GTPBP2

GTP binding protein 2

Basic information

Region (hg38): 6:43605316-43629264

Links

ENSG00000172432 ∙ NCBI:54676 ∙ OMIM:607434 ∙ HGNC:4670 ∙ Uniprot:Q9BX10 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Jaberi-Elahi syndrome (Definitive), mode of inheritance: AR
• Jaberi-Elahi syndrome (Strong), mode of inheritance: AR
• Jaberi-Elahi syndrome (Moderate), mode of inheritance: AR
• Jaberi-Elahi syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Jaberi-Elahi syndrome	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; Musculoskeletal; Neurologic; Ophthalmologic	26675814; 29449720

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GTPBP2 gene.

• Jaberi-Elahi syndrome (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTPBP2 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			1	49	6	56
missense			44	2	1	47
nonsense	1		1			2
start loss						0
frameshift	2	2				4
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			3	4		7
non coding				19	9	28
Total	3	3	46	70	16

Variants in GTPBP2

This is a list of pathogenic ClinVar variants found in the GTPBP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-43605319-T-G		Xeroderma pigmentosum variant type	Uncertain significance (Jan 12, 2018)
6-43605326-T-G		Xeroderma pigmentosum variant type	Conflicting classifications of pathogenicity (Jun 16, 2023)
6-43605326-TTTTC-T			Likely benign (Feb 21, 2023)
6-43605327-T-A			Likely benign (Nov 10, 2023)
6-43605330-C-A			Likely benign (Jan 25, 2024)
6-43605497-T-G			Benign (Jul 10, 2018)
6-43605580-C-T			Likely benign (Jul 14, 2018)
6-43610271-GC-G			Likely benign (Jul 05, 2018)
6-43610541-T-C			Likely benign (Mar 13, 2023)
6-43610541-T-G			Likely benign (Jan 03, 2024)
6-43610544-C-A			Likely benign (Oct 28, 2023)
6-43610548-C-T			Likely benign (Dec 13, 2022)
6-43610550-A-G			Likely benign (Dec 05, 2023)
6-43610556-T-TG		Xeroderma pigmentosum	Pathogenic (Feb 05, 2023)
6-43610571-C-G			Likely benign (Jan 29, 2023)
6-43610579-T-C		Inborn genetic diseases	Likely benign (May 08, 2023)
6-43610589-T-C			Likely benign (Oct 29, 2023)
6-43610590-C-T			Uncertain significance (Apr 29, 2019)
6-43610592-T-C			Likely benign (Apr 11, 2023)
6-43610596-C-T		Xeroderma pigmentosum variant type	Pathogenic (Aug 01, 2023)
6-43610610-C-T			Likely benign (Feb 01, 2024)
6-43610619-C-T			Likely benign (Apr 14, 2023)
6-43610642-C-A		Xeroderma pigmentosum variant type • Inborn genetic diseases	Uncertain significance (May 23, 2023)
6-43610644-C-T			Uncertain significance (Apr 12, 2022)
6-43610660-A-G		Xeroderma pigmentosum	Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTPBP2	protein_coding	protein_coding	ENST00000307126	12	23847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.317	0.683	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.43	182	367	0.496	0.0000230	3869
Missense in Polyphen		49	152.8	0.32068		1598
Synonymous	-0.0964	151	150	1.01	0.00000877	1290
Loss of Function	3.93	7	30.4	0.231	0.00000200	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000615	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.516
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.358
• hipred: Y
• hipred_score: 0.685
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gtpbp2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: platelet degranulation;translational elongation;biological_process
• Cellular component: extracellular region;platelet alpha granule lumen;intracellular membrane-bounded organelle
• Molecular function: translation elongation factor activity;GTPase activity;protein binding;GTP binding