FIBCD1

gene
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Also known as FLJ14810

Summary

FIBCD1 (fibrinogen C domain containing 1, HGNC:25922) is a protein-coding gene on chromosome 9q34.12, encoding Fibrinogen C domain-containing protein 1 (Q8N539). Acetyl group-binding receptor which shows a high-affinity and calcium-dependent binding to acetylated structures such as chitin, some N-acetylated carbohydrates, and amino acids, but not to their non-acetylated counterparts.

FIBCD1 is a conserved type II transmembrane endocytic receptor that binds chitin and is located primarily in the intestinal brush border (Schlosser et al., 2009 [PubMed 19710473]).

Source: NCBI Gene 84929 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 137 total
  • Druggable target: yes
  • MANE Select transcript: NM_032843

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25922
Approved symbolFIBCD1
Namefibrinogen C domain containing 1
Location9q34.12
Locus typegene with protein product
StatusApproved
AliasesFLJ14810
Ensembl geneENSG00000130720
Ensembl biotypeprotein_coding
OMIM613357
Entrez84929

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000372337, ENST00000372338, ENST00000444139, ENST00000448616, ENST00000451466, ENST00000463475, ENST00000486250, ENST00000872083, ENST00000872084, ENST00000933855, ENST00000933856, ENST00000933857

RefSeq mRNA: 2 — MANE Select: NM_032843 NM_001145106, NM_032843

CCDS: CCDS6937

Canonical transcript exons

ENST00000372338 — 7 exons

ExonStartEnd
ENSE00001457570130902440130904323
ENSE00001613459130924237130924396
ENSE00001636266130923744130923880
ENSE00001767299130911792130911888
ENSE00001772617130905234130905413
ENSE00001920779130938536130939247
ENSE00003515123130929567130930046

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 90.47.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7253 / max 41.7642, expressed in 545 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1028081.0504372
1028070.3998198
1028060.2402140
1028050.03489

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481990.47gold quality
right adrenal gland cortexUBERON:003582783.30gold quality
pancreatic ductal cellCL:000207982.49silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099181.28gold quality
right adrenal glandUBERON:000123380.96gold quality
heart right ventricleUBERON:000208080.50gold quality
adrenal cortexUBERON:000123579.71gold quality
left adrenal gland cortexUBERON:003582579.59gold quality
left testisUBERON:000453379.40gold quality
vena cavaUBERON:000408779.28gold quality
mucosa of transverse colonUBERON:000499179.27gold quality
left adrenal glandUBERON:000123478.95gold quality
left ventricle myocardiumUBERON:000656678.93gold quality
right testisUBERON:000453478.47gold quality
cardiac muscle of right atriumUBERON:000337977.80gold quality
parotid glandUBERON:000183177.57gold quality
testisUBERON:000047377.11gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450276.94silver quality
oocyteCL:000002376.78silver quality
gingival epitheliumUBERON:000194976.58gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047375.70silver quality
superficial temporal arteryUBERON:000161475.06gold quality
biceps brachiiUBERON:000150774.28silver quality
cerebellar vermisUBERON:000472074.26silver quality
gingivaUBERON:000182874.05gold quality
tendon of biceps brachiiUBERON:000818873.98gold quality
body of tongueUBERON:001187673.72gold quality
adrenal glandUBERON:000236973.44gold quality
upper arm skinUBERON:000426373.29gold quality
Ammon’s hornUBERON:000195473.16gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no1.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

104 targeting FIBCD1, 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-4481100.0066.421669
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-451499.9967.101870
HSA-MIR-6744-5P99.9366.82748
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-22-3P99.9368.13917
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-449299.8768.253611
HSA-MIR-444799.8567.812900
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-450399.8571.451869
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-674599.7465.331321
HSA-MIR-149-3P99.7268.223963
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-1296-3P99.7264.04636
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-6883-5P99.6968.053785
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-6762-3P99.6666.941188

Literature-anchored findings (GeneRIF, showing 10)

  • FIBCD1 is a high-affinity receptor for chitin and chitin fragments, and may play an important role in controlling the exposure of intestine to chitin and chitin fragments (PMID:19710473)
  • The recognition unit of FIBCD1 organizes into a noncovalently linked tetrameric structure and uses a hydrophobic funnel (S1) for acetyl group recognition. (PMID:19892701)
  • The high affinity ligand N-acetylmannosamine (ManNAc) binds FIBCD1 in the S1 site, predominantly via the acetyl group with the oxygen and acetamide nitrogen hydrogen-bonded to the protein and the methyl group inserted into a hydrophobic pocket. (PMID:24293368)
  • FIBCD1 is expressed in epithelial cells derived from all three germ layers. Endodermal-derived epithelial cells throughout the gastrointestinal tract and the respiratory system showed high expression of FIBCD1 and also mesodermal-derived cells in the genitourinary system and ectodermal-derived epidermis and sebaceous glands cells expressed FIBCD1. (PMID:29220632)
  • FIBCD1 may be a novel biomarker to evaluate the prognosis of gastric cancer. (PMID:29659669)
  • thses findings support FIBCD1 as a lung epithelial pattern recognition receptor that recognizes the complex Aspergillus fumigatus cell wall polysaccharides and modulates the lung epithelial inflammatory response by suppressing inflammatory mediators and mucins (PMID:30279687)
  • The myokine Fibcd1 is an endogenous determinant of myofiber size and mitigates cancer-induced myofiber atrophy. (PMID:35501350)
  • FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder. (PMID:35916241)
  • The role of FIBCD1 in response to Aspergillus fumigatus in lung epithelial cells. (PMID:36888604)
  • Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen-associated carbohydrate motifs. (PMID:38072065)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriofibcd1bENSDARG00000060393
danio_reriofibcd1aENSDARG00000074640
mus_musculusFibcd1ENSMUSG00000026841
rattus_norvegicusFibcd1ENSRNOG00000009735

Paralogs (25): TNC (ENSG00000041982), FCN1 (ENSG00000085265), ANGPT2 (ENSG00000091879), ANGPT4 (ENSG00000101280), FGL1 (ENSG00000104760), FN1 (ENSG00000115414), TNR (ENSG00000116147), ANGPTL1 (ENSG00000116194), TNN (ENSG00000120332), FGL2 (ENSG00000127951), ANGPTL6 (ENSG00000130812), ANGPTL3 (ENSG00000132855), ANGPTL2 (ENSG00000136859), FCN3 (ENSG00000142748), FNDC7 (ENSG00000143107), ANGPT1 (ENSG00000154188), FCN2 (ENSG00000160339), MFAP4 (ENSG00000166482), ANGPTL4 (ENSG00000167772), TNXB (ENSG00000168477), FGG (ENSG00000171557), FGA (ENSG00000171560), FGB (ENSG00000171564), ANGPTL7 (ENSG00000171819), ANGPTL5 (ENSG00000187151)

Protein

Protein identifiers

Fibrinogen C domain-containing protein 1Q8N539 (reviewed: Q8N539)

All UniProt accessions (4): Q8N539, A3KFJ8, H0Y4Y8, X6RDH7

UniProt curated annotations — full annotation on UniProt →

Function. Acetyl group-binding receptor which shows a high-affinity and calcium-dependent binding to acetylated structures such as chitin, some N-acetylated carbohydrates, and amino acids, but not to their non-acetylated counterparts. Can facilitate the endocytosis of acetylated components.

Subunit / interactions. Homotetramer; disulfide-linked.

Subcellular location. Membrane.

Tissue specificity. Expressed in the small and large intestinal epithelial cells with a highly polarized localization to the apical surface corresponding to the brush border and in the ducts of the salivary gland.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N539-11yes
Q8N539-22

RefSeq proteins (2): NP_001138578, NP_116232* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002181Fibrinogen_a/b/g_C_domDomain
IPR014716Fibrinogen_a/b/g_C_1Homologous_superfamily
IPR020837Fibrinogen_CSConserved_site
IPR036056Fibrinogen-like_CHomologous_superfamily
IPR050373Fibrinogen_C-term_domainFamily

Pfam: PF00147

UniProt features (50 total): strand 14, mutagenesis site 7, helix 7, site 4, splice variant 3, topological domain 2, disulfide bond 2, region of interest 2, binding site 2, chain 1, glycosylation site 1, transmembrane region 1, sequence conflict 1, turn 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
6ZQXX-RAY DIFFRACTION1.84
6ZQYX-RAY DIFFRACTION1.85
6ZQRX-RAY DIFFRACTION1.93
6ZR0X-RAY DIFFRACTION1.94
6ZR3X-RAY DIFFRACTION1.97
4M7HX-RAY DIFFRACTION2
6ZR4X-RAY DIFFRACTION2
4M7FX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N539-F180.610.50

Functional residue map

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

Catalytic / active sites (4): 405 (implicated in ligand binding); 415 (implicated in ligand binding); 431 (implicated in ligand binding); 432 (implicated in ligand binding)

Ligand- & substrate-binding residues (2): 393; 395

Disulfide bonds (2): 244–273, 401–414

Glycosylation sites (1): 340

Mutagenesis-validated functional residues (7):

PositionPhenotype
393complete loss of binding to acetylated bovine serum albumin and reduced binding to chitin; when associated with a-395.
395complete loss of binding to acetylated bovine serum albumin and reduced binding to chitin; when associated with n-395.
405significantly reduced binding to acetylated bovine serum albumin and loss of binding to chitin; when associated with s-4
415complete loss of binding to acetylated bovine serum albumin and chitin.
431significantly reduced binding to acetylated bovine serum albumin and loss of binding to chitin; when associated with s-4
432complete loss of binding to acetylated bovine serum albumin and chitin.
443slight reduction in binding to acetylated bovine serum albumin and no effect on binding to chitin.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): EFC_Q6, IRF7_01, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, RFX1_01, WANG_SMARCE1_TARGETS_UP, TAL1BETAITF2_01, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K27ME3, MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN, GOMF_CHITIN_BINDING, chr9q34, GOCC_EXTERNAL_ENCAPSULATING_STRUCTURE, GSE14415_NATURAL_TREG_VS_TCONV_DN

GO Biological Process (0):

GO Molecular Function (3): chitin binding (GO:0008061), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
carbohydrate derivative binding1
cation binding1
binding1
cellular anatomical structure1

Protein interactions and networks

STRING

564 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FIBCD1ALBP02768495
FIBCD1WFIKKN2Q8TEU8456
FIBCD1QRFPP83859441
FIBCD1OR10W1Q8NGF6422
FIBCD1IGFBP2P18065400
FIBCD1MPPED1O15442398
FIBCD1NOD2Q9HC29392
FIBCD1CLEC7AQ9BXN2386
FIBCD1TMTC4Q5T4D3371
FIBCD1OR9I1Q8NGQ6371
FIBCD1OR2L2Q8NH16366
FIBCD1SOCS3O14543360
FIBCD1WFS1O76024358
FIBCD1PEX5LQ8IYB4351
FIBCD1ZNF586Q9NXT0348

IntAct

15 interactions, top by confidence:

ABTypeScore
NRP1CSNK2A2psi-mi:“MI:0914”(association)0.790
FIBCD1MALpsi-mi:“MI:0915”(physical association)0.720
MALFIBCD1psi-mi:“MI:0915”(physical association)0.720
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
CLDND1TNFRSF10Bpsi-mi:“MI:0914”(association)0.350
TSPAN3SCAMP3psi-mi:“MI:0914”(association)0.350
TMUB2TMEM259psi-mi:“MI:0914”(association)0.350
CD80RIMOC1psi-mi:“MI:0914”(association)0.350
GDPD5TMEM120Bpsi-mi:“MI:0914”(association)0.350
SAAL1TMEM223psi-mi:“MI:0914”(association)0.350
MALFIBCD1psi-mi:“MI:0915”(physical association)0.000

BioGRID (8): FIBCD1 (Two-hybrid), FIBCD1 (Affinity Capture-RNA), MAL (Two-hybrid), FIBCD1 (Phenotypic Suppression), FIBCD1 (Affinity Capture-MS), FIBCD1 (Affinity Capture-MS), FIBCD1 (Affinity Capture-MS), FIBCD1 (Affinity Capture-MS)

ESM2 similar proteins: A2AV25, A5PJQ2, O35764, O43278, O43827, O70165, O95841, O95897, P02675, P02678, P04115, P12804, P14480, P30203, P33573, Q0P4P2, Q14314, Q1RMR1, Q24K15, Q29041, Q29042, Q29RY7, Q2KJ51, Q2TNK5, Q568Y7, Q5EA66, Q5FB95, Q5I2E5, Q5XK91, Q640P2, Q6AX44, Q6TMA8, Q8BM13, Q8IUK5, Q8K0E8, Q8N539, Q8NI99, Q8R0Z6, Q8R1Q3, Q91ZV7

Diamond homologs: A0A8J8, A2AV25, D8VNS7, D8VNS8, D8VNS9, D8VNT0, E2IYB3, E9PV24, O00602, O08538, O15123, O18920, O35460, O35462, O35608, O43827, O70165, O70497, O75636, O77802, O93526, O95841, P02671, P02675, P02676, P02678, P02679, P02680, P04115, P06399, P10039, P12799, P12804, P14448, P14480, P17634, P19477, P21520, P22105, P24821

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance119
Likely benign9
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1316 predictions. Top by Δscore:

