FBXO48

protein-coding

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

Gene summary

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in SCF-dependent proteasomal ubiquitin-dependent protein catabolic process. Predicted to be part of SCF ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001024680.3

Inheritance

—

ClinVar variants

U:15B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr2:68,459,422-68,467,294

External References & Databases

Ensembl (ENSG00000204923)

Transcript & Mutation Effects

hg38 • Region Span ~7.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FBXO48 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001024680.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar	4 clinvar		19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	4	0	19

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001024680.3	RefSeq	NP_001019851.1	2	MANE Select
ENST00000377957.4	Ensembl	ENSP00000367193.2	2	MANE Select
ENST00000865605.1	Ensembl	ENSP00000535664.1	2	Standard
ENST00000865605.2	Ensembl	ENSP00000535664.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein ubiquitination
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process

Molecular Function

ubiquitin-protein transferase activity

Cellular Component

cytoplasm
SCF ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377957
Coding exons: 2
Length: 7840
Individuals with no LoFs: 125688
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125719
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.634	63	78.8	0.799	0.00000372	1040
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0015	0.0015	notable
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.725
RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0762

Gene Damage Prediction

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