FBXL15

protein-coding

F-box and leucine rich repeat protein 15, the group of F-box and leucine rich repeat proteins

Gene summary

Involved in several processes, including G2/M transition of mitotic cell cycle; SCF-dependent proteasomal ubiquitin-dependent protein catabolic process; and positive regulation of BMP signaling pathway. Located in cytoplasm. Part of SCF ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FBXO37

MANE transcript

NM_024326.4

Inheritance

—

ClinVar variants

U:38B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr10:102,419,189-102,423,136

External References & Databases

Ensembl (ENSG00000107872)

Transcript & Mutation Effects

hg38 • Region Span ~3.9 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 FBXL15 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 34

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024326.4. 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			1 clinvar	1 clinvar		2
missense			37 clinvar			37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	1	0	39

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024326.4	RefSeq	NP_077302.3	4	MANE Select
ENST00000369956.8	Ensembl	ENSP00000358972.3	4	MANE Select
NM_001387294.1	RefSeq	NP_001374223.1	4	Standard
ENST00000425536.1	Ensembl	ENSP00000403646.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
fbxl15	Danio rerio	Structure: trunk Quality: increased curvature abnormal

Gene / Model

Organism

Observed Phenotype

fbxl15

Danio rerio

Structure: trunk

Quality: increased curvature

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
Immune System
Adaptive Immune System
Antigen processing: Ubiquitination & Proteasome degradation

Biological Process

G2/M transition of mitotic cell cycle
protein polyubiquitination
ubiquitin-dependent protein catabolic process
dorsal/ventral pattern formation
protein ubiquitination

Molecular Function

ubiquitin-protein transferase activity
protein binding

Cellular Component

cytoplasm
cytosol
SCF ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000224862
Coding exons: 4
Length: 3948
Individuals with no LoFs: 123953
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 123960
p: 0.0000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	98	157	0.624	0.00000727	1824
Missense (PolyPhen)		30	55.982	0.53589		730
Synonymous	-0.209	80	77.7	1.03	0.00000371	678
Loss of Function	1.35	4	8.18	0.489	3.49e-7	99

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000069	0.000063	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000030	0.000027	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of SMURF1, thereby acting as a positive regulator of the BMP signaling pathway. Required for dorsal/ventral pattern formation and bone mass maintenance. Also mediates ubiquitination of SMURF2 and WWP2. {ECO:0000269|PubMed:21572392}.;

Recessive Scores

pRec: 0.105

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.579

Gene Damage Prediction

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