FBXO48

Summary

FBXO48 (F-box protein 48, HGNC:33857) is a protein-coding gene on chromosome 2p13.3, encoding F-box only protein 48 (Q5FWF7).

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.

Source: NCBI Gene 554251 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_001024680

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33857
Approved symbol	FBXO48
Name	F-box protein 48
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204923
Ensembl biotype	protein_coding
OMIM	620549
Entrez	554251

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000377957, ENST00000865605, ENST00000865606, ENST00000865607, ENST00000865608, ENST00000865609, ENST00000865610, ENST00000931500, ENST00000962929, ENST00000962930

RefSeq mRNA: 1 — MANE Select: NM_001024680 NM_001024680

CCDS: CCDS33213

Canonical transcript exons

ENST00000377957 — 4 exons

Exon	Start	End
ENSE00001475630	68459422	68464370
ENSE00001475632	68464840	68465178
ENSE00001475634	68466144	68466470
ENSE00001475636	68467211	68467294

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 94.98.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6415 / max 331.1897, expressed in 906 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
28883	1.0843	756
28884	0.2812	33
28882	0.2761	103

Top tissues by expression

138 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
quadriceps femoris	UBERON:0001377	94.98	gold quality
cerebellar vermis	UBERON:0004720	91.64	gold quality
thymus	UBERON:0002370	83.46	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.18	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.64	gold quality
islet of Langerhans	UBERON:0000006	69.68	gold quality
skeletal muscle tissue	UBERON:0001134	69.29	gold quality
hindlimb stylopod muscle	UBERON:0004252	68.58	gold quality
muscle tissue	UBERON:0002385	67.00	gold quality
duodenum	UBERON:0002114	66.67	gold quality
leukocyte	CL:0000738	66.38	gold quality
lymph node	UBERON:0000029	66.35	gold quality
monocyte	CL:0000576	66.01	gold quality
muscle of leg	UBERON:0001383	65.41	gold quality
gastrocnemius	UBERON:0001388	65.06	gold quality
granulocyte	CL:0000094	64.96	gold quality
colonic epithelium	UBERON:0000397	64.57	silver quality
vermiform appendix	UBERON:0001154	64.22	gold quality
tonsil	UBERON:0002372	64.18	gold quality
bone marrow cell	CL:0002092	64.14	silver quality
endometrium	UBERON:0001295	63.92	gold quality
cortical plate	UBERON:0005343	63.50	gold quality
pancreas	UBERON:0001264	63.49	gold quality
liver	UBERON:0002107	63.49	gold quality
ganglionic eminence	UBERON:0004023	63.38	gold quality
rectum	UBERON:0001052	63.24	gold quality
placenta	UBERON:0001987	62.62	gold quality
ventricular zone	UBERON:0003053	62.56	gold quality
prefrontal cortex	UBERON:0000451	62.46	gold quality
lower esophagus mucosa	UBERON:0035834	62.43	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.96
E-GEOD-137537	no	3001.69
E-HCAD-8	no	908.75

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting FBXO48, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839

Literature-anchored findings (GeneRIF, showing 1)

• mutations in the coding region of the FBXO48 gene play little or no role in the development of Parkinson diseases. (PMID:23485738)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	fbxo48	ENSDARG00000086184
mus_musculus	Fbxo48	ENSMUSG00000044966
rattus_norvegicus	Fbxo48	ENSRNOG00000075916

Protein

Protein identifiers

F-box only protein 48 — Q5FWF7 (reviewed: Q5FWF7)

Alternative names: F-box protein 48

All UniProt accessions (1): Q5FWF7

RefSeq proteins (1): NP_001019851* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001810	F-box_dom	Domain
IPR036047	F-box-like_dom_sf	Homologous_superfamily

Pfam: PF12937

UniProt features (5 total): chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5FWF7-F1	82.25	0.59

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_SCF_DEPENDENT_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, ATCATGA_MIR433, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEIN_CATABOLIC_PROCESS, GOCC_SCF_UBIQUITIN_LIGASE_COMPLEX, GOCC_TRANSFERASE_COMPLEX, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOBP_PROTEOLYSIS, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_UBIQUITIN_LIGASE_COMPLEX, chr2p13, DMRT1_TARGET_GENES, E2F5_TARGET_GENES

GO Biological Process (1): SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): cytoplasm (GO:0005737), SCF ubiquitin ligase complex (GO:0019005)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
proteasome-mediated ubiquitin-dependent protein catabolic process	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
cullin-RING ubiquitin ligase complex	1

Protein interactions and networks

STRING

244 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FBXO48	ECT2L	Q008S8	590
FBXO48	OR5AP2	Q8NGF4	570
FBXO48	FBXO47	Q5MNV8	567
FBXO48	OR8B4	Q96RC9	550
FBXO48	ZNF684	Q5T5D7	543
FBXO48	OR1L8	Q8NGR8	511
FBXO48	FOXD4L6	Q3SYB3	510
FBXO48	ETAA1	Q9NY74	504
FBXO48	PNO1	Q9NRX1	488
FBXO48	ZNF793	Q6ZN11	486
FBXO48	ZNF18	P17022	473
FBXO48	NUP62CL	Q9H1M0	473
FBXO48	BHLHA9	Q7RTU4	472
FBXO48	OR2I1	Q8NGU4	471
FBXO48	Q8WV35	Q8WV35	462

IntAct

6 interactions, top by confidence:

A	B	Type	Score
SKP1	FBXO48	psi-mi:“MI:0915”(physical association)	0.560
SKP1	FBXO48	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): FBXO48 (Synthetic Lethality), FBXO48 (Two-hybrid), FBXO48 (Affinity Capture-RNA), FBXO48 (Affinity Capture-MS), FBXO48 (Affinity Capture-MS)

ESM2 similar proteins: A1A5R8, F4I7C7, O22977, O55036, P53804, P54274, P70371, Q008S8, Q08AX9, Q0P4S5, Q28GK6, Q4V7W2, Q566M8, Q5DTZ6, Q5FWF7, Q5XGI3, Q68FF0, Q6NPP4, Q6NQ79, Q6NSI8, Q7TSG3, Q84JU6, Q8CAT8, Q8GSA7, Q8GYY7, Q8GZ42, Q8LG03, Q8NCQ5, Q8NG08, Q8RWD6, Q8S8Y8, Q8S8Y9, Q90Z80, Q9C5Q8, Q9CAZ0, Q9FHK0, Q9FLX3, Q9FY74, Q9GKV7, Q9LK24

Diamond homologs: A1C7E4, A1DHW6, A2QCU8, B0XTS1, B2RZ17, B6GZA1, B6Q4Z5, B8M7Q5, B8NGT5, C5FP68, D4AM37, D4D8P3, L7N1X6, P0DL28, P39014, P87053, Q00659, Q008S8, Q01277, Q0CY32, Q2UFN8, Q4X0A9, Q58D00, Q5E9G6, Q5FWF7, Q8BIA4, Q8IX29, Q8N3Y1, Q9NRD0, Q9QZM9, Q9QZN3, Q9UKT8, Q8CAT8, Q9VZF4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

22 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

811 predictions. Top by Δscore:

Variant	Effect	Δscore
2:68464212:T:C	donor_gain	1.0000
2:68466272:T:TA	donor_gain	1.0000
2:68466337:G:C	donor_gain	1.0000
2:68466373:G:C	donor_gain	1.0000
2:68466273:C:A	donor_gain	0.9900
2:68466325:T:TA	donor_gain	0.9900
2:68466372:A:AC	donor_gain	0.9900
2:68466372:AG:A	donor_gain	0.9900
2:68467209:A:AC	donor_gain	0.9900
2:68467210:C:CC	donor_gain	0.9900
2:68467210:CTAGG:C	donor_gain	0.9900
2:68466482:T:TC	acceptor_gain	0.9800
2:68464216:T:A	donor_gain	0.9700
2:68464249:T:C	donor_gain	0.9700
2:68466482:T:C	acceptor_gain	0.9700
2:68467021:T:A	donor_gain	0.9700
2:68464267:A:C	donor_gain	0.9600
2:68466390:G:A	donor_gain	0.9600
2:68466408:C:CA	donor_gain	0.9600
2:68466491:G:GC	acceptor_gain	0.9600
2:68466323:CTT:C	donor_gain	0.9500
2:68466475:T:C	acceptor_gain	0.9500
2:68466491:G:C	acceptor_gain	0.9500
2:68464311:T:C	donor_gain	0.9400
2:68466862:T:A	donor_gain	0.9400
2:68464321:AGC:A	donor_gain	0.9300
2:68466332:A:C	donor_gain	0.9300
2:68466349:T:C	donor_gain	0.9300
2:68466428:G:C	donor_gain	0.9300
2:68466620:CG:C	donor_gain	0.9300

AlphaMissense

1044 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:68464325:A:G	W118R	0.991
2:68464325:A:T	W118R	0.991
2:68464244:A:G	W145R	0.990
2:68464244:A:T	W145R	0.990
2:68464953:A:G	W65R	0.988
2:68464953:A:T	W65R	0.988
2:68464332:T:A	K115N	0.986
2:68464332:T:G	K115N	0.986
2:68464242:C:A	W145C	0.983
2:68464242:C:G	W145C	0.983
2:68464323:C:A	W118C	0.983
2:68464323:C:G	W118C	0.983
2:68464234:A:G	I148T	0.980
2:68464234:A:C	I148S	0.978
2:68464918:C:A	W76C	0.974
2:68464918:C:G	W76C	0.974
2:68464226:C:G	A151P	0.973
2:68464845:A:G	W101R	0.973
2:68464845:A:T	W101R	0.973
2:68464920:A:G	W76R	0.973
2:68464920:A:T	W76R	0.973
2:68464231:A:G	L149P	0.972
2:68464212:T:A	R155S	0.968
2:68464212:T:G	R155S	0.968
2:68464324:C:G	W118S	0.968
2:68464984:A:C	S54R	0.968
2:68464984:A:T	S54R	0.968
2:68464986:T:G	S54R	0.968
2:68464951:C:A	W65C	0.965
2:68464951:C:G	W65C	0.965

dbSNP variants (sampled 300 via entrez): RS1000125900 (2:68468988 G>C), RS1000208879 (2:68460539 T>C), RS1000361613 (2:68466883 A>C), RS1000392815 (2:68467045 G>A,C), RS1000408231 (2:68469231 A>C), RS1000878944 (2:68465423 C>T), RS1001058257 (2:68459089 T>C), RS1001634975 (2:68469161 G>A,C,T), RS1002064917 (2:68465627 A>G), RS1002378411 (2:68464807 A>G), RS1002696340 (2:68462113 G>A,C), RS1002834960 (2:68467590 G>A,C), RS1002908350 (2:68467729 G>A,T), RS1003168589 (2:68468597 C>T), RS1003247103 (2:68468835 A>G)

Disease associations

OMIM: gene MIM:620549 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001341_19	Multiple sclerosis	2.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, decreases expression	2
Smoke	decreases expression, increases abundance	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
trichostatin A	affects expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Niclosamide	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Aflatoxin B1	increases methylation	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.