FBXW9

F-box and WD repeat domain containing 9, the group of WD repeat domain containing|F-box and WD repeat domain containing

Basic information

Region (hg38): 19:12688053-12696631

Links

ENSG00000132004 ∙ NCBI:84261 ∙ OMIM:609074 ∙ HGNC:28136 ∙ Uniprot:Q5XUX1 ∙ 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 FBXW9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXW9 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			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	0	0

Variants in FBXW9

This is a list of pathogenic ClinVar variants found in the FBXW9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12688261-C-T			Likely benign (Nov 01, 2022)
19-12689239-C-G		not specified	Uncertain significance (May 18, 2022)
19-12689247-A-C		not specified	Uncertain significance (May 23, 2023)
19-12689542-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-12689618-C-A		not specified	Uncertain significance (Jun 22, 2021)
19-12689786-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-12689787-G-A		not specified	Uncertain significance (Mar 07, 2023)
19-12689794-G-C		not specified	Uncertain significance (Feb 21, 2024)
19-12689837-G-A		not specified	Uncertain significance (Mar 07, 2025)
19-12689871-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-12689969-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-12689970-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-12689979-C-A		not specified	Uncertain significance (Mar 29, 2023)
19-12689979-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-12689990-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-12690042-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-12690042-G-C		not specified	Uncertain significance (Aug 22, 2023)
19-12690050-G-A		not specified	Uncertain significance (Mar 03, 2022)
19-12691199-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-12691201-G-A		not specified	Uncertain significance (May 02, 2024)
19-12691231-G-T		not specified	Uncertain significance (Dec 21, 2022)
19-12691369-G-A		not specified	Uncertain significance (Apr 10, 2023)
19-12691409-C-T		not specified	Uncertain significance (Nov 10, 2024)
19-12691420-C-T		not specified	Uncertain significance (Oct 12, 2024)
19-12691421-G-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXW9	protein_coding	protein_coding	ENST00000393261	10	8591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.09e-9	0.802	125661	0	86	125747	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.622	259	289	0.897	0.0000171	2889
Missense in Polyphen		89	107.94	0.82453		1135
Synonymous	0.654	123	133	0.928	0.00000819	985
Loss of Function	1.55	17	25.5	0.668	0.00000144	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000790	0.000774
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000492	0.000489
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000363	0.000360
Middle Eastern	0.000492	0.000489
South Asian	0.000328	0.000327
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. {ECO:0000250}.
• Pathway: 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: 0.0806

Intolerance Scores

• loftool: 0.820
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.272
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.722

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxw9
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; skeleton phenotype; respiratory 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); hematopoietic system phenotype; vision/eye phenotype; immune system phenotype

Gene ontology

• Biological process: protein polyubiquitination;post-translational protein modification
• Cellular component: cytosol;preribosome, large subunit precursor;PeBoW complex
• Molecular function: ubiquitin-protein transferase activity;protein binding