FBXO39

protein-coding

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

Gene summary

Members of the F-box protein family, such as FBXO39, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_153230.3

Inheritance

—

ClinVar variants

U:67B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr17:6,776,215-6,797,101

External References & Databases

Ensembl (ENSG00000177294)

Transcript & Mutation Effects

hg38 • Region Span ~20.9 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 FBXO39 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153230.3. 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			1 clinvar			1
missense			65 clinvar	4 clinvar	1 clinvar	70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	67	4	1	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153230.3	RefSeq	NP_694962.1	3	MANE Select
ENST00000321535.5	Ensembl	ENSP00000321386.4	3	MANE Select
ENST00000572251.1	Ensembl	ENSP00000459284.1	2	Standard
ENST00000575022.1	Ensembl	ENSP00000458890.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

SCF-dependent proteasomal ubiquitin-dependent protein catabolic process

Cellular Component

SCF ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321535
Coding exons: 3
Length: 20879
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125748
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0559	250	248	1.01	0.0000141	2941
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00018	0.00017	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.127

Gene Damage Prediction

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