FBXW2

F-box and WD repeat domain containing 2, the group of WD repeat domain containing|F-box and WD repeat domain containing

Basic information

Region (hg38): 9:120751978-120793416

Links

ENSG00000119402 ∙ NCBI:26190 ∙ OMIM:609071 ∙ HGNC:13608 ∙ Uniprot:Q9UKT8 ∙ 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 FBXW2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXW2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in FBXW2

This is a list of pathogenic ClinVar variants found in the FBXW2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-120764579-A-C		not specified	Uncertain significance (Jan 22, 2024)
9-120764629-G-A		not specified	Uncertain significance (Jul 31, 2024)
9-120764726-G-A		not specified	Uncertain significance (Oct 08, 2024)
9-120764756-T-A		not specified	Uncertain significance (Dec 06, 2023)
9-120764770-C-T		not specified	Uncertain significance (May 14, 2024)
9-120764771-G-A		not specified	Uncertain significance (Oct 31, 2023)
9-120764773-T-C		not specified	Uncertain significance (Aug 04, 2023)
9-120764795-T-C		not specified	Likely benign (Oct 19, 2024)
9-120764828-T-C		not specified	Uncertain significance (Dec 02, 2024)
9-120764839-T-C		not specified	Uncertain significance (Jan 23, 2023)
9-120771363-C-G		not specified	Uncertain significance (Feb 27, 2024)
9-120771451-T-G		not specified	Uncertain significance (Jan 19, 2024)
9-120772810-G-C		not specified	Uncertain significance (Jul 09, 2021)
9-120772831-G-C		not specified	Uncertain significance (May 23, 2023)
9-120778353-G-C		not specified	Uncertain significance (Aug 09, 2021)
9-120778492-A-G		not specified	Uncertain significance (Nov 14, 2023)
9-120787789-T-C		not specified	Uncertain significance (Aug 16, 2022)
9-120787904-A-T		not specified	Uncertain significance (Nov 26, 2024)
9-120787913-C-T		not specified	Uncertain significance (Jul 25, 2023)
9-120787945-A-C		not specified	Uncertain significance (Sep 09, 2024)
9-120787976-T-C		not specified	Uncertain significance (Jan 06, 2023)
9-120788086-T-C		not specified	Uncertain significance (Sep 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXW2	protein_coding	protein_coding	ENST00000608872	6	41435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00123	124792	0	4	124796	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	137	244	0.561	0.0000126	2990
Missense in Polyphen		28	74.33	0.3767		922
Synonymous	-0.170	103	101	1.02	0.00000573	858
Loss of Function	4.09	0	19.5	0.00	8.24e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000556	0.0000556
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.
• Pathway: Wnt Signaling Pathway and Pluripotency;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: 0.0935

Intolerance Scores

• loftool: 0.199
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.728
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxw2

Gene ontology

• Biological process: protein polyubiquitination;cellular protein modification process;proteolysis;post-translational protein modification
• Cellular component: cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding