FBXO3

F-box protein 3, the group of F-boxes other

Basic information

Region (hg38): 11:33740939-33774543

Links

ENSG00000110429 ∙ NCBI:26273 ∙ OMIM:609089 ∙ HGNC:13582 ∙ Uniprot:Q9UK99 ∙ 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 FBXO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO3 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				2		2
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	21	2	1

Variants in FBXO3

This is a list of pathogenic ClinVar variants found in the FBXO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-33741918-C-G		not specified	Uncertain significance (Sep 27, 2021)
11-33741927-C-T		not specified	Uncertain significance (Jun 19, 2024)
11-33741928-G-A		not specified	Uncertain significance (Dec 03, 2021)
11-33741930-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-33742003-C-G		not specified	Uncertain significance (Mar 05, 2024)
11-33747149-C-T		not specified	Uncertain significance (Jun 17, 2024)
11-33747176-C-T		not specified	Uncertain significance (Dec 06, 2021)
11-33747185-G-A		not specified	Uncertain significance (Oct 02, 2023)
11-33747298-T-C			Likely benign (Jun 01, 2022)
11-33750639-C-T		not specified	Uncertain significance (Jan 10, 2023)
11-33751545-T-G		not specified	Uncertain significance (Jan 31, 2022)
11-33755788-C-T			Benign (Jul 15, 2020)
11-33755940-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-33758582-G-A			Likely benign (Jun 01, 2022)
11-33768935-G-A		not specified	Uncertain significance (Jul 02, 2024)
11-33768940-A-G		not specified	Uncertain significance (Jul 31, 2024)
11-33768945-T-A		not specified	Uncertain significance (May 06, 2024)
11-33768958-G-C		not specified	Uncertain significance (May 23, 2023)
11-33768994-T-A		not specified	Uncertain significance (May 08, 2023)
11-33770792-C-T		not specified	Uncertain significance (Oct 07, 2024)
11-33774407-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-33774472-G-C		not specified	Uncertain significance (May 31, 2023)
11-33774472-G-T		not specified	Uncertain significance (May 20, 2024)
11-33774487-A-G		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO3	protein_coding	protein_coding	ENST00000265651	11	33605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0108	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	168	267	0.630	0.0000143	3074
Missense in Polyphen		41	92.671	0.44242		1121
Synonymous	1.00	80	92.3	0.867	0.00000497	864
Loss of Function	4.52	4	31.3	0.128	0.00000201	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000613	0.0000613
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. Mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. In the presence of PML, HIPK2 ubiquitination still occurs, but degradation is prevented. PML, HIPK2 and FBXO3 may act synergically to activate p53/TP53- dependent transactivation. {ECO:0000269|PubMed:18809579}.

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.430
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.313
• hipred: Y
• hipred_score: 0.783
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo3

Gene ontology

• Biological process: proteolysis;protein ubiquitination
• Cellular component: nucleoplasm;cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding