GTPBP1

GTP binding protein 1

Basic information

Region (hg38): 22:38705741-38738299

Links

ENSG00000100226 ∙ NCBI:9567 ∙ OMIM:602245 ∙ HGNC:4669 ∙ Uniprot:O00178 ∙ 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 GTPBP1 gene.

• Inborn genetic diseases (15 variants)

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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	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
22-38706014-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)
22-38706079-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)
22-38729478-A-C		not specified	Uncertain significance (Aug 28, 2023)
22-38729608-A-T		not specified	Uncertain significance (Jun 07, 2023)
22-38729613-C-T		not specified	Uncertain significance (Mar 02, 2023)
22-38730652-G-A		not specified	Uncertain significance (Aug 17, 2022)
22-38736270-G-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Feb 03, 2021)
22-38736274-G-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (May 04, 2022)
22-38736276-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Nov 19, 2023)
22-38736281-C-T		Emery-Dreifuss muscular dystrophy • not specified	Uncertain significance (Aug 31, 2021)
22-38736299-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (May 13, 2022)

GnomAD

Source: gnomAD

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: 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

	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