GTPBP1

GTP binding protein 1

Basic information

Region (hg38): 22:38705742-38738299

Links

ENSG00000100226 ∙ NCBI:9567 ∙ OMIM:602245 ∙ HGNC:4669 ∙ Uniprot:O00178 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with characteristic facial and ectodermal features and tetraparesis 1 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with characteristic facial and ectodermal features and tetraparesis 1	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Dermatologic; Neurologic	38118446

ClinVar

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

• not_specified (55 variants)
• Neurodevelopmental_disorder_with_characteristic_facial_and_ectodermal_features_and_tetraparesis_1 (3 variants)
• not_provided (1 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. These statistics are base on transcript: NM_000004286.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense	1		55		1	57
nonsense	2					2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	0	55	0	1

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