FBXO10

F-box protein 10, the group of F-boxes other

Basic information

Region (hg38): 9:37510891-37576380

Links

ENSG00000147912 ∙ NCBI:26267 ∙ OMIM:609092 ∙ HGNC:13589 ∙ Uniprot:Q9UK96 ∙ 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 FBXO10 gene.

• Inborn genetic diseases (21 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO10 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					4	4
missense			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	5

Variants in FBXO10

This is a list of pathogenic ClinVar variants found in the FBXO10 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-37512614-G-A		not specified	Uncertain significance (Dec 14, 2023)
9-37512715-A-T		not specified	Uncertain significance (Jun 11, 2021)
9-37516043-C-T		not specified	Uncertain significance (Feb 27, 2024)
9-37516073-G-A		not specified	Uncertain significance (Mar 16, 2022)
9-37518133-C-T		not specified	Uncertain significance (Nov 08, 2021)
9-37518257-G-C			Benign (Jul 04, 2018)
9-37518300-C-T		not specified	Uncertain significance (Oct 22, 2021)
9-37518385-T-A		not specified	Uncertain significance (Feb 08, 2023)
9-37521629-G-A		not specified	Uncertain significance (Jan 19, 2024)
9-37521676-T-A		not specified	Uncertain significance (Aug 13, 2021)
9-37521695-G-C		not specified	Uncertain significance (Dec 13, 2022)
9-37521767-T-C		not specified	Uncertain significance (Mar 25, 2022)
9-37521785-T-C		not specified	Uncertain significance (Feb 14, 2023)
9-37521794-G-C		not specified	Uncertain significance (Nov 18, 2023)
9-37521799-A-C		not specified	Uncertain significance (Dec 28, 2022)
9-37525149-C-T		not specified	Uncertain significance (Sep 26, 2022)
9-37529172-T-C		not specified	Uncertain significance (Jun 12, 2023)
9-37529211-T-C		not specified	Uncertain significance (Aug 13, 2021)
9-37531993-G-A			Benign (Mar 29, 2018)
9-37532054-A-C		not specified	Uncertain significance (Sep 29, 2022)
9-37537157-T-C		not specified	Uncertain significance (Apr 13, 2023)
9-37537196-A-C		not specified	Uncertain significance (Jan 23, 2024)
9-37537229-T-C		not specified	Uncertain significance (Feb 02, 2024)
9-37537236-G-A			Benign (Jul 20, 2018)
9-37537250-C-T		not specified	Uncertain significance (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO10	protein_coding	protein_coding	ENST00000432825	10	77983

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000238	1.00	124573	0	110	124683	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	466	596	0.782	0.0000370	6263
Missense in Polyphen		115	189.97	0.60535		1966
Synonymous	1.85	200	236	0.847	0.0000146	1924
Loss of Function	3.25	16	37.5	0.427	0.00000210	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000560	0.000559
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.0000557	0.0000556
Finnish	0.00237	0.00237
European (Non-Finnish)	0.000251	0.000248
Middle Eastern	0.0000557	0.0000556
South Asian	0.000406	0.000327
Other	0.000839	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. The SCF(FBXO10) complex mediates ubiquitination and degradation of BCL2, an antiapoptotic protein, thereby playing a role in apoptosis by controlling the stability of BCL2. {ECO:0000269|PubMed:23431138}.
• Disease: DISEASE: Note=Defects in FBXO10 may be a cause of diffuse large B- cell lymphoma by allowing the accumulation of BCL2, an oncoprotein that has a critical role in lymphomas. {ECO:0000269|PubMed:23431138}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Intolerance Scores

• loftool: 0.719
• rvis_EVS: -1.99
• rvis_percentile_EVS: 1.76

Haploinsufficiency Scores

• pHI: 0.349
• hipred: N
• hipred_score: 0.476
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo10

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;apoptotic process;protein ubiquitination;regulation of apoptotic process;post-translational protein modification
• Cellular component: ubiquitin ligase complex;cytoplasm;cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding