FBXO42

F-box protein 42, the group of F-boxes other

Basic information

Region (hg38): 1:16246839-16352480

Links

ENSG00000037637 ∙ NCBI:54455 ∙ OMIM:609109 ∙ HGNC:29249 ∙ Uniprot:Q6P3S6 ∙ 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 FBXO42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO42 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in FBXO42

This is a list of pathogenic ClinVar variants found in the FBXO42 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-16250683-C-T		not specified	Uncertain significance (May 11, 2022)
1-16250744-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-16250834-C-T		not specified	Uncertain significance (Nov 03, 2023)
1-16250908-A-G		not specified	Uncertain significance (Aug 02, 2022)
1-16250965-C-T		not specified	Uncertain significance (May 07, 2024)
1-16250966-G-A		not specified	Uncertain significance (May 13, 2024)
1-16251100-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-16251126-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-16251173-C-T		not specified	Uncertain significance (Jun 10, 2022)
1-16251206-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-16251211-T-C		not specified	Uncertain significance (Mar 14, 2023)
1-16251302-G-C		not specified	Uncertain significance (Apr 08, 2024)
1-16251383-A-G		not specified	Uncertain significance (Jun 29, 2023)
1-16251406-C-G		not specified	Uncertain significance (Jan 05, 2022)
1-16251451-C-A		not specified	Uncertain significance (Apr 20, 2024)
1-16251505-T-C		not specified	Uncertain significance (May 10, 2024)
1-16251521-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-16251551-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-16251554-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-16251680-G-A		not specified	Uncertain significance (Jun 17, 2024)
1-16251724-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-16252289-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-16252368-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-16252377-T-C		not specified	Uncertain significance (Apr 17, 2023)
1-16253667-G-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO42	protein_coding	protein_coding	ENST00000375592	9	105616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00497	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	298	419	0.712	0.0000228	4663
Missense in Polyphen		82	162.22	0.50549		1781
Synonymous	-0.111	156	154	1.01	0.00000869	1475
Loss of Function	4.71	4	33.4	0.120	0.00000191	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of some SCF (SKP1-CUL1- F-box protein)-type E3 ubiquitin ligase complex. Specifically recognizes p53/TP53, promoting its ubiquitination and degradation. {ECO:0000269|PubMed:19509332}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.389
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.36

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.673
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.658

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo42

Gene ontology

• Molecular function: protein binding