FBXO40

F-box protein 40, the group of Zinc fingers TRAF-type|F-boxes other

Basic information

Region (hg38): 3:121593378-121630295

Links

ENSG00000163833 ∙ NCBI:51725 ∙ OMIM:609107 ∙ HGNC:29816 ∙ Uniprot:Q9UH90 ∙ 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 FBXO40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO40 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			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	4	0

Variants in FBXO40

This is a list of pathogenic ClinVar variants found in the FBXO40 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-121621465-C-G		not specified	Uncertain significance (Jan 19, 2022)
3-121621493-C-A		not specified	Uncertain significance (May 11, 2022)
3-121621679-C-A		not specified	Uncertain significance (Nov 18, 2022)
3-121621697-G-A		not specified	Uncertain significance (Dec 15, 2023)
3-121621748-T-C		not specified	Uncertain significance (Nov 14, 2023)
3-121621773-T-G		not specified	Uncertain significance (Jul 20, 2022)
3-121621835-G-T		not specified	Uncertain significance (Jul 14, 2021)
3-121621943-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-121622057-A-T		not specified	Uncertain significance (Oct 12, 2021)
3-121622100-A-G		not specified	Uncertain significance (May 09, 2022)
3-121622131-A-G			Likely benign (Feb 01, 2023)
3-121622168-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-121622223-A-G		not specified	Uncertain significance (Jun 17, 2024)
3-121622258-G-A		not specified	Uncertain significance (Feb 27, 2023)
3-121622261-G-A		not specified	Likely benign (Apr 19, 2023)
3-121622265-G-A		not specified	Likely benign (Nov 14, 2023)
3-121622346-A-C		not specified	Uncertain significance (Mar 01, 2024)
3-121622481-A-G		not specified	Uncertain significance (Oct 03, 2022)
3-121622508-G-A		not specified	Uncertain significance (Dec 13, 2022)
3-121622554-C-A		not specified	Uncertain significance (Jun 18, 2024)
3-121622557-G-C		not specified	Uncertain significance (Dec 07, 2021)
3-121622655-A-G		not specified	Uncertain significance (Apr 07, 2023)
3-121622684-A-G		not specified	Uncertain significance (Sep 19, 2022)
3-121622712-C-T		not specified	Uncertain significance (Jun 17, 2022)
3-121622756-G-C		not specified	Uncertain significance (Apr 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO40	protein_coding	protein_coding	ENST00000338040	3	37174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.53e-9	0.638	125458	2	288	125748	0.00115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.217	376	388	0.969	0.0000205	4701
Missense in Polyphen		107	124.74	0.85775		1544
Synonymous	-0.0717	152	151	1.01	0.00000843	1359
Loss of Function	1.26	16	22.5	0.712	0.00000118	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00228	0.00229
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000635	0.000633
Middle Eastern	0.00228	0.00229
South Asian	0.00444	0.00439
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that may function in myogenesis. {ECO:0000250}.
• 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: 0.103

Intolerance Scores

• loftool: 0.801
• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.57

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.282
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.366

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo40

Gene ontology

• Biological process: protein polyubiquitination;muscle cell differentiation;post-translational protein modification
• Cellular component: cytoplasm;cytosol
• Molecular function: molecular_function;ubiquitin-protein transferase activity;zinc ion binding;ubiquitin protein ligase activity