CIDEB

gene
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Summary

CIDEB (cell death inducing DFFA like effector b, HGNC:1977) is a protein-coding gene on chromosome 14q12, encoding Lipid transferase CIDEB (Q9UHD4). Lipid transferase specifically expressed in hepatocytes, which promotes unilocular lipid droplet formation by mediating lipid droplet fusion.

Enables identical protein binding activity. Involved in lipid droplet fusion and positive regulation of apoptotic process. Acts upstream of or within apoptotic process. Located in cytosol and perinuclear region of cytoplasm. Is active in lipid droplet.

Source: NCBI Gene 27141 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 117 total
  • MANE Select transcript: NM_001393339

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1977
Approved symbolCIDEB
Namecell death inducing DFFA like effector b
Location14q12
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000136305
Ensembl biotypeprotein_coding
OMIM604441
Entrez27141

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 22 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000258807, ENST00000336557, ENST00000554411, ENST00000555471, ENST00000555817, ENST00000556756, ENST00000885634, ENST00000885635, ENST00000885636, ENST00000885637, ENST00000885638, ENST00000885639, ENST00000885640, ENST00000885641, ENST00000885642, ENST00000885643, ENST00000885644, ENST00000885645, ENST00000885646, ENST00000885647, ENST00000885648, ENST00000885649, ENST00000885650, ENST00000967605

RefSeq mRNA: 9 — MANE Select: NM_001393339 NM_001318807, NM_001393334, NM_001393335, NM_001393336, NM_001393337, NM_001393338, NM_001393339, NM_001393340, NM_014430

CCDS: CCDS32056

Canonical transcript exons

ENST00000554411 — 5 exons

ExonStartEnd
ENSE000006544282430594724306137
ENSE000006544292430637424306523
ENSE000006544302430737124307515
ENSE000022365722430518724305765
ENSE000024565282430781824307977

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.37.

FANTOM5 (CAGE): breadth broad, TPM avg 6.1223 / max 800.5828, expressed in 771 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1425932.8201570
1425881.729783
1425890.715669
1425900.3889195
1425910.2928163
1425940.094741
1425870.046414
1425920.034112

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111498.37gold quality
liverUBERON:000210798.33gold quality
duodenumUBERON:000211498.27gold quality
spleenUBERON:000210695.77gold quality
granulocyteCL:000009493.63gold quality
leukocyteCL:000073892.55gold quality
monocyteCL:000057692.54gold quality
bloodUBERON:000017892.11gold quality
adrenal tissueUBERON:001830391.82gold quality
small intestineUBERON:000210891.48gold quality
small intestine Peyer’s patchUBERON:000345491.15gold quality
esophagus mucosaUBERON:000246990.27gold quality
adult mammalian kidneyUBERON:000008289.83gold quality
left adrenal gland cortexUBERON:003582589.29gold quality
lower esophagus mucosaUBERON:003583488.90gold quality
left adrenal glandUBERON:000123488.65gold quality
adrenal glandUBERON:000236988.37gold quality
right adrenal glandUBERON:000123388.28gold quality
left ovaryUBERON:000211987.97gold quality
right adrenal gland cortexUBERON:003582787.60gold quality
kidneyUBERON:000211387.55gold quality
ovaryUBERON:000099287.36gold quality
right ovaryUBERON:000211887.33gold quality
cortex of kidneyUBERON:000122586.89gold quality
bone marrowUBERON:000237186.81gold quality
olfactory segment of nasal mucosaUBERON:000538686.14gold quality
bone marrow cellCL:000209285.87gold quality
skin of abdomenUBERON:000141685.85gold quality
zone of skinUBERON:000001485.65gold quality
skin of legUBERON:000151185.54gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.26

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF

miRNA regulators (miRDB)

35 targeting CIDEB, 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-211099.9666.681930
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-427199.8868.322244
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-430799.8270.453374
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-509399.6769.262291
HSA-MIR-320299.6667.702737
HSA-MIR-431099.5968.842527
HSA-MIR-4728-3P99.4768.94981
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-431699.3765.751360
HSA-MIR-450599.2767.812678
HSA-MIR-578799.2267.862628
HSA-MIR-491-5P99.1365.981468
HSA-MIR-66199.0965.942062
HSA-MIR-4695-5P99.0664.871151
HSA-MIR-3145-3P98.8569.072031
HSA-MIR-4700-5P98.6367.431915
HSA-MIR-445098.2668.35725
HSA-MIR-1212698.0964.82637
HSA-MIR-63797.9164.051517
HSA-MIR-6728-5P97.7966.33891
HSA-MIR-6783-5P97.6767.211528
HSA-MIR-3127-5P97.5265.24786
HSA-MIR-606997.4565.88357
HSA-MIR-194-3P97.3665.961027
HSA-MIR-215-3P97.0268.011209
HSA-MIR-4695-3P96.7167.21836

Literature-anchored findings (GeneRIF, showing 14)

  • A novel mechanism for the cell-specific transcription of the human CIDE-B gene, which involves epigenetic and genetic control at separate respective promoters is reported. (PMID:16248853)
  • PGC-1alpha plays an important role in partitioning cytoplasmic TG toward the VLDL secretory compartments and promoting VLDL secretion via transcriptional induction of CideB. (PMID:20551328)
  • CIDE proteins expression correlate with tumor and survival characteristics in patients with renal cell carcinoma. (PMID:23475172)
  • this work highlights CIDEB’s role in lipid droplet (LD) fusion, and presents a new model system to study the PGC-1alpha/CIDEB pathway’s role in LD dynamics and the VLDL pathway. (PMID:24161736)
  • Authors found CIDEB to be an essential cofactor for hepatitis C virus entry into hepatocytes. (PMID:24829338)
  • these data revealed that Cideb plays an important role in controlling intestinal chylomicron lipidation. (PMID:24831470)
  • CIDEB can act as an anti-HCV host factor and contribute to altered triglyceride homeostasis. (PMID:24980280)
  • CIDEB downregulation may contribute to HCV-induced hepatic steatosis (PMID:26865724)
  • this study shows that C5a signaling induces apoptosis in brain vascular endothelial cells in experimental lupus through activation of CIDEB (PMID:27213693)
  • CIDEB interacts with the HCV NS5A protein, and the N terminus of CIDEB and the domain I of NS5A are involved in this interaction. (PMID:27282740)
  • High Cideb expression is associated with Ulcerative Colitis. (PMID:28719542)
  • The Differential Expression of Cide Family Members is Associated with Nafld Progression from Steatosis to Steatohepatitis. (PMID:31097771)
  • Association of CIDEB gene promoter methylation with overweight or obesity in adults. (PMID:35475772)
  • Germline Mutations in CIDEB and Protection against Liver Disease. (PMID:35939579)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocidebENSDARG00000012640
mus_musculusCidebENSMUSG00000022219
rattus_norvegicusCidebENSRNOG00000020377
drosophila_melanogasterDrep2FBGN0028408

Paralogs (3): DFFA (ENSG00000160049), CIDEA (ENSG00000176194), CIDEC (ENSG00000187288)

Protein

Protein identifiers

Lipid transferase CIDEBQ9UHD4 (reviewed: Q9UHD4)

Alternative names: Cell death activator CIDE-B, Cell death-inducing DFFA-like effector B

