FBXO46

F-box protein 46, the group of F-boxes other

Basic information

Region (hg38): 19:45710629-45730896

Previous symbols: [ "FBXO34L" ]

Links

ENSG00000177051 ∙ NCBI:23403 ∙ OMIM:609117 ∙ HGNC:25069 ∙ Uniprot:Q6PJ61 ∙ 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 FBXO46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO46 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					1	1
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	1

Variants in FBXO46

This is a list of pathogenic ClinVar variants found in the FBXO46 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45711700-C-T		not specified	Uncertain significance (Feb 10, 2023)
19-45711709-C-G		not specified	Uncertain significance (Sep 26, 2023)
19-45711725-C-T		not specified	Uncertain significance (Dec 06, 2024)
19-45711860-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-45712052-C-T		not specified	Uncertain significance (Jan 21, 2025)
19-45712213-G-A		not specified	Uncertain significance (Nov 21, 2024)
19-45712237-G-T		not specified	Uncertain significance (Jan 21, 2025)
19-45712240-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-45712246-T-G		not specified	Uncertain significance (Jun 18, 2021)
19-45712265-G-T		not specified	Uncertain significance (Feb 01, 2025)
19-45712352-T-G		not specified	Uncertain significance (Jan 18, 2025)
19-45712412-A-C		not specified	Uncertain significance (Jun 03, 2024)
19-45712417-C-T		not specified	Uncertain significance (Jun 01, 2023)
19-45712433-G-T		not specified	Uncertain significance (Dec 28, 2023)
19-45712504-T-A		not specified	Uncertain significance (Aug 23, 2021)
19-45712615-G-A		not specified	Uncertain significance (Jun 30, 2024)
19-45712682-G-A		not specified	Uncertain significance (May 03, 2023)
19-45712757-G-C		not specified	Uncertain significance (Mar 11, 2025)
19-45712759-A-G		not specified	Uncertain significance (Apr 19, 2024)
19-45712806-G-A			Benign (Nov 16, 2018)
19-45712819-C-T		not specified	Uncertain significance (Oct 01, 2024)
19-45712881-C-A		not specified	Uncertain significance (Nov 28, 2024)
19-45712886-C-G		not specified	Uncertain significance (Feb 01, 2025)
19-45712886-C-T		not specified	Uncertain significance (Sep 22, 2022)
19-45712918-G-C		not specified	Uncertain significance (Jul 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO46	protein_coding	protein_coding	ENST00000317683	1	20276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.694	0.306	124578	0	8	124586	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	283	426	0.665	0.0000312	3811
Missense in Polyphen		111	194.52	0.57063		1615
Synonymous	-0.753	213	199	1.07	0.0000160	1337
Loss of Function	3.14	3	17.0	0.177	0.00000113	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000462	0.0000443
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000178	0.000165

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.775
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.381

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo46

Gene ontology

• Molecular function: protein binding