VariantEffectΔscore
9:130905231:CAC:Cdonor_loss1.0000
9:130905232:A:ACdonor_gain1.0000
9:130905233:C:CCdonor_gain1.0000
9:130905233:CCTG:Cdonor_gain1.0000
9:130905411:GCCC:Gacceptor_loss1.0000
9:130905412:CC:Cacceptor_gain1.0000
9:130905413:CC:Cacceptor_gain1.0000
9:130905414:C:CCacceptor_gain1.0000
9:130905415:T:Cacceptor_loss1.0000
9:130905420:T:TCacceptor_gain1.0000
9:130911787:CTCA:Cdonor_loss1.0000
9:130911790:A:ATdonor_loss1.0000
9:130911884:AACAC:Aacceptor_gain1.0000
9:130911885:ACAC:Aacceptor_gain1.0000
9:130911886:CAC:Cacceptor_gain1.0000
9:130911886:CACC:Cacceptor_gain1.0000
9:130911889:C:CAacceptor_loss1.0000
9:130911889:C:CCacceptor_gain1.0000
9:130911890:T:Gacceptor_loss1.0000
9:130923736:ACACT:Adonor_loss1.0000
9:130923737:CACTC:Cdonor_loss1.0000
9:130923738:ACTC:Adonor_loss1.0000
9:130923739:CTCA:Cdonor_loss1.0000
9:130923740:TCA:Tdonor_loss1.0000
9:130923741:C:CGdonor_loss1.0000
9:130923742:A:ACdonor_gain1.0000
9:130923742:ACCGT:Adonor_gain1.0000
9:130923743:C:CCdonor_gain1.0000
9:130923743:C:CTdonor_loss1.0000
9:130923743:CCGT:Cdonor_gain1.0000

AlphaMissense

2977 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:130904139:C:AW437C1.000
9:130904139:C:GW437C1.000
9:130904141:A:GW437R1.000
9:130904141:A:TW437R1.000
9:130904208:G:CC414W1.000
9:130904209:C:TC414Y1.000
9:130904220:C:AW410C1.000
9:130904220:C:GW410C1.000
9:130904222:A:GW410R1.000
9:130904222:A:TW410R1.000
9:130904247:A:CC401W1.000
9:130904248:C:AC401F1.000
9:130904248:C:GC401S1.000
9:130904248:C:TC401Y1.000
9:130904249:A:TC401S1.000
9:130904290:A:GF387S1.000
9:130904140:C:GW437S0.999
9:130904182:T:CY423C0.999
9:130904183:A:CY423D0.999
9:130904188:C:AG421V0.999
9:130904188:C:TG421E0.999
9:130904189:C:AG421W0.999
9:130904190:A:CN420K0.999
9:130904190:A:TN420K0.999
9:130904196:G:CN418K0.999
9:130904196:G:TN418K0.999
9:130904200:G:AS417F0.999
9:130904200:G:TS417Y0.999
9:130904207:G:CH415D0.999
9:130904209:C:AC414F0.999

dbSNP variants (sampled 300 via entrez): RS1000000314 (9:130928131 T>A), RS1000011666 (9:130902133 T>C), RS1000021119 (9:130933026 T>A), RS1000066641 (9:130909705 T>C), RS1000109547 (9:130927850 G>A), RS1000145613 (9:130923791 C>T), RS1000202996 (9:130919306 A>G), RS1000265589 (9:130923639 T>C,G), RS1000392947 (9:130920669 C>G), RS1000392988 (9:130915468 C>T), RS1000424873 (9:130919566 C>T), RS1000713593 (9:130917247 C>T), RS1000730943 (9:130937111 T>A), RS1000756267 (9:130919768 G>A,T), RS1000905587 (9:130908768 C>G,T)

Disease associations

OMIM: gene MIM:613357 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST006479_86Diverticular disease1.000000e-06
GCST008667_2Smoking status (heavy vs never)4.000000e-07
GCST010988_435Adult body size1.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0009959diverticular disease
EFO:0006527smoking status measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523397 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
entinostatincreases expression, affects cotreatment2
aminomethylphosphonic acid (AMPA)decreases expression1
bisphenol Adecreases methylation1
kojic aciddecreases expression1
ethyl-p-hydroxybenzoatedecreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arseniteincreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
aflatoxin B2decreases methylation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Amiodaroneincreases expression1
Atrazineincreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1
Diazinonincreases methylation1
Estradiolaffects cotreatment, increases expression1
Fluorouracildecreases expression1
Plant Extractsdecreases expression, affects cotreatment1
Silicon Dioxidedecreases expression1
Testosteronedecreases expression1
Urethanedecreases expression1
Valproic Acidaffects expression1
2,4-Dichlorophenoxyacetic Aciddecreases expression1
Aflatoxin B1decreases methylation1
Cadmium Chlorideincreases abundance, increases palmitoylation, decreases reaction1
Okadaic Aciddecreases expression1

ChEMBL screening assays

4 unique, capped per target: 4 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4419299BindingBinding affinity to V5-His tagged FIBCD1 ecto-domain (54 to 461 residues) (unknown origin) assessed as reduction in binding between FIBCD1 and acetylated BSA at 50 mM by ELISA relative to controlFibcd1 for the prevention and treatment of diseases

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.