GTPBP6

GTP binding protein 6 (putative), the group of Pseudoautosomal region 1

Basic information

Region (hg38): X:304528-318796

Links

ENSG00000178605 ∙ NCBI:8225 ∙ OMIM:300124 ∙ HGNC:30189 ∙ Uniprot:O43824 ∙ 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 GTPBP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTPBP6 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTPBP6	protein_coding	protein_coding	ENST00000326153	6	10862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.16e-7	0.200	124796	0	37	124833	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.77	262	193	1.36	0.0000145	1798
Missense in Polyphen		104	78.366	1.3271		798
Synonymous	-2.52	127	95.6	1.33	0.00000828	617
Loss of Function	0.178	11	11.7	0.944	5.81e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000150
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000222	0.000222
Middle Eastern	0.000111	0.000111
South Asian	0.000164	0.000163
Other	0.000166	0.000164

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.129
• ghis: 0.404

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtpbp6

Gene ontology

• Cellular component: cytoplasm
• Molecular function: GTP binding;ribosome binding;metal ion binding