All UniProt accessions (2): Q9UHD4, G3V4E2

UniProt curated annotations — full annotation on UniProt →

Function. Lipid transferase specifically expressed in hepatocytes, which promotes unilocular lipid droplet formation by mediating lipid droplet fusion. Lipid droplet fusion promotes their enlargement, restricting lipolysis and favoring lipid storage. Localizes on the lipid droplet surface, at focal contact sites between lipid droplets, and mediates atypical lipid droplet fusion by promoting directional net neutral lipid transfer from the smaller to larger lipid droplets. The transfer direction may be driven by the internal pressure difference between the contacting lipid droplet pair. Promotes lipid exchange and lipid droplet fusion in both small and large lipid droplet-containing hepatocytes. In addition to its role in lipid droplet fusion, also involved in cytoplasmic vesicle biogenesis and transport. Required for very-low-density lipoprotein (VLDL) lipidation and maturation. Probably involved in the biogenesis of VLDL transport vesicles by forming a COPII vesicle coat and facilitating the formation of endoplasmic reticulum-derived large vesicles. Also involved in sterol-regulated export of the SCAP-SREBP complex, composed of SCAP, SREBF1/SREBP1 and SREBF2/SREBP2, by promoting loading of SCAP-SREBP into COPII vesicles. May also activate apoptosis. (Microbial infection) Involved in Hepatatis C virus (HCV) assembly and required for HCV entry into hepatocytes.

Subunit / interactions. Interacts with DFFA. Interacts with DFFB; inhibited by DFFB. Interacts with APOB. Interacts with PREB/SEC12; facilitating loading of SCAP-SREBP into COPII vesicles. (Microbial infection) Interacts (via N-terminus) with HCV non-structural protein 5A (via N-terminus); this interaction seems to regulate the association of HCV particles with ApoE.

Subcellular location. Lipid droplet. Endoplasmic reticulum membrane. Golgi apparatus. Cytoplasmic vesicle. COPI-coated vesicle.

Tissue specificity. Highly expressed in liver and small intestine and, at lower levels, in colon, kidney and spleen.

Similarity. Belongs to the CIDE family.

RefSeq proteins (9): NP_001305736, NP_001380263, NP_001380264, NP_001380265, NP_001380266, NP_001380267, NP_001380268, NP_001380269, NP_055245 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003508CIDE-N_domDomain

Pfam: PF02017

UniProt features (15 total): strand 7, sequence conflict 3, helix 2, chain 1, domain 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1D4BSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UHD4-F173.400.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 177 (showing top): GOBP_REGULATION_OF_TRIGLYCERIDE_METABOLIC_PROCESS, GNF2_GSTM1, GOBP_VESICLE_ORGANIZATION, GCANCTGNY_MYOD_Q6, GNF2_HPN, LUCAS_HNF4A_TARGETS_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_LIPID_COMPLEX_ASSEMBLY, chr14q12, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOCC_COATED_VESICLE, GNF2_LCAT

GO Biological Process (11): apoptotic process (GO:0006915), intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630), lipid storage (GO:0019915), response to nutrient levels (GO:0031667), very-low-density lipoprotein particle assembly (GO:0034379), positive regulation of apoptotic process (GO:0043065), COPII-coated vesicle cargo loading (GO:0090110), regulation of triglyceride metabolic process (GO:0090207), execution phase of apoptosis (GO:0097194), lipid droplet fusion (GO:0160077), intermembrane lipid transfer (GO:0120009)

GO Molecular Function (5): identical protein binding (GO:0042802), molecular adaptor activity (GO:0060090), phosphatidic acid binding (GO:0070300), lipid transfer activity (GO:0120013), protein binding (GO:0005515)

GO Cellular Component (11): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), lipid droplet (GO:0005811), cytosol (GO:0005829), COPII vesicle coat (GO:0030127), COPI-coated vesicle (GO:0030137), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm5
cellular anatomical structure4
apoptotic process2
binding2
endomembrane system2
intracellular membrane-bounded organelle2
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
DNA damage response1
intrinsic apoptotic signaling pathway1
nutrient storage1
response to stimulus1
plasma lipoprotein particle assembly1
regulation of apoptotic process1
positive regulation of programmed cell death1
vesicle cargo loading1
intracellular transport1
COPII-coated vesicle budding1
triglyceride metabolic process1
regulation of lipid metabolic process1
cellular process1
bