FBXO48

F-box protein 48, the group of F-boxes other

Basic information

Region (hg38): 2:68459421-68467294

Links

ENSG00000204923 ∙ NCBI:554251 ∙ ∙ HGNC:33857 ∙ Uniprot:Q5FWF7 ∙ 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 FBXO48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBXO48 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			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in FBXO48

This is a list of pathogenic ClinVar variants found in the FBXO48 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-68464841-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-68464865-T-C		not specified	Uncertain significance (May 06, 2024)
2-68464905-T-A		not specified	Likely benign (May 18, 2022)
2-68464974-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-68464989-G-A		not specified	Uncertain significance (Jun 13, 2023)
2-68465084-A-C		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBXO48	protein_coding	protein_coding	ENST00000377957	2	7840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000107	0.379	125688	0	31	125719	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.634	63	78.8	0.799	0.00000372	1040
Missense in Polyphen		10	18.935	0.52813		273
Synonymous	0.668	24	28.5	0.841	0.00000140	272
Loss of Function	0.0563	6	6.15	0.976	3.46e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00156	0.00156
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.725
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.171
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0762

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbxo48

Gene ontology

• Biological process: protein ubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
• Cellular component: cytoplasm;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity