GTPBP8

GTP binding protein 8 (putative)

Basic information

Region (hg38): 3:112990984-113015060

Links

ENSG00000163607 ∙ NCBI:29083 ∙ ∙ HGNC:25007 ∙ Uniprot:Q8N3Z3 ∙ 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 GTPBP8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTPBP8 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in GTPBP8

This is a list of pathogenic ClinVar variants found in the GTPBP8 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-112991030-G-A		not specified	Uncertain significance (Mar 13, 2023)
3-112991083-C-G		not specified	Uncertain significance (Oct 21, 2024)
3-112991094-C-T		not specified	Uncertain significance (Sep 08, 2024)
3-112991145-A-G		not specified	Uncertain significance (Nov 10, 2024)
3-112991156-G-A		not specified	Uncertain significance (Jul 16, 2024)
3-112991223-C-T		not specified	Likely benign (Aug 17, 2022)
3-112991237-A-G		not specified	Uncertain significance (Jun 30, 2022)
3-112991264-G-C		not specified	Uncertain significance (Apr 15, 2024)
3-112991316-C-T		not specified	Uncertain significance (Sep 14, 2023)
3-112993081-T-G		not specified	Uncertain significance (Feb 13, 2024)
3-112993121-A-C		not specified	Uncertain significance (Oct 06, 2024)
3-112995163-A-G		not specified	Uncertain significance (Nov 10, 2022)
3-112995186-G-A		not specified	Uncertain significance (Nov 13, 2024)
3-112999468-A-G		not specified	Uncertain significance (Apr 15, 2024)
3-112999497-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-112999498-T-G		not specified	Uncertain significance (Dec 01, 2022)
3-113000887-T-C		not specified	Uncertain significance (Apr 12, 2022)
3-113005531-A-G		NEPRO-related disorder	Likely benign (May 08, 2019)
3-113005711-C-A		Abnormal cerebral white matter morphology;Microcephaly	Uncertain significance (May 12, 2021)
3-113005866-C-T		NEPRO-related disorder	Benign (Jul 01, 2024)
3-113005886-GT-G		NEPRO-related disorder	Uncertain significance (Dec 05, 2022)
3-113008202-G-A		NEPRO-related disorder	Uncertain significance (Mar 27, 2024)
3-113008238-C-T		Abnormal cerebral white matter morphology;Microcephaly	Uncertain significance (May 12, 2021)
3-113008337-A-T		Anauxetic dysplasia 3	Benign (Jul 14, 2021)
3-113008375-G-T		NEPRO-related disorder	Benign (Apr 24, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTPBP8	protein_coding	protein_coding	ENST00000383678	6	24143

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-7	0.228	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.565	173	153	1.13	0.00000683	1840
Missense in Polyphen		39	39.657	0.98343		507
Synonymous	-0.477	66	61.2	1.08	0.00000283	568
Loss of Function	0.259	11	12.0	0.919	5.96e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00151
Ashkenazi Jewish	0.00	0.00
East Asian	0.000229	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000189	0.000185
Middle Eastern	0.000229	0.000217
South Asian	0.000993	0.000915
Other	0.000180	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0992

Intolerance Scores

• loftool: 0.907
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• pHI: 0.0787
• hipred: N
• hipred_score: 0.177
• ghis: 0.458

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0374

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtpbp8

Gene ontology

• Cellular component: mitochondrion
• Molecular function: GTP binding;metal ion binding