FBXL16

gene
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Also known as MGC33974Fbl16

Summary

FBXL16 (F-box and leucine rich repeat protein 16, HGNC:14150) is a protein-coding gene on chromosome 16p13.3, encoding F-box/LRR-repeat protein 16 (Q8N461). Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.

Members of the F-box protein family, such as FBXL16, 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]).

Source: NCBI Gene 146330 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 53 total
  • MANE Select transcript: NM_153350

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14150
Approved symbolFBXL16
NameF-box and leucine rich repeat protein 16
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesMGC33974, Fbl16
Ensembl geneENSG00000127585
Ensembl biotypeprotein_coding
OMIM609082
Entrez146330

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000397621, ENST00000562563, ENST00000562585, ENST00000562648, ENST00000926353, ENST00000926354

RefSeq mRNA: 1 — MANE Select: NM_153350 NM_153350

CCDS: CCDS10421

Canonical transcript exons

ENST00000397621 — 6 exons

ExonStartEnd
ENSE00000873939695415695923
ENSE00001227237696773697419
ENSE00001529427705512705801
ENSE00003530942692500694423
ENSE00003541344694992695076
ENSE00003678142694634694697

Expression profiles

Bgee: expression breadth ubiquitous, 227 present calls, max score 99.79.

FANTOM5 (CAGE): breadth broad, TPM avg 13.5949 / max 984.9750, expressed in 652 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
15576911.7487347
1557660.5431230
1557670.4083137
1557620.3474194
1557630.2876103
1557640.167377
1557650.071438
1557680.021110

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
Brodmann (1909) area 46UBERON:000648399.79gold quality
postcentral gyrusUBERON:000258199.73gold quality
parietal lobeUBERON:000187299.71gold quality
entorhinal cortexUBERON:000272899.71gold quality
endothelial cellCL:000011599.66gold quality
superior frontal gyrusUBERON:000266199.65gold quality
lateral globus pallidusUBERON:000247699.55gold quality
temporal lobeUBERON:000187199.42gold quality
putamenUBERON:000187499.42gold quality
cerebellar vermisUBERON:000472099.42gold quality
caudate nucleusUBERON:000187399.32gold quality
right frontal lobeUBERON:000281099.32gold quality
amygdalaUBERON:000187699.27gold quality
occipital lobeUBERON:000202199.27gold quality
lateral nuclear group of thalamusUBERON:000273699.27gold quality
nucleus accumbensUBERON:000188299.25gold quality
dorsolateral prefrontal cortexUBERON:000983499.19gold quality
frontal cortexUBERON:000187099.18gold quality
primary visual cortexUBERON:000243699.18gold quality
Ammon’s hornUBERON:000195499.14gold quality
middle temporal gyrusUBERON:000277199.13gold quality
Brodmann (1909) area 23UBERON:001355499.00gold quality
anterior cingulate cortexUBERON:000983598.99gold quality
prefrontal cortexUBERON:000045198.93gold quality
cerebral cortexUBERON:000095698.81gold quality
Brodmann (1909) area 9UBERON:001354098.75gold quality
neocortexUBERON:000195098.68gold quality
ponsUBERON:000098898.62gold quality
right hemisphere of cerebellumUBERON:001489097.86gold quality
forebrainUBERON:000189097.82gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.34

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

123 targeting FBXL16, 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-7110-3P100.0073.182486
HSA-MIR-4283100.0066.422097
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4455100.0065.481587
HSA-MIR-3924100.0072.092394
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-9-5P100.0072.282361
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-607799.9968.042299
HSA-MIR-366299.9973.825684
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-185-3P99.9567.011743
HSA-LET-7C-3P99.9573.422862
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-338-5P99.9272.342951
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-449299.8768.253611
HSA-MIR-3151-5P99.8663.831069

Literature-anchored findings (GeneRIF, showing 6)

  • the expression of FBXL16 reproducibly upregulated in p16INK4A and p14ARF knockdown HeLa cells (PMID:20043084)
  • The F-box protein FBXL16 up-regulates the stability of C-MYC oncoprotein by antagonizing the activity of the F-box protein FBW7. (PMID:32345600)
  • FBXL16 modulates the proliferation and autophagy in breast cancer cells via activating SRC-3-AKT signaling pathway. (PMID:34333223)
  • Suppression of breast cancer progression by FBXL16 via oxygen-independent regulation of HIF1alpha stability. (PMID:34818544)
  • FBXL16 Promotes Endometrial Progesterone Resistance via PP2A(B55alpha) /Cyclin D1 Axis in Ishikawa. (PMID:36106050)
  • MiR-1307-5p enhances fibroblast transdifferentiation to exacerbate chronic obstructive pulmonary disease through regulating FBXL16/HIF1alpha axis. (PMID:39420370)

Cross-species orthologs

19 orthologs

OrganismSymbolGene ID
danio_reriofbxl16ENSDARG00000060915
mus_musculusFbxl16ENSMUSG00000025738
rattus_norvegicusFbxl16ENSRNOG00000022248
drosophila_melanogasterCG32085FBGN0052085
caenorhabditis_elegansWBGENE00008177
caenorhabditis_elegansWBGENE00009689
caenorhabditis_elegansgadr-6WBGENE00009823
caenorhabditis_elegansWBGENE00010365
caenorhabditis_elegansK05C4.9WBGENE00010585
caenorhabditis_elegansWBGENE00012655
caenorhabditis_elegansWBGENE00018561
caenorhabditis_elegansWBGENE00018613
caenorhabditis_elegansWBGENE00018766
caenorhabditis_elegansWBGENE00019239
caenorhabditis_elegansWBGENE00021053
caenorhabditis_elegansWBGENE00021180
caenorhabditis_eleganszeel-1WBGENE00021463
caenorhabditis_elegansWBGENE00044459
caenorhabditis_elegansgadr-5WBGENE00045058

Paralogs (15): FBXL3 (ENSG00000005812), FBXL19 (ENSG00000099364), FBXL15 (ENSG00000107872), FBXL20 (ENSG00000108306), FBXL4 (ENSG00000112234), FBXL5 (ENSG00000118564), SKP2 (ENSG00000145604), FBXL17 (ENSG00000145743), FBXL2 (ENSG00000153558), FBXL18 (ENSG00000155034), FBXL13 (ENSG00000161040), FBXL14 (ENSG00000171823), FBXL6 (ENSG00000182325), FBXL7 (ENSG00000183580), FBXL22 (ENSG00000197361)

Protein

Protein identifiers

F-box/LRR-repeat protein 16Q8N461 (reviewed: Q8N461)

Alternative names: F-box and leucine-rich repeat protein 16

All UniProt accessions (1): Q8N461

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.

Subunit / interactions. Interacts with SKP1 and CUL1.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N461-11yes
Q8N461-22

RefSeq proteins (1): NP_699181* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006553Leu-rich_rpt_Cys-con_subtypRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR036047F-box-like_dom_sfHomologous_superfamily
IPR050648F-box_LRR-repeatFamily
IPR057207FBXL15_LRRDomain

Pfam: PF25372

UniProt features (14 total): repeat 7, chain 1, domain 1, compositionally biased region 1, modified residue 1, splice variant 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N461-F184.530.78

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 92

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

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

MSigDB gene sets: 118 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, KOINUMA_COLON_CANCER_MSI_UP, AAGCCAT_MIR135A_MIR135B, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGTGGRR_PAX4_03, GOBP_SCF_DEPENDENT_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, ATAACCT_MIR154, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_PROTEIN_CATABOLIC_PROCESS, SENESE_HDAC3_TARGETS_DN, GOCC_SCF_UBIQUITIN_LIGASE_COMPLEX, GOCC_TRANSFERASE_COMPLEX, GOBP_PROTEOLYSIS

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 (3): cytosol (GO:0005829), SCF ubiquitin ligase complex (GO:0019005), cytoplasm (GO:0005737)

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
cellular anatomical structure2
proteasome-mediated ubiquitin-dependent protein catabolic process1
binding1
cytoplasm1
cullin-RING ubiquitin ligase complex1
intracellular anatomical structure1

Protein interactions and networks

STRING

1404 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FBXL16SKP1P34991813
FBXL16CUL1Q13616703
FBXL16FBXO16Q8IX29593
FBXL16FBXL6Q8N531532
FBXL16CEP97Q8IW35471
FBXL16CETN2P41208453
FBXL16FBXL8Q96CD0448
FBXL16CEP164Q9UPV0445
FBXL16NEU4Q8WWR8433
FBXL16AP2A2O94973421
FBXL16RUNDC3AQ59EK9416
FBXL16NGEFQ8N5V2410
FBXL16PROSER2Q86WR7407
FBXL16KDM4BO94953396
FBXL16FAM199XQ6PEV8396

IntAct

31 interactions, top by confidence:

ABTypeScore
PPP2R2BMYO9Apsi-mi:“MI:0914”(association)0.640
FBXL16HIF1Apsi-mi:“MI:0915”(physical association)0.620
FBXL16HIF1Apsi-mi:“MI:2364”(proximity)0.620
FBXL16UBBpsi-mi:“MI:0914”(association)0.530
Lats2MPDZpsi-mi:“MI:0914”(association)0.420
FBXL16MAPK6psi-mi:“MI:0915”(physical association)0.370
Ppp2r1aCCHCR1psi-mi:“MI:0914”(association)0.350
MARK2WDR46psi-mi:“MI:0914”(association)0.350
Skp1XPO1psi-mi:“MI:0914”(association)0.350
PPP2R1AINTS2psi-mi:“MI:0914”(association)0.350
PPP2R2ARBM7psi-mi:“MI:0914”(association)0.350
Ppp2r2dKLF4psi-mi:“MI:0914”(association)0.350
PPP2CAENSApsi-mi:“MI:0914”(association)0.350
PPP2CBENSApsi-mi:“MI:0914”(association)0.350
SKP1BHLHE40psi-mi:“MI:0914”(association)0.350
COMTD1TARS3psi-mi:“MI:0914”(association)0.350
FBXL16POTEFpsi-mi:“MI:0914”(association)0.350
SKP1RNASET2psi-mi:“MI:0914”(association)0.350
IGFBP5RPP40psi-mi:“MI:0914”(association)0.350
FBXL16HSPA8psi-mi:“MI:0914”(association)0.350
FBXL16STK25psi-mi:“MI:0914”(association)0.350
SKP1NDUFAB1psi-mi:“MI:0914”(association)0.350
PPP2R1Apsi-mi:“MI:0914”(association)0.350
DSCR9FBXL16psi-mi:“MI:0915”(physical association)0.000

BioGRID (42): FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), FBXL16 (Affinity Capture-MS), DAAM1 (Affinity Capture-MS), UBB (Affinity Capture-MS), FBXL18 (Affinity Capture-MS), SKP1 (Affinity Capture-Western), SKP1 (Affinity Capture-Western), MYC (Affinity Capture-Western), HSPA8 (Affinity Capture-MS)

ESM2 similar proteins: A1A5X2, A2RT62, A6H639, A8Y3R9, B3FL73, D3Z902, D3ZXS4, G5EDB9, O49286, P34284, P87053, Q09299, Q0P4D1, Q0VD31, Q17R01, Q19857, Q32PG9, Q4R642, Q570C0, Q5BJ29, Q5JU00, Q5MJ12, Q65XV2, Q8BFZ4, Q8BH70, Q8BID8, Q8BVU0, Q8C4V4, Q8CDU4, Q8CFJ9, Q8J2J3, Q8LB33, Q8N1E6, Q8N461, Q8W104, Q96S15, Q9EPX5, Q9LPL4, Q9LW29, Q9NXK8

Diamond homologs: A2RT62, Q5MJ12, Q8N461

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 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
Cyclin A/B1/B2 associated events during G2/M transition570.2×1e-06
Cyclin D associated events in G1663.6×1e-07
Degradation of beta-catenin by the destruction complex539.3×1e-05
Separation of Sister Chromatids513.8×4e-04

GO biological processes:

GO termPartnersFoldFDR
intracellular signal transduction79.2×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance40
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

869 predictions. Top by Δscore:

VariantEffectΔscore
16:694628:TCTCA:Tdonor_loss1.0000
16:694629:CTCA:Cdonor_loss1.0000
16:694630:TCA:Tdonor_loss1.0000
16:694631:CAC:Cdonor_loss1.0000
16:694696:ACC:Aacceptor_loss1.0000
16:694697:CCTGT:Cacceptor_loss1.0000
16:694698:C:Aacceptor_loss1.0000
16:694699:T:Aacceptor_loss1.0000
16:695410:CGCA:Cdonor_loss1.0000
16:695411:GCAC:Gdonor_loss1.0000
16:695412:CACC:Cdonor_loss1.0000
16:695413:ACCT:Adonor_loss1.0000
16:695414:C:CGdonor_loss1.0000
16:694420:CAGC:Cacceptor_gain0.9900
16:694424:C:CCacceptor_gain0.9900
16:694424:CTGCG:Cacceptor_loss0.9900
16:694695:CAC:Cacceptor_gain0.9900
16:694698:C:CCacceptor_gain0.9900
16:694703:G:Tacceptor_gain0.9900
16:695409:GCGCA:Gdonor_loss0.9900
16:695413:A:ACdonor_gain0.9900
16:695414:C:CCdonor_gain0.9900
16:695414:CCTGT:Cdonor_gain0.9900
16:696768:CACA:Cdonor_loss0.9900
16:696769:ACACC:Adonor_loss0.9900
16:696771:ACCT:Adonor_loss0.9900
16:696772:CCTCG:Cdonor_loss0.9900
16:696786:T:TAdonor_gain0.9900
16:697416:CGCT:Cacceptor_gain0.9900
16:697418:CT:Cacceptor_gain0.9900

AlphaMissense

3063 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:694354:A:GL454P1.000
16:694360:A:GL452P1.000
16:694423:C:TG431D1.000
16:695001:C:AW406C1.000
16:695001:C:GW406C1.000
16:695003:A:GW406R1.000
16:695003:A:TW406R1.000
16:695053:C:TG389D1.000
16:695054:C:GG389R1.000
16:695059:T:AD387V1.000
16:695073:A:CC382W1.000
16:695074:C:TC382Y1.000
16:695075:A:GC382R1.000
16:695415:C:AR381M1.000
16:695415:C:GR381T1.000
16:695418:T:AD380V1.000
16:695421:A:TL379H1.000
16:695427:A:GL377P1.000
16:695427:A:TL377H1.000
16:695475:T:AD361V1.000
16:695476:C:AD361Y1.000
16:695476:C:GD361H1.000
16:695478:G:AT360I1.000
16:695489:G:CC356W1.000
16:695491:A:GC356R1.000
16:695494:A:GW355R1.000
16:695494:A:TW355R1.000
16:695499:A:CL353R1.000
16:695499:A:GL353P1.000
16:695499:A:TL353H1.000

dbSNP variants (sampled 300 via entrez): RS1000003040 (16:693954 G>A), RS1000175819 (16:702879 G>A), RS1000480062 (16:697918 T>A,G), RS1000607163 (16:692806 C>A,T), RS1000610108 (16:702682 G>A,C), RS1000827165 (16:695354 G>A,C,T), RS1001041321 (16:692495 A>G), RS1001061565 (16:700701 C>A), RS1001358685 (16:692934 A>T), RS1001405810 (16:700449 C>A,T), RS1001483948 (16:697691 GT>G,GTT), RS1001720914 (16:702812 G>A,C), RS1001821864 (16:702358 T>C), RS1002010215 (16:701601 C>G,T), RS1002097573 (16:692159 G>A)

Disease associations

OMIM: gene MIM:609082 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST007327_175Smoking status (ever vs never smokers)7.000000e-13
GCST012226_124Waist circumference adjusted for body mass index3.000000e-08
GCST012226_126Waist circumference adjusted for body mass index4.000000e-08
GCST012597_2Attention deficit hyperactivity disorder2.000000e-07

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004318smoking behavior
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

35 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation8
trichostatin Aincreases expression2
entinostatincreases expression, affects cotreatment2
Benzo(a)pyreneincreases methylation, affects methylation, increases expression2
Tobacco Smoke Pollutiondecreases expression2
bisphenol Adecreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
manganese chlorideincreases abundance, increases expression1
beta-methylcholineaffects expression1
pentanalincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
abrinedecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Calcitriolincreases expression1
Catechinaffects cotreatment, increases expression1
Cisplatindecreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diethylhexyl Phthalatedecreases expression1
Hydrogen Peroxideaffects expression1
Manganeseincreases abundance, increases expression1
Plant Extractsaffects cotreatment, decreases expression1
Polychlorinated Biphenylsaffects expression1
Silicon Dioxideincreases expression1
Dihydrotestosteronedecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): attention deficit-hyperactivity disorder