FBXO39

F-box protein 39, the group of F-boxes other

Basic information

Region (hg38): 17:6776215-6797101

Links

ENSG00000177294 ∙ NCBI:162517 ∙ OMIM:609106 ∙ HGNC:28565 ∙ Uniprot:Q8N4B4 ∙ 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 FBXO39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO39 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			41		1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	41	0	2

Variants in FBXO39

This is a list of pathogenic ClinVar variants found in the FBXO39 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6779873-A-G		not specified	Uncertain significance (Oct 07, 2024)
17-6779875-G-A		not specified	Uncertain significance (May 30, 2024)
17-6779899-C-G		not specified	Uncertain significance (Oct 20, 2021)
17-6779996-G-A		not specified	Uncertain significance (Sep 15, 2021)
17-6780019-T-C		not specified	Uncertain significance (Dec 21, 2024)
17-6780038-G-A		not specified	Uncertain significance (Feb 28, 2025)
17-6780067-C-T		not specified	Uncertain significance (May 29, 2024)
17-6780073-A-G		not specified	Uncertain significance (Dec 02, 2021)
17-6780081-T-G		not specified	Uncertain significance (Apr 15, 2024)
17-6780138-G-T		not specified	Uncertain significance (Mar 04, 2025)
17-6780151-A-C		not specified	Uncertain significance (Oct 03, 2023)
17-6780205-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-6780206-G-A		not specified	Uncertain significance (Jan 18, 2023)
17-6780241-C-T		not specified	Uncertain significance (Jun 17, 2022)
17-6780259-A-G		not specified	Uncertain significance (Jan 10, 2023)
17-6780332-T-G		not specified	Uncertain significance (Apr 15, 2024)
17-6780341-A-G		not specified	Uncertain significance (Apr 08, 2022)
17-6780345-G-T		not specified	Uncertain significance (Dec 05, 2024)
17-6780346-A-G		not specified	Uncertain significance (Mar 07, 2024)
17-6780387-G-C		not specified	Uncertain significance (Dec 15, 2023)
17-6780572-G-C		not specified	Uncertain significance (Jun 07, 2023)
17-6780622-C-T		not specified	Likely benign (Jan 29, 2025)
17-6780623-G-A		not specified	Uncertain significance (Mar 23, 2022)
17-6780637-A-C		not specified	Uncertain significance (Aug 08, 2022)
17-6780643-C-T		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO39	protein_coding	protein_coding	ENST00000321535	3	20879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000673	0.915	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0559	250	248	1.01	0.0000141	2941
Missense in Polyphen		69	69.108	0.99843		874
Synonymous	1.28	82	98.2	0.835	0.00000550	817
Loss of Function	1.58	9	15.8	0.570	7.59e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000377	0.000377
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000176	0.000167
Middle Eastern	0.000598	0.000598
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0800

Intolerance Scores

• loftool: 0.819
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.4

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.379

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.127

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo39

Gene ontology

• Biological process: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
• Cellular component: SCF ubiquitin ligase complex