GTPBP4

GTP binding protein 4

Basic information

Region (hg38): 10:988434-1019932

Links

ENSG00000107937 ∙ NCBI:23560 ∙ OMIM:619169 ∙ HGNC:21535 ∙ Uniprot:Q9BZE4 ∙ 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 GTPBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTPBP4 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	2	3
missense			41	1		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7			7
Total	0	0	48	2	2

Variants in GTPBP4

This is a list of pathogenic ClinVar variants found in the GTPBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-992565-G-A		not specified	Uncertain significance (Nov 10, 2023)
10-992565-G-T		not specified	Uncertain significance (Oct 27, 2021)
10-995929-G-T		not specified	Uncertain significance (Feb 26, 2024)
10-996022-T-G		not specified	Uncertain significance (Sep 20, 2023)
10-996145-C-G		not specified	Uncertain significance (Jul 13, 2021)
10-996177-C-T		not specified	Uncertain significance (Oct 03, 2022)
10-996193-G-A		not specified	Uncertain significance (Jul 13, 2021)
10-996239-C-G		not specified	Uncertain significance (May 24, 2024)
10-997240-G-C		not specified	Uncertain significance (Nov 12, 2021)
10-997256-C-T		not specified	Uncertain significance (May 05, 2023)
10-999031-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-999087-C-T		not specified	Uncertain significance (Aug 30, 2022)
10-999094-A-T		not specified	Uncertain significance (Feb 15, 2023)
10-1000765-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-1000772-G-A			Benign (Oct 10, 2019)
10-1000849-G-C		not specified	Uncertain significance (Mar 13, 2023)
10-1000864-A-G		not specified	Uncertain significance (Mar 29, 2023)
10-1000951-C-G		not specified	Uncertain significance (Jun 02, 2023)
10-1000976-A-G		not specified	Uncertain significance (Aug 02, 2021)
10-1000978-G-A		not specified	Uncertain significance (Jan 09, 2024)
10-1005818-A-G		not specified	Uncertain significance (May 27, 2022)
10-1007050-A-G			Benign (Mar 29, 2018)
10-1008967-C-T		not specified	Uncertain significance (Jan 24, 2023)
10-1008977-C-G		not specified	Uncertain significance (Apr 25, 2023)
10-1009551-T-C		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTPBP4	protein_coding	protein_coding	ENST00000360803	17	31539

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000152	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0779	359	363	0.989	0.0000203	4217
Missense in Polyphen		82	103.07	0.79555		1211
Synonymous	0.129	128	130	0.986	0.00000744	1158
Loss of Function	5.66	0	37.4	0.00	0.00000216	434

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biogenesis of the 60S ribosomal subunit. {ECO:0000250}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.46

Haploinsufficiency Scores

• pHI: 0.915
• hipred: Y
• hipred_score: 0.825
• ghis: 0.583

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtpbp4

Zebrafish Information Network

• Gene name: gtpbp4
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased thickness

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);osteoblast differentiation;negative regulation of DNA replication;negative regulation of cell population proliferation;negative regulation of cell-cell adhesion;negative regulation of cell migration;negative regulation of protein ubiquitination;negative regulation of collagen binding;protein stabilization
• Cellular component: nucleus;nucleolus;cytoplasm;Golgi apparatus;cytosol;membrane;nuclear membrane;perinuclear region of cytoplasm
• Molecular function: RNA binding;GTPase activity;protein binding;GTP binding