Dec 16, 2023)
3-114018859-G-A		not specified	Uncertain significance (Dec 20, 2021)
3-114031696-T-C		not specified	Uncertain significance (Jan 11, 2023)
3-114031737-T-G		not specified	Uncertain significance (Jan 03, 2024)
3-114034947-T-C		not specified	Uncertain significance (Dec 21, 2023)
3-114034968-C-G		not specified	Uncertain significance (Dec 22, 2023)
3-114035046-C-G		not specified	Uncertain significance (Mar 16, 2024)
3-114035051-A-T		not specified	Uncertain significance (May 13, 2024)
3-114036641-A-T		not specified	Uncertain significance (Nov 17, 2023)
3-114036691-T-C		not specified	Uncertain significance (Mar 19, 2024)
3-114036742-G-T		not specified	Uncertain significance (Jun 29, 2023)
3-114036756-T-C		not specified	Uncertain significance (Jun 13, 2022)
3-114042711-T-C		not specified	Likely benign (Aug 04, 2021)
3-114042756-C-A		not specified	Uncertain significance (Jan 03, 2024)
3-114042787-C-T		not specified	Uncertain significance (Jan 20, 2023)
3-114046662-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-114056387-G-A		not specified	Uncertain significance (Nov 09, 2023)
3-114056411-C-A		not specified	Uncertain significance (Jan 03, 2024)
3-114056424-T-C		not specified	Uncertain significance (Apr 20, 2024)
3-114056459-A-G		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QTRT2	protein_coding	protein_coding	ENST00000485050	9	82590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.85e-10	0.368	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	205	232	0.884	0.0000125	2770
Missense in Polyphen		48	67.794	0.70802		781
Synonymous	-0.00543	89	88.9	1.00	0.00000483	839
Loss of Function	0.959	17	21.8	0.778	0.00000130	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000633	0.000633
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000336	0.000323
European (Non-Finnish)	0.000452	0.000431
Middle Eastern	0.000109	0.000109
South Asian	0.000369	0.000359
Other	0.000509	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-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). {ECO:0000255|HAMAP- Rule:MF_03043}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.0362
• hipred: N
• hipred_score: 0.218
• ghis: 0.561

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Qtrt2

Gene ontology

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