FBXO44

gene
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Also known as FBX30FBG3MGC14140Fbxo6aFbx44

Summary

FBXO44 (F-box protein 44, HGNC:24847) is a protein-coding gene on chromosome 1p36.22, encoding F-box only protein 44 (Q9H4M3). Substrate-recognition component of two distinct E3 ligase complexes, the SKP1-CUL1-FBXO44 complex and the CUL4B-DDB1-FBXO44 complex.

This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. It is also a member of the NFB42 (neural F Box 42 kDa) family, similar to F-box only protein 2 and F-box only protein 6. Several alternatively spliced transcript variants encoding two distinct isoforms have been found for this gene.

Source: NCBI Gene 93611 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 73 total
  • MANE Select transcript: NM_033182

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24847
Approved symbolFBXO44
NameF-box protein 44
Location1p36.22
Locus typegene with protein product
StatusApproved
AliasesFBX30, FBG3, MGC14140, Fbxo6a, Fbx44
Ensembl geneENSG00000132879
Ensembl biotypeprotein_coding
OMIM609111
Entrez93611

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 23 protein_coding

ENST00000251546, ENST00000251547, ENST00000376760, ENST00000376762, ENST00000376768, ENST00000376770, ENST00000425796, ENST00000471895, ENST00000475435, ENST00000858192, ENST00000858193, ENST00000858194, ENST00000858195, ENST00000858196, ENST00000858197, ENST00000858198, ENST00000858199, ENST00000933204, ENST00000933205, ENST00000933206, ENST00000933207, ENST00000968217, ENST00000968218

RefSeq mRNA: 7 — MANE Select: NM_033182 NM_001014765, NM_001304790, NM_001304791, NM_001330355, NM_033182, NM_183412, NM_183413

CCDS: CCDS131, CCDS132, CCDS81261

Canonical transcript exons

ENST00000251547 — 6 exons

ExonStartEnd
ENSE000008189141165826711658393
ENSE000009556771165580611656100
ENSE000017552401166113011663327
ENSE000018758911165487711654952
ENSE000034853151165853311658628
ENSE000036237131165873611658871

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 99.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.0798 / max 217.7808, expressed in 1756 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
62416.67951755
6230.225696
6250.126377
6220.048421

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489099.07gold quality
cerebellar hemisphereUBERON:000224598.98gold quality
cerebellar cortexUBERON:000212998.93gold quality
right frontal lobeUBERON:000281098.40gold quality
Brodmann (1909) area 9UBERON:001354097.97gold quality
cerebellumUBERON:000203797.92gold quality
anterior cingulate cortexUBERON:000983597.76gold quality
prefrontal cortexUBERON:000045197.71gold quality
nucleus accumbensUBERON:000188297.45gold quality
putamenUBERON:000187497.13gold quality
amygdalaUBERON:000187696.68gold quality
caudate nucleusUBERON:000187396.63gold quality
hypothalamusUBERON:000189896.62gold quality
adenohypophysisUBERON:000219696.20gold quality
dorsolateral prefrontal cortexUBERON:000983495.47gold quality
frontal cortexUBERON:000187095.35gold quality
frontal lobeUBERON:001652595.35gold quality
C1 segment of cervical spinal cordUBERON:000646995.19gold quality
neocortexUBERON:000195095.09gold quality
pituitary glandUBERON:000000795.01gold quality
tendon of biceps brachiiUBERON:000818894.48gold quality
brainUBERON:000095594.32gold quality
forebrainUBERON:000189094.21gold quality
pancreatic ductal cellCL:000207994.08silver quality
spinal cordUBERON:000224093.97gold quality
metanephros cortexUBERON:001053393.93gold quality
granulocyteCL:000009493.86gold quality
cortical plateUBERON:000534393.61gold quality
cerebral cortexUBERON:000095693.51gold quality
kidney epitheliumUBERON:000481993.29silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-84465yes6.50
E-ANND-3no2.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting FBXO44, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4283100.0066.422097
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-651-3P99.9473.485177
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-427199.8868.322244
HSA-MIR-383-3P99.8565.841359
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-320A-3P99.7769.732107
HSA-MIR-320B99.7769.732107
HSA-MIR-320C99.7769.732107
HSA-MIR-320D99.7769.732107
HSA-MIR-442999.7769.622111
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-674599.7465.331321
HSA-MIR-10393-3P99.7266.56961
HSA-MIR-6801-5P99.7266.50981
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-6762-3P99.6666.941188
HSA-MIR-182799.6368.573265

Literature-anchored findings (GeneRIF, showing 6)

  • Skp1 and Fbg3 were co-expressed in E. coli. The plate-shaped crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 34.1, b = 76.6, c = 193.9 A and one molecule per asymmetric unit. (PMID:20057081)
  • FBXO44 mediates BRCA1 ubiquitination and degradation (PMID:23086937)
  • FBXO44-mediated degradation of RGS2 protein uniquely depends on a Cul4B/DDB1 complex. (PMID:25970626)
  • Although the overall structure of FBG3 is similar to that of Fbs1, the residues that form the Fbs1 carbohydrate-binding pocket failed to be superposed with the corresponding residues of FBG3. (PMID:26460611)
  • N-Terminal Targeting of Regulator of G Protein Signaling Protein 2 for F-Box Only Protein 44-Mediated Proteasomal Degradation. (PMID:33008920)
  • FBXO44 promotes DNA replication-coupled repetitive element silencing in cancer cells. (PMID:33357448)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_reriofbxo44.5ENSDARG00000012035
danio_reriofbxo44.1ENSDARG00000022623
danio_reriofbxo6.3ENSDARG00000037645
danio_reriofbxo44.7ENSDARG00000057884
danio_reriofbxo6.2ENSDARG00000057899
danio_reriofbxo44.9ENSDARG00000071029
danio_reriofbxo44.3ENSDARG00000071044
danio_reriofbxo44.10ENSDARG00000092077
danio_reriofbxo44.8ENSDARG00000092166
danio_reriofbxo6.1ENSDARG00000115843
mus_musculusFbxo44ENSMUSG00000029001
rattus_norvegicusFbxo44ENSRNOG00000009298

Paralogs (5): FBXO2 (ENSG00000116661), FBXO6 (ENSG00000116663), FBXO27 (ENSG00000161243), NCCRP1 (ENSG00000188505), FBXO17 (ENSG00000269190)

Protein

Protein identifiers

F-box only protein 44Q9H4M3 (reviewed: Q9H4M3)

Alternative names: F-box protein FBX30, F-box/G-domain protein 3

All UniProt accessions (5): A0A0A0MSI6, B7Z1P2, Q9H4M3, R4GMZ8, R4GNH4

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-recognition component of two distinct E3 ligase complexes, the SKP1-CUL1-FBXO44 complex and the CUL4B-DDB1-FBXO44 complex. The complex SCF(FBXO44) complex ubiquitinates and mediates BRCA1 degradation. In association with cullin 4B/CUL4B and DDB1, mediates the ubiquitination of RGS2 leading to its degradation. Additionally, regulates the pregnane X receptor/NR1I2 protein level by ubiquitination and degradation.

Subunit / interactions. Part of a SCF (SKP1-cullin-F-box) protein ligase complex. Interacts with SKP1 and CUL1. Interacts with CUL4B and DDB1. Interacts wwith BRCA1; this interaction mediates BRCA1 ubiquitination and subsequent degradation. Interacts with RGS2; this interaction mediates RGS2 ubiquitination and subsequent degradation. Interacts with PXR/NR1I2; this interaction mediates PXR/NR1I2 ubiquitination and subsequent degradation.

Subcellular location. Nucleus.

Tissue specificity. Abundantly expressed in brain and kidney. Expressed at lower levels in heart, spleen and liver.

Miscellaneous. In contrast to other FBA domain containing proteins, FBXO44 demonstrates no significant binding to any of the 200 glycans tested.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H4M3-11yes
Q9H4M3-22

RefSeq proteins (7): NP_001014765, NP_001291719, NP_001291720, NP_001317284, NP_149438, NP_904319, NP_904320 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001810F-box_domDomain
IPR007397F-box-assoc_domDomain
IPR008979Galactose-bd-like_sfHomologous_superfamily
IPR036047F-box-like_dom_sfHomologous_superfamily
IPR039752F-box_onlyFamily

Pfam: PF04300, PF12937

UniProt features (33 total): strand 14, helix 11, domain 2, splice variant 2, sequence conflict 2, chain 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5B4NX-RAY DIFFRACTION2.3
3WSOX-RAY DIFFRACTION2.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H4M3-F192.600.82

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-8951664Neddylation
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 93 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, WANG_CLIM2_TARGETS_UP, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, AP1_Q4_01, TGANTCA_AP1_C, AACTTT_UNKNOWN, GOBP_SCF_DEPENDENT_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_ERAD_PATHWAY

GO Biological Process (5): glycoprotein catabolic process (GO:0006516), proteasomal protein catabolic process (GO:0010498), SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146), ERAD pathway (GO:0036503), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (3): ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515), ubiquitin protein ligase activity (GO:0061630)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), SCF ubiquitin ligase complex (GO:0019005)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Post-translational protein modification1
Class I MHC mediated antigen processing & presentation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein catabolic process2
proteasomal protein catabolic process2
cellular anatomical structure2
glycoprotein metabolic process1
carbohydrate derivative catabolic process1
proteasome-mediated ubiquitin-dependent protein catabolic process1
response to endoplasmic reticulum stress1
response to chemical1
ubiquitin-dependent protein catabolic process1
enzyme-substrate adaptor activity1
binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
cullin-RING ubiquitin ligase complex1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

33 interactions, top by confidence:

ABTypeScore
CDK13CCNKpsi-mi:“MI:0914”(association)0.830
FBXO44SKP1psi-mi:“MI:0915”(physical association)0.800
SKP1FBXO44psi-mi:“MI:0915”(physical association)0.800
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730
SKP1MYCBP2psi-mi:“MI:0914”(association)0.640
FBXO44BORCS6psi-mi:“MI:0915”(physical association)0.600
BORCS6FBXO44psi-mi:“MI:0915”(physical association)0.600
CUL1FBXO21psi-mi:“MI:0914”(association)0.600
FBXO44SERTAD3psi-mi:“MI:0915”(physical association)0.560
SERTAD3FBXO44psi-mi:“MI:0915”(physical association)0.560
FBXO44CUL1psi-mi:“MI:0914”(association)0.530
FBXO44DDX21psi-mi:“MI:0915”(physical association)0.400
PRNPCARNS1psi-mi:“MI:0914”(association)0.350
CUL1LGALS8psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
COPS6DDX3Xpsi-mi:“MI:0914”(association)0.350
COPS6psi-mi:“MI:0914”(association)0.350
SKP1BHLHE40psi-mi:“MI:0914”(association)0.350
PHLDA3HSPA8psi-mi:“MI:0914”(association)0.350
ERCC8CCT2psi-mi:“MI:0914”(association)0.350
FBXO44A2ML1psi-mi:“MI:0914”(association)0.350

BioGRID (99): FBXO44 (Two-hybrid), FBXO44 (Two-hybrid), FBXO44 (Two-hybrid), BRCA1 (Biochemical Activity), SKP1 (Affinity Capture-MS), CUL1 (Affinity Capture-MS), SPA17 (Affinity Capture-MS), FBXO44 (Affinity Capture-MS), FBXO44 (Affinity Capture-Western), RGS2 (Affinity Capture-Western), CUL4B (Affinity Capture-Western), CUL1 (Affinity Capture-Western), SKP1 (Affinity Capture-Western), DDB1 (Affinity Capture-Western), SKP1 (Co-crystal Structure)

ESM2 similar proteins: B2GV54, D3K5L7, E2R222, O60656, O95803, P16152, P52848, Q08DW9, Q0VCJ8, Q0VD27, Q15645, Q1JQE6, Q2HJ19, Q3U129, Q3UA06, Q3UHN9, Q4R766, Q5E9T4, Q5R8Y5, Q5RCU5, Q5XHZ9, Q5XIJ5, Q5ZIN0, Q5ZMH6, Q67FW5, Q6AYT7, Q6DD70, Q6GL10, Q6GV29, Q6PIU2, Q8BGB7, Q8BK26, Q8BLF1, Q8BWB6, Q8MI29, Q8N2K0, Q8NFT2, Q8VDI9, Q99JW1, Q99LR1

Diamond homologs: G3X9C2, Q17QK6, Q3SX24, Q568V3, Q6AY27, Q6DIA9, Q6ZVX7, Q80UW2, Q8NI29, Q923V4, Q96EF6, Q9H4M3, Q9N0C8, Q9NRD1, Q9QZM8, Q9UK22, Q8BK26, Q9QZN4

SIGNOR signaling

2 interactions.

AEffectBMechanism
FBXO44“down-regulates quantity by destabilization”BRCA1binding
FBXO44“up-regulates activity”“Cullin 1-RBX1-Skp1”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 25 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Neddylation615.8×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance40
Likely benign23
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1638 predictions. Top by Δscore:

VariantEffectΔscore
1:11650831:CTCT:Cacceptor_gain1.0000
1:11650833:CT:Cacceptor_gain1.0000
1:11650842:C:CTacceptor_gain1.0000
1:11656072:G:GTdonor_gain1.0000
1:11656073:A:Tdonor_gain1.0000
1:11658262:A:AGacceptor_gain1.0000
1:11658263:T:Gacceptor_gain1.0000
1:11658265:A:AGacceptor_gain1.0000
1:11658265:A:ATacceptor_loss1.0000
1:11658265:AGAG:Aacceptor_gain1.0000
1:11658265:AGAGG:Aacceptor_gain1.0000
1:11658266:G:GGacceptor_gain1.0000
1:11658266:GA:Gacceptor_gain1.0000
1:11658266:GAGG:Gacceptor_gain1.0000
1:11658266:GAGGG:Gacceptor_gain1.0000
1:11658343:G:GTdonor_gain1.0000
1:11658362:CAGG:Cdonor_loss1.0000
1:11658363:AG:Adonor_loss1.0000
1:11658365:GTCA:Gdonor_loss1.0000
1:11658394:G:GGdonor_gain1.0000
1:11658624:GACTG:Gdonor_gain1.0000
1:11658626:CTG:Cdonor_gain1.0000
1:11658627:TG:Tdonor_gain1.0000
1:11658627:TGGT:Tdonor_loss1.0000
1:11658628:GG:Gdonor_gain1.0000
1:11658628:GGT:Gdonor_loss1.0000
1:11658629:G:GGdonor_gain1.0000
1:11658629:GTG:Gdonor_loss1.0000
1:11658630:T:Gdonor_loss1.0000
1:11658631:GAGT:Gdonor_loss1.0000

AlphaMissense

1678 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:11658311:T:AW104R0.998
1:11658311:T:CW104R0.998
1:11658545:G:CK135N0.997
1:11658545:G:TK135N0.997
1:11658863:T:AW206R0.997
1:11658863:T:CW206R0.997
1:11661241:A:CS246R0.997
1:11661243:C:AS246R0.997
1:11661243:C:GS246R0.997
1:11658313:G:CW104C0.995
1:11658313:G:TW104C0.995
1:11658377:T:CF126L0.995
1:11658379:C:AF126L0.995
1:11658379:C:GF126L0.995
1:11658865:G:CW206C0.995
1:11658865:G:TW206C0.995
1:11661179:T:CF225S0.995
1:11658281:T:AW94R0.994
1:11658281:T:CW94R0.994
1:11661224:G:AG240D0.994
1:11658562:T:AL141H0.993
1:11658624:G:CD162H0.993
1:11661142:T:CF213L0.993
1:11661144:C:AF213L0.993
1:11661144:C:GF213L0.993
1:11658312:G:CW104S0.992
1:11658546:T:CS136P0.992
1:11661178:T:CF225L0.992
1:11661180:T:AF225L0.992
1:11661180:T:GF225L0.992

dbSNP variants (sampled 300 via entrez): RS1000097533 (1:11663779 C>T), RS1000641466 (1:11661435 C>G,T), RS1000704875 (1:11660438 G>C), RS1001074408 (1:11656176 T>A), RS1001165716 (1:11653494 A>T), RS1001269221 (1:11663454 TCAC>T), RS1001957857 (1:11660796 G>A), RS1002202050 (1:11655771 G>A), RS1002303826 (1:11652748 G>C), RS1002378695 (1:11655587 G>T), RS1002582379 (1:11658426 C>T), RS1002862438 (1:11658186 A>C,G), RS1002881033 (1:11657006 AG>A), RS1002952831 (1:11662157 A>G), RS1003075233 (1:11658681 C>T)

Disease associations

OMIM: gene MIM:609111 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008478_1Neurological blood protein biomarker levels3.000000e-10
GCST010654_5Arterial stiffness (brachial-femoral pulse wave velocity)1.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004517arterial stiffness measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
alpha phellandreneincreases expression1
trichostatin Aaffects expression1
beta-lapachonedecreases expression, increases expression1
di-n-butylphosphoric acidaffects expression1
jinfukangaffects cotreatment, increases expression1
Acetaminophenincreases expression1
Benzo(a)pyreneaffects methylation1
Cisplatinaffects cotreatment, increases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Doxorubicinincreases expression1
Smokedecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Urethaneincreases expression1
Valproic Acidincreases methylation1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.