QTRT2
protein-codingqueuine tRNA-ribosyltransferase accessory subunit 2
Gene summary
This gene encodes a subunit of tRNA-guanine transglycosylase. tRNA-guanine transglycosylase is a heterodimeric enzyme complex that plays a critical role in tRNA modification by synthesizing the 7-deazaguanosine queuosine, which is found in tRNAs that code for asparagine, aspartic acid, histidine, and tyrosine. The encoded protein may play a role in the queuosine 5'-monophosphate salvage pathway. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]
- QTRTD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~82.6 kbGenCC 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 QTRT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024638.4. 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 | 0 | |||||
| missense | 8 | 1 | 9 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 12 | 1 | 0 | 13 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078914.1 | 8 | MANE Select | |
| Ensembl | ENSP00000281273.4 | 8 | MANE Select | |
| RefSeq | NP_001243764.1 | 9 | Standard | |
| RefSeq | NP_001243765.1 | 6 | 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-guanine transglycosylation
Molecular Function
- queuine tRNA-ribosyltransferase activity
- protein homodimerization activity
- metal ion binding
- protein heterodimerization activity
Cellular Component
- cytoplasm
- mitochondrion
- mitochondrial outer membrane
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000485050
- Coding exons
- 9
- Length
- 82590
- Individuals with no LoFs
- 125657
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 91
- Defined
- 125748
- p
- 0.000362
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.628 | 205 | 232 | 0.884 | 0.0000125 | 2770 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00057 | 0.00052 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00034 | 0.00032 | rare |
| European (Non-Finnish) | 0.00045 | 0.00043 | rare |
| South Asian | 0.00037 | 0.00036 | rare |
| Other | 0.00051 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.22
Essentials
- Essential (gene trap)
- N