FNDC4

gene
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Also known as FLJ22362FRCP1

Summary

FNDC4 (fibronectin type III domain containing 4, HGNC:20239) is a protein-coding gene on chromosome 2p23.3, encoding Fibronectin type III domain-containing protein 4 (Q9H6D8). Has anti-inflammatory properties.

Involved in response to transforming growth factor beta. Predicted to be located in endoplasmic reticulum; extracellular space; and plasma membrane.

Source: NCBI Gene 64838 — RefSeq curated summary.

At a glance

  • GWAS associations: 38
  • Clinical variants (ClinVar): 21 total
  • MANE Select transcript: NM_022823

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20239
Approved symbolFNDC4
Namefibronectin type III domain containing 4
Location2p23.3
Locus typegene with protein product
StatusApproved
AliasesFLJ22362, FRCP1
Ensembl geneENSG00000115226
Ensembl biotypeprotein_coding
OMIM611905
Entrez64838

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 retained_intron

ENST00000264703, ENST00000476197, ENST00000491414, ENST00000934124, ENST00000934125, ENST00000951222

RefSeq mRNA: 1 — MANE Select: NM_022823 NM_022823

CCDS: CCDS1756

Canonical transcript exons

ENST00000264703 — 7 exons

ExonStartEnd
ENSE000008091922749266627492790
ENSE000009630442749188327492478
ENSE000013487542749487827495200
ENSE000034786902749454727494703
ENSE000035156312749338927493478
ENSE000036152522749393027494134
ENSE000036861112749435127494466

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 98.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6875 / max 193.9208, expressed in 1282 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
275157.98401276
2021280.3764211
275120.150651
275160.092827
275140.062927
275130.02099

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left adrenal gland cortexUBERON:003582598.00gold quality
left adrenal glandUBERON:000123497.87gold quality
right adrenal glandUBERON:000123397.66gold quality
adrenal cortexUBERON:000123597.05gold quality
right adrenal gland cortexUBERON:003582797.00gold quality
right lobe of liverUBERON:000111496.10gold quality
right frontal lobeUBERON:000281095.56gold quality
adrenal glandUBERON:000236995.40gold quality
anterior cingulate cortexUBERON:000983594.92gold quality
cingulate cortexUBERON:000302794.90gold quality
prefrontal cortexUBERON:000045194.84gold quality
lower esophagus mucosaUBERON:003583494.44gold quality
cortical plateUBERON:000534393.44gold quality
neocortexUBERON:000195093.41gold quality
frontal cortexUBERON:000187093.32gold quality
Brodmann (1909) area 9UBERON:001354093.31gold quality
dorsolateral prefrontal cortexUBERON:000983493.10gold quality
nucleus accumbensUBERON:000188293.09gold quality
caudate nucleusUBERON:000187392.90gold quality
right hemisphere of cerebellumUBERON:001489092.77gold quality
cerebellar hemisphereUBERON:000224592.58gold quality
left ovaryUBERON:000211992.54gold quality
cerebellar cortexUBERON:000212992.53gold quality
amygdalaUBERON:000187692.52gold quality
cerebral cortexUBERON:000095692.00gold quality
putamenUBERON:000187491.94gold quality
telencephalonUBERON:000189391.58gold quality
cerebellumUBERON:000203791.33gold quality
liverUBERON:000210791.23gold quality
right ovaryUBERON:000211891.21gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting FNDC4, 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-607799.9968.042299
HSA-MIR-314899.9775.066478
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-4671-3P99.8872.461045
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-3913-5P99.7867.26968
HSA-MIR-7-5P99.6770.531809
HSA-MIR-312299.5066.33821
HSA-MIR-548B-3P99.3867.261000
HSA-MIR-397899.2468.392201
HSA-MIR-432499.0470.141569
HSA-MIR-2355-5P98.8365.511589
HSA-MIR-331-3P98.7664.91793
HSA-MIR-58398.7167.441791
HSA-MIR-6776-5P98.5467.431304
HSA-MIR-6838-3P98.4065.88559
HSA-MIR-1233-5P98.1966.711201
HSA-MIR-6778-5P98.1966.591239
HSA-MIR-6881-5P98.1667.38665
HSA-MIR-392197.8167.451431
HSA-MIR-144-5P97.6669.90531
HSA-MIR-296-5P97.6164.02851
HSA-MIR-431497.5067.301369
HSA-MIR-2467-5P97.3667.71991
HSA-MIR-4653-5P97.2267.721429
HSA-MIR-6841-5P97.1967.29409
HSA-MIR-364996.8564.10340

Literature-anchored findings (GeneRIF, showing 8)

  • Reports the cloning, expression and subcellular localization of the related mouse protein. (PMID:12384288)
  • FNDC4 as a factor with direct therapeutic potential in inflammatory bowel disease and possibly other inflammatory diseases. (PMID:27066907)
  • The novel adipokine FNDC4 reduces lipogenesis and increases fat browning in human visceral adipocytes. (PMID:32407726)
  • Orphan GPR116 mediates the insulin sensitizing effects of the hepatokine FNDC4 in adipose tissue. (PMID:34016966)
  • FNDC4 and FNDC5 reduce SARS-CoV-2 entry points and spike glycoprotein S1-induced pyroptosis, apoptosis, and necroptosis in human adipocytes. (PMID:34465884)
  • Irisin and the fibronectin type III domain-containing family: structure, signaling and role in female reproduction. (PMID:35521900)
  • FNDC4 reduces inflammation, proliferation, invasion and migration of rheumatoid synovial cells by inhibiting CCL2/ERK signaling. (PMID:38181585)
  • FNDC4 reduces hepatocyte inflammatory cell death via AMPKalpha in metabolic dysfunction-associated steatotic liver disease. (PMID:39173437)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusFndc4ENSMUSG00000038552
rattus_norvegicusFndc4ENSRNOG00000051056

Paralogs (1): FNDC5 (ENSG00000160097)

Protein

Protein identifiers

Fibronectin type III domain-containing protein 4Q9H6D8 (reviewed: Q9H6D8)

Alternative names: Fibronectin type III repeat-containing protein 1

All UniProt accessions (1): Q9H6D8

UniProt curated annotations — full annotation on UniProt →

Function. Has anti-inflammatory properties. In the colon, acts on macrophages to down-regulate inflammation. May suppress osteoclastogenesis and mature osteoclast resorptive function. In white adipose tissue, decreases local inflammation, via interaction with GPR116. Also required for proper systemic glucose tolerance, specifically sensitizing white adipocytes to insulin and promoting glucose uptake. The insulin sensitizing function in adipose tissue is mediated by interaction with ADGRF5/GPR116 and activation of cAMP signaling.

Subcellular location. Membrane Secreted.

Tissue specificity. Highly expressed in the liver and the brain, including in the cortex, hypothalamus and hippocampus. Also expressed in adipose tissue.

Induction. Up-regulated by inflammation in the intestine. Up-regulated by TGFB1 in a colorectal adenocarcinoma cell line.

RefSeq proteins (1): NP_073734* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003961FN3_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR052120FNDC_type_III_4/5Family

Pfam: PF00041

UniProt features (13 total): glycosylation site 3, chain 2, topological domain 2, region of interest 2, signal peptide 1, transmembrane region 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H6D8-F170.270.35

Functional residue map

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

Glycosylation sites (3): 52, 97, 147

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): GOBP_INFLAMMATORY_RESPONSE, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_NEGATIVE_REGULATION_OF_DEFENSE_RESPONSE, LASTOWSKA_COAMPLIFIED_WITH_MYCN, GOBP_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE, GOBP_RESPONSE_TO_GROWTH_FACTOR, GOBP_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_INFLAMMATORY_RESPONSE, GOBP_REGULATION_OF_DEFENSE_RESPONSE, CUI_TCF21_TARGETS_2_UP

GO Biological Process (2): negative regulation of inflammatory response (GO:0050728), response to transforming growth factor beta (GO:0071559)

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

GO Cellular Component (5): obsolete extracellular space (GO:0005615), endoplasmic reticulum (GO:0005783), plasma membrane (GO:0005886), extracellular region (GO:0005576), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
inflammatory response1
negative regulation of defense response1
negative regulation of response to external stimulus1
regulation of inflammatory response1
response to growth factor1
binding1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
membrane1
cell periphery1

Protein interactions and networks

STRING

572 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FNDC4FN1P02751643
FNDC4ADGRF5Q8IZF2633
FNDC4ZNF512Q96ME7594
FNDC4EIF2B4Q9UI10584
FNDC4SPATA31H1Q68DN1570
FNDC4KRTCAP3Q53RY4565
FNDC4ATRAIDQ6UW56557
FNDC4CCDC121Q6ZUS5542
FNDC4SNX17Q15036541
FNDC4CCDC61Q9Y6R9536
FNDC4NRBP1Q9UHY1512
FNDC4PINLYPA6NC86505
FNDC4FNDC3AQ9Y2H6505
FNDC4GTF3C2Q8WUA4469
FNDC4HIC2Q96JB3462

IntAct

4 interactions, top by confidence:

ABTypeScore
FNDC4POLR2Gpsi-mi:“MI:0915”(physical association)0.370
FNDC4MT-ND2psi-mi:“MI:0914”(association)0.350
FNDC4NDUFB3psi-mi:“MI:0914”(association)0.350

BioGRID (39): SAFB2 (Affinity Capture-MS), GHITM (Affinity Capture-MS), AGPAT3 (Affinity Capture-MS), LIMA1 (Affinity Capture-MS), GALNT11 (Affinity Capture-MS), TRPM4 (Affinity Capture-MS), SLC9A6 (Affinity Capture-MS), CAV1 (Affinity Capture-MS), NDUFB3 (Affinity Capture-MS), INTS7 (Affinity Capture-MS), PPP1R10 (Affinity Capture-MS), MPRIP (Affinity Capture-MS), ND5 (Affinity Capture-MS), ALG10 (Affinity Capture-MS), HLA-DRB1 (Affinity Capture-MS)

ESM2 similar proteins: A6NLX4, A6QNY1, A6QPL2, A9CBA0, B2RTN2, D3ZF92, O43278, O75509, O88472, P30203, P98154, P98162, Q1JQE1, Q1RMT9, Q29RT9, Q3U515, Q56A20, Q5BIR3, Q5HZW5, Q5RCS3, Q5XIX0, Q61003, Q64322, Q6AXU5, Q6UWV7, Q7TMJ8, Q7TQH7, Q7Z4F1, Q86T13, Q86XT9, Q8BH27, Q8BSU2, Q8CB67, Q8TEF2, Q8VCP9, Q91ZV2, Q91ZV3, Q921R4, Q96FE7, Q96PD2

Diamond homologs: A6QPL2, O18016, O18023, Q1L867, Q3TR08, Q8K3V5, Q8K4Z2, Q8NAU1, Q8WZ42, Q98949, Q9H6D8, B0V2N1, F1NWE3, G5EF96, Q13332, Q64605, Q8AV57, P16621

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance15
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

895 predictions. Top by Δscore:

VariantEffectΔscore
2:27492476:TTTC:Tacceptor_loss1.0000
2:27492477:TTCTG:Tacceptor_loss1.0000
2:27492478:TC:Tacceptor_loss1.0000
2:27492479:C:CCacceptor_gain1.0000
2:27492479:CTGT:Cacceptor_loss1.0000
2:27492687:T:TAdonor_gain1.0000
2:27492688:C:Adonor_gain1.0000
2:27492788:CAG:Cacceptor_gain1.0000
2:27492791:C:CCacceptor_gain1.0000
2:27493383:A:ACdonor_gain1.0000
2:27493384:C:CCdonor_gain1.0000
2:27493385:TCAC:Tdonor_loss1.0000
2:27493386:CAC:Cdonor_loss1.0000
2:27493387:A:ACdonor_gain1.0000
2:27493387:ACCAG:Adonor_gain1.0000
2:27493388:C:CCdonor_gain1.0000
2:27493388:CCAG:Cdonor_gain1.0000
2:27493388:CCAGC:Cdonor_gain1.0000
2:27493407:C:CTdonor_gain1.0000
2:27493427:T:TAdonor_gain1.0000
2:27493428:C:Adonor_gain1.0000
2:27493475:TCAC:Tacceptor_gain1.0000
2:27493476:CACC:Cacceptor_gain1.0000
2:27493479:C:CAacceptor_loss1.0000
2:27493479:C:CCacceptor_gain1.0000
2:27494349:A:ACdonor_gain1.0000
2:27494350:C:CCdonor_gain1.0000
2:27494350:CTTG:Cdonor_gain1.0000
2:27494462:CCGGT:Cacceptor_gain1.0000
2:27494463:CGGT:Cacceptor_gain1.0000

AlphaMissense

1498 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:27493395:A:GW180R1.000
2:27493395:A:TW180R1.000
2:27494399:C:AW67C1.000
2:27494399:C:GW67C1.000
2:27494401:A:GW67R0.999
2:27494401:A:TW67R0.999
2:27492774:G:CF187L0.998
2:27492774:G:TF187L0.998
2:27492776:A:GF187L0.998
2:27494400:C:GW67S0.998
2:27494412:G:TA63D0.998
2:27493980:A:GF135S0.997
2:27494368:A:CY78D0.997
2:27494436:A:TV55D0.997
2:27493980:A:CF135C0.996
2:27494361:A:TI80N0.996
2:27494370:C:TG77D0.996
2:27494400:C:AW67L0.996
2:27493979:G:CF135L0.995
2:27493979:G:TF135L0.995
2:27493981:A:GF135L0.995
2:27494066:C:AW106C0.995
2:27494066:C:GW106C0.995
2:27494416:A:GS62P0.995
2:27492784:A:TI184N0.994
2:27494406:A:TV65E0.994
2:27492750:C:AK195N0.993
2:27492750:C:GK195N0.993
2:27492775:A:GF187S0.993
2:27494070:A:TL105H0.993

dbSNP variants (sampled 300 via entrez): RS1000571428 (2:27492517 G>C), RS1001692053 (2:27495844 G>A,T), RS1001797559 (2:27497146 G>A), RS1002560298 (2:27496293 G>T), RS1002694619 (2:27495977 T>C), RS1003144153 (2:27492847 C>A), RS1003562709 (2:27495216 C>T), RS1003708065 (2:27494889 C>A,T), RS1004765645 (2:27496328 T>C), RS1005637442 (2:27494914 G>A,C), RS1005733035 (2:27494905 C>A), RS1005764269 (2:27495231 C>G), RS1006001097 (2:27495078 C>T), RS1007502218 (2:27495330 AC>A), RS1007824753 (2:27491673 T>A,C)

Disease associations

OMIM: gene MIM:611905 | disease phenotypes: MIM:615630, MIM:616394

GenCC curated gene-disease

Mondo (2): short-rib thoracic dysplasia 10 with or without polydactyly (MONDO:0014284), retinitis pigmentosa 71 (MONDO:0014618)

Orphanet (2): Jeune syndrome (Orphanet:474), Retinitis pigmentosa (Orphanet:791)

HPO phenotypes

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

GWAS associations

38 associations (top):

StudyTraitp-value
GCST000649_21Chronic kidney disease3.000000e-14
GCST000769_3Calcium levels7.000000e-06
GCST001381_11Menopause (age at onset)2.000000e-12
GCST001698_12Serum total protein levels4.000000e-06
GCST001698_9Serum total protein levels6.000000e-08
GCST001699_7Serum albumin levels3.000000e-14
GCST001699_9Serum albumin levels2.000000e-08
GCST001905_4Hypertriglyceridemia2.000000e-13
GCST002650_1Coffee consumption (cups per day)7.000000e-08
GCST004131_72Inflammatory bowel disease1.000000e-07
GCST004132_64Crohn’s disease6.000000e-11
GCST009391_1135Metabolite levels1.000000e-09
GCST009391_1193Metabolite levels8.000000e-12
GCST009391_1334Metabolite levels7.000000e-08
GCST009391_134Metabolite levels5.000000e-06
GCST009391_1399Metabolite levels3.000000e-06
GCST009391_1436Metabolite levels2.000000e-07
GCST009391_1449Metabolite levels3.000000e-08
GCST009391_1458Metabolite levels5.000000e-08
GCST009391_1504Metabolite levels3.000000e-07
GCST009391_1521Metabolite levels3.000000e-06
GCST009391_1600Metabolite levels3.000000e-08
GCST009391_1613Metabolite levels7.000000e-08
GCST009391_1731Metabolite levels6.000000e-06
GCST009391_1763Metabolite levels6.000000e-06
GCST009391_1815Metabolite levels1.000000e-06
GCST009391_1821Metabolite levels2.000000e-08
GCST009391_1832Metabolite levels2.000000e-07
GCST009391_1840Metabolite levels1.000000e-07
GCST009391_1867Metabolite levels3.000000e-09

EFO canonical traits (33, from GWAS)

EFO IDTrait name
EFO:0004838calcium measurement
EFO:0004704age at menopause
EFO:0004536total blood protein measurement
EFO:0004530triglyceride measurement
EFO:0004330coffee consumption
EFO:0006782cups of coffee per day measurement
EFO:0010458alpha-hydroxybutyric acid measurement
EFO:0009765alanine measurement
EFO:0010362lysophosphatidylcholine 20:3 measurement
EFO:0010355diacylglycerol 36:2 measurement
EFO:0010369lysophosphatidylethanolamine 18:2 measurement
EFO:0010409triacylglycerol 50:2 measurement
EFO:0010410triacylglycerol 50:3 measurement
EFO:0010406triacylglycerol 48:3 measurement
EFO:0010417triacylglycerol 52:5 measurement
EFO:0010418triacylglycerol 52:6 measurement
EFO:0010377phosphatidylcholine 34:3 measurement
EFO:0010378phosphatidylcholine 34:4 measurement
EFO:0010375phosphatidylcholine 34:1 measurement
EFO:0010370lysophosphatidylethanolamine 20:4 measurement
EFO:0010404triacylglycerol 48:1 measurement
EFO:0010405triacylglycerol 48:2 measurement
EFO:0010412triacylglycerol 50:5 measurement
EFO:0010413triacylglycerol 52:1 measurement
EFO:0010411triacylglycerol 50:4 measurement
EFO:0010414triacylglycerol 52:2 measurement
EFO:0010373phosphatidylcholine 32:1 measurement
EFO:0010374phosphatidylcholine 32:2 measurement
EFO:0007745lactate measurement
EFO:0010356lysophosphatidylcholine 14:0 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, increases methylation, affects methylation3
Fluoxetineincreases expression3
Ketoconazoleincreases expression3
mercuric bromidedecreases expression, affects cotreatment2
Amiodaroneincreases expression2
Amitriptylineincreases expression2
Chlorpromazineincreases expression2
Clozapineincreases expression2
Flecainidedecreases expression, increases expression2
Imipramineincreases expression2
Perhexilineincreases expression2
Silicon Dioxidedecreases expression, increases expression2
Tamoxifenincreases expression2
Thioridazineincreases expression2
Valproic Aciddecreases methylation, affects expression2
Zimeldineincreases expression2
Cyclosporineincreases expression2
Sertralineincreases expression2
bisphenol Aaffects expression1
2,2’-methylenebis(4-methyl-6-tert-butylphenol)affects response to substance, affects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
diallyl trisulfideincreases expression1
chlorcyclizineincreases expression1
CGP 52608affects binding, increases reaction1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
nutlin 3affects cotreatment, increases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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