FBXO6

F-box protein 6, the group of F-boxes other

Basic information

Region (hg38): 1:11664200-11674354

Links

ENSG00000116663 ∙ NCBI:26270 ∙ OMIM:605647 ∙ HGNC:13585 ∙ Uniprot:Q9NRD1 ∙ 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 FBXO6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO6 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			24	3	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	4	1

Variants in FBXO6

This is a list of pathogenic ClinVar variants found in the FBXO6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-11668687-T-G		not specified	Uncertain significance (Oct 19, 2024)
1-11668710-G-A		not specified	Uncertain significance (Nov 15, 2024)
1-11668734-A-G		not specified	Uncertain significance (Jun 30, 2023)
1-11668735-C-T		not specified	Uncertain significance (Feb 07, 2025)
1-11668736-G-A		not specified	Likely benign (Apr 20, 2024)
1-11668746-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-11668796-C-A		not specified	Uncertain significance (May 17, 2023)
1-11668857-G-A		not specified	Uncertain significance (Nov 22, 2022)
1-11668868-G-C		not specified	Uncertain significance (Mar 03, 2025)
1-11668872-G-A		not specified	Uncertain significance (Apr 19, 2023)
1-11668913-T-A		not specified	Uncertain significance (Dec 13, 2022)
1-11668917-A-G		not specified	Uncertain significance (Jun 03, 2024)
1-11668942-A-C		not specified	Uncertain significance (Oct 21, 2024)
1-11671308-G-A			Benign (Aug 03, 2017)
1-11671320-A-G		not specified	Uncertain significance (Dec 10, 2024)
1-11671383-C-T		not specified	Uncertain significance (Feb 28, 2025)
1-11671941-T-G		not specified	Uncertain significance (Jul 07, 2024)
1-11671999-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-11671999-G-T		not specified	Uncertain significance (Apr 07, 2022)
1-11672010-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-11673285-C-G		not specified	Uncertain significance (Oct 29, 2024)
1-11673344-T-G		not specified	Uncertain significance (May 26, 2023)
1-11673347-G-C		not specified	Uncertain significance (Nov 15, 2024)
1-11673395-A-G		not specified	Likely benign (Mar 22, 2023)
1-11673642-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO6	protein_coding	protein_coding	ENST00000376753	5	10231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0152	0.961	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.251	190	181	1.05	0.0000113	1916
Missense in Polyphen		61	68.378	0.89211		726
Synonymous	-0.179	79	77.0	1.03	0.00000497	575
Loss of Function	1.97	5	12.5	0.400	6.22e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000260	0.000260
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.000381	0.000381
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of some SCF (SKP1-CUL1- F-box protein)-type E3 ubiquitin ligase complexes. Involved in endoplasmic reticulum-associated degradation pathway (ERAD) for misfolded lumenal proteins by recognizing and binding sugar chains on unfolded glycoproteins that are retrotranslocated into the cytosol and promoting their ubiquitination and subsequent degradation. Able to recognize and bind denatured glycoproteins, which are modified with not only high-mannose but also complex- type oligosaccharides. Also recognizes sulfated glycans. Also involved in DNA damage response by specifically recognizing activated CHEK1 (phosphorylated on 'Ser-345'), promoting its ubiquitination and degradation. Ubiquitination of CHEK1 is required to insure that activated CHEK1 does not accumulate as cells progress through S phase, or when replication forks encounter transient impediments during normal DNA replication. {ECO:0000269|PubMed:18203720, ECO:0000269|PubMed:19716789}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Chaperonin-mediated protein folding;Immune System;Association of TriC/CCT with target proteins during biosynthesis;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation;Protein folding (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.862
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.461
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo6

Gene ontology

• Biological process: DNA damage checkpoint;protein polyubiquitination;DNA repair;proteolysis;glycoprotein catabolic process;response to unfolded protein;ubiquitin-dependent ERAD pathway;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;post-translational protein modification
• Cellular component: cytoplasm;cytosol;SCF ubiquitin ligase complex;endoplasmic reticulum quality control compartment
• Molecular function: ubiquitin-protein transferase activity;protein binding;carbohydrate binding;ubiquitin protein ligase activity