FBXO9

F-box protein 9, the group of F-boxes other

Basic information

Region (hg38): 6:53051990-53100873

Links

ENSG00000112146 ∙ NCBI:26268 ∙ OMIM:609091 ∙ HGNC:13588 ∙ Uniprot:Q9UK97 ∙ 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 FBXO9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO9 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in FBXO9

This is a list of pathogenic ClinVar variants found in the FBXO9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-53071051-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-53071130-A-C		not specified	Uncertain significance (Aug 02, 2021)
6-53073514-T-G		not specified	Uncertain significance (Sep 27, 2021)
6-53073559-C-A		not specified	Uncertain significance (Jun 17, 2024)
6-53073581-C-T		not specified	Uncertain significance (Dec 07, 2021)
6-53076490-G-A		not specified	Uncertain significance (Dec 02, 2022)
6-53078841-T-C		not specified	Uncertain significance (Apr 13, 2023)
6-53078885-G-A		not specified	Uncertain significance (Aug 08, 2022)
6-53081015-A-G		not specified	Uncertain significance (Nov 10, 2022)
6-53081065-C-T		not specified	Uncertain significance (Dec 17, 2023)
6-53082551-A-C		not specified	Uncertain significance (Apr 07, 2023)
6-53092446-G-A		not specified	Uncertain significance (Dec 20, 2023)
6-53092533-G-A		not specified	Uncertain significance (Aug 16, 2022)
6-53095524-C-G		not specified	Uncertain significance (Jan 16, 2024)
6-53097726-A-G		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO9	protein_coding	protein_coding	ENST00000244426	12	48883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000122	0.998	124636	0	18	124654	0.0000722

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	162	236	0.687	0.0000126	2928
Missense in Polyphen		38	76.444	0.49709		922
Synonymous	1.51	60	76.8	0.781	0.00000382	795
Loss of Function	2.72	11	26.0	0.424	0.00000134	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000654	0.0000646
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.000280	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.0000719	0.0000708
Middle Eastern	0.000280	0.000278
South Asian	0.0000655	0.0000654
Other	0.000496	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of TTI1 and TELO2 in a CK2-dependent manner, thereby directly regulating mTOR signaling. SCF(FBXO9) recognizes and binds mTORC1-bound TTI1 and TELO2 when they are phosphorylated by CK2 following growth factor deprivation, leading to their degradation. In contrast, the SCF(FBXO9) does not mediate ubiquitination of TTI1 and TELO2 when they are part of the mTORC2 complex. As a consequence, mTORC1 is inactivated to restrain cell growth and protein translation, while mTORC2 is activated due to the relief of feedback inhibition by mTORC1. {ECO:0000269|PubMed:23263282}.
• 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)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.442
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: Y
• hipred_score: 0.786
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.415

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo9
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein polyubiquitination;protein ubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;regulation of TOR signaling;post-translational protein modification;innate immune response;fat cell differentiation
• Cellular component: ubiquitin ligase complex;cytoplasm;cytosol;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding