GTPBP1

GTP binding protein 1

Basic information

Region (hg38): 22:38705742-38738299

Links

ENSG00000100226NCBI:9567OMIM:602245HGNC:4669Uniprot:O00178AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GTPBP1 gene.

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
clinvar
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)3283112
22-38706014-C-A not specified Uncertain significance (Nov 28, 2023)3103197
22-38706038-C-T not specified Uncertain significance (Jan 05, 2022)2270574
22-38706061-G-A not specified Uncertain significance (Apr 14, 2023)2568825
22-38706077-G-T not specified Uncertain significance (Apr 23, 2024)3283118
22-38706079-T-G not specified Uncertain significance (Aug 23, 2021)2394621
22-38708891-G-A not specified Uncertain significance (Mar 03, 2022)2278011
22-38716032-G-T not specified Uncertain significance (Mar 12, 2024)3103195
22-38716069-A-G not specified Uncertain significance (Oct 05, 2023)3103196
22-38716826-T-G not specified Uncertain significance (Sep 29, 2022)2314804
22-38724353-G-A not specified Uncertain significance (Jan 26, 2022)2394990
22-38726013-C-G not specified Uncertain significance (Aug 23, 2021)2246896
22-38726043-G-A not specified Uncertain significance (Apr 04, 2023)2532781
22-38726085-C-T not specified Uncertain significance (Jan 29, 2024)3103192
22-38726286-C-T not specified Uncertain significance (Jul 25, 2023)2614064
22-38727322-C-A not specified Uncertain significance (Nov 15, 2023)3103193
22-38727324-A-C not specified Uncertain significance (Jul 09, 2021)2235586
22-38728010-C-G not specified Uncertain significance (May 06, 2022)2287922
22-38728087-C-G not specified Uncertain significance (Mar 18, 2024)3283113
22-38729478-A-C not specified Uncertain significance (Aug 28, 2023)2593607
22-38729523-C-T not specified Uncertain significance (Apr 08, 2024)3283114
22-38729552-G-A not specified Uncertain significance (Apr 22, 2024)3283116
22-38729568-C-T not specified Uncertain significance (Apr 24, 2024)3283119
22-38729608-A-T not specified Uncertain significance (Jun 07, 2023)2516997
22-38729613-C-T not specified Uncertain significance (Mar 02, 2023)2467563

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GTPBP1protein_codingprotein_codingENST00000216044 1232577
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9300.07001257240121257360.0000477
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.362053920.5230.00002414330
Missense in Polyphen45174.250.258241775
Synonymous1.341361570.8640.000009561398
Loss of Function4.01426.10.1530.00000146299

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.0001990.000198
East Asian0.000.00
Finnish0.0001070.0000924
European (Non-Finnish)0.00003570.0000352
Middle Eastern0.000.00
South Asian0.00006540.0000653
Other0.0001820.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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