GBP6

guanylate binding protein family member 6, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89364058-89388160

Links

ENSG00000183347 ∙ NCBI:163351 ∙ OMIM:612467 ∙ HGNC:25395 ∙ Uniprot:Q6ZN66 ∙ 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 GBP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP6 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	1
missense			35	2	3	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	4

Variants in GBP6

This is a list of pathogenic ClinVar variants found in the GBP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-89368562-G-T		not specified	Uncertain significance (Dec 21, 2022)
1-89368582-G-A		not specified	Likely benign (Jul 19, 2022)
1-89368623-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-89368682-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-89368694-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-89369592-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-89369606-C-T		not specified	Uncertain significance (Mar 05, 2024)
1-89369633-T-C		not specified	Uncertain significance (Oct 04, 2022)
1-89378128-T-C		not specified	Uncertain significance (Dec 20, 2021)
1-89378166-T-C		not specified	Uncertain significance (Nov 29, 2023)
1-89378425-C-T		not specified	Uncertain significance (Dec 02, 2021)
1-89378437-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-89378503-T-G		not specified	Uncertain significance (Aug 21, 2023)
1-89378603-G-C		not specified	Uncertain significance (May 09, 2023)
1-89380397-A-G		not specified	Uncertain significance (Mar 21, 2023)
1-89380413-A-G		not specified	Uncertain significance (Dec 12, 2023)
1-89380426-G-A			Benign (Oct 17, 2017)
1-89380470-A-T		not specified	Uncertain significance (Mar 08, 2024)
1-89380472-C-T		not specified	Uncertain significance (May 25, 2022)
1-89380494-T-C		not specified	Uncertain significance (Mar 31, 2024)
1-89380521-A-G		not specified	Uncertain significance (Jan 22, 2024)
1-89380536-C-G		not specified	Uncertain significance (Jan 09, 2024)
1-89380538-A-C		not specified	Uncertain significance (Feb 06, 2023)
1-89380581-C-T		not specified	Uncertain significance (Mar 15, 2024)
1-89381727-C-T		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP6	protein_coding	protein_coding	ENST00000370456	10	22404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.23e-16	0.0254	125658	0	88	125746	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00135	339	339	1.00	0.0000173	4192
Missense in Polyphen		82	97.684	0.83944		1335
Synonymous	0.218	124	127	0.975	0.00000663	1170
Loss of Function	0.446	25	27.5	0.908	0.00000135	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000507
Ashkenazi Jewish	0.00	0.00
East Asian	0.000871	0.000761
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000871	0.000761
South Asian	0.00128	0.000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds GTP, GDP and GMP. {ECO:0000250}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• loftool: 0.925
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.88

Haploinsufficiency Scores

• pHI: 0.0605
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0485

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gbp9

Gene ontology

• Biological process: immune response;defense response to bacterium;cellular response to interferon-gamma
• Cellular component: extracellular exosome
• Molecular function: GTPase activity;GTP binding