GTPBP1
Basic information
Region (hg38): 22:38705742-38738299
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTPBP1 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 | 20 | 20 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 20 | 0 | 0 |
Variants in GTPBP1
This is a list of pathogenic ClinVar variants found in the GTPBP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-38705978-C-G | not specified | Uncertain significance (Apr 08, 2024) | ||
22-38706014-C-A | not specified | Uncertain significance (Nov 28, 2023) | ||
22-38706038-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
22-38706061-G-A | not specified | Uncertain significance (Apr 14, 2023) | ||
22-38706077-G-T | not specified | Uncertain significance (Apr 23, 2024) | ||
22-38706079-T-G | not specified | Uncertain significance (Aug 23, 2021) | ||
22-38708891-G-A | not specified | Uncertain significance (Mar 03, 2022) | ||
22-38716032-G-T | not specified | Uncertain significance (Mar 12, 2024) | ||
22-38716069-A-G | not specified | Uncertain significance (Oct 05, 2023) | ||
22-38716826-T-G | not specified | Uncertain significance (Sep 29, 2022) | ||
22-38724353-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
22-38726013-C-G | not specified | Uncertain significance (Aug 23, 2021) | ||
22-38726043-G-A | not specified | Uncertain significance (Apr 04, 2023) | ||
22-38726085-C-T | not specified | Uncertain significance (Jan 29, 2024) | ||
22-38726286-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
22-38727322-C-A | not specified | Uncertain significance (Nov 15, 2023) | ||
22-38727324-A-C | not specified | Uncertain significance (Jul 09, 2021) | ||
22-38728010-C-G | not specified | Uncertain significance (May 06, 2022) | ||
22-38728087-C-G | not specified | Uncertain significance (Mar 18, 2024) | ||
22-38729478-A-C | not specified | Uncertain significance (Aug 28, 2023) | ||
22-38729523-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
22-38729552-G-A | not specified | Uncertain significance (Apr 22, 2024) | ||
22-38729568-C-T | not specified | Uncertain significance (Apr 24, 2024) | ||
22-38729608-A-T | not specified | Uncertain significance (Jun 07, 2023) | ||
22-38729613-C-T | not specified | Uncertain significance (Mar 02, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GTPBP1 | protein_coding | protein_coding | ENST00000216044 | 12 | 32577 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.930 | 0.0700 | 125724 | 0 | 12 | 125736 | 0.0000477 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.36 | 205 | 392 | 0.523 | 0.0000241 | 4330 |
Missense in Polyphen | 45 | 174.25 | 0.25824 | 1775 | ||
Synonymous | 1.34 | 136 | 157 | 0.864 | 0.00000956 | 1398 |
Loss of Function | 4.01 | 4 | 26.1 | 0.153 | 0.00000146 | 299 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.000199 | 0.000198 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000107 | 0.0000924 |
European (Non-Finnish) | 0.0000357 | 0.0000352 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.000182 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Promotes degradation of target mRNA species. Plays a role in the regulation of circadian mRNA stability. Binds GTP and has GTPase activity (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.173
Intolerance Scores
- loftool
- 0.271
- rvis_EVS
- -0.78
- rvis_percentile_EVS
- 12.88
Haploinsufficiency Scores
- pHI
- 0.303
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.884
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gtpbp1
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- translational elongation;immune response;signal transduction;GTP metabolic process;positive regulation of mRNA catabolic process
- Cellular component
- cytoplasmic exosome (RNase complex);cytosol;membrane
- Molecular function
- RNA binding;translation elongation factor activity;GTPase activity;GTP binding