FBXO4

F-box protein 4, the group of F-boxes other

Basic information

Region (hg38): 5:41925253-41941743

Links

ENSG00000151876 ∙ NCBI:26272 ∙ OMIM:609090 ∙ HGNC:13583 ∙ Uniprot:Q9UKT5 ∙ 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 FBXO4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO4 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in FBXO4

This is a list of pathogenic ClinVar variants found in the FBXO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-41925329-G-C		not specified	Uncertain significance (Jul 05, 2022)
5-41925342-C-G		not specified	Uncertain significance (Dec 19, 2022)
5-41925359-T-G		not specified	Uncertain significance (Jun 24, 2022)
5-41925365-A-G		not specified	Uncertain significance (Sep 29, 2022)
5-41925380-A-T		not specified	Uncertain significance (Mar 29, 2022)
5-41925443-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-41925454-C-T		not specified	Uncertain significance (May 30, 2024)
5-41925460-G-A		not specified	Uncertain significance (Oct 12, 2022)
5-41925491-G-A		not specified	Uncertain significance (May 18, 2023)
5-41927077-C-G		not specified	Uncertain significance (Oct 20, 2021)
5-41927079-A-T		not specified	Uncertain significance (Mar 29, 2023)
5-41927181-G-T		not specified	Uncertain significance (Mar 11, 2022)
5-41927223-G-C		not specified	Uncertain significance (Jul 20, 2021)
5-41929793-G-A			Likely benign (Apr 01, 2023)
5-41929804-G-A		not specified	Uncertain significance (Oct 25, 2022)
5-41929893-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-41934143-G-T		not specified	Uncertain significance (Dec 08, 2023)
5-41934192-G-A		not specified	Uncertain significance (Dec 14, 2022)
5-41934206-G-A		not specified	Uncertain significance (Feb 21, 2024)
5-41934231-G-T		not specified	Uncertain significance (Feb 15, 2023)
5-41934237-T-A		not specified	Uncertain significance (Jan 03, 2022)
5-41934237-T-G		not specified	Uncertain significance (Dec 22, 2023)
5-41939548-G-A		not specified	Uncertain significance (Sep 29, 2023)
5-41941208-C-T		not specified	Uncertain significance (Dec 19, 2023)
5-41941271-G-A		not specified	Likely benign (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO4	protein_coding	protein_coding	ENST00000281623	7	16490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000401	0.838	125704	0	39	125743	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.649	156	181	0.864	0.00000847	2524
Missense in Polyphen		60	69.502	0.86328		930
Synonymous	-0.316	63	59.9	1.05	0.00000262	723
Loss of Function	1.40	11	17.3	0.636	8.93e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000101	0.0000924
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000402	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Promotes ubiquitination of CCND1 and its subsequent proteasomal degradation. Recognizes TERF1 and promotes its ubiquitination together with UBE2D1. {ECO:0000269|PubMed:10531035, ECO:0000269|PubMed:16275645, ECO:0000269|PubMed:18598945, ECO:0000269|PubMed:20159592, ECO:0000269|PubMed:20181953}.
• Pathway: Ubiquitin mediated proteolysis - 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: 0.101

Intolerance Scores

• loftool: 0.792
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.111
• hipred: Y
• hipred_score: 0.673
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo4
• Phenotype: immune system phenotype; neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; cellular phenotype

Gene ontology

• Biological process: protein polyubiquitination;aging;posttranscriptional regulation of gene expression;protein ubiquitination;cellular homeostasis;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;positive regulation of protein ubiquitination;regulation of protein stability;protein destabilization;positive regulation of telomere maintenance via telomerase;common myeloid progenitor cell proliferation;post-translational protein modification;negative regulation of fibroblast proliferation;cellular response to ionizing radiation;negative regulation of protein localization to nucleus;positive regulation of protein polyubiquitination;regulation of DNA damage checkpoint
• Cellular component: ubiquitin ligase complex;cytoplasm;cytosol;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding;protein homodimerization activity;ubiquitin protein ligase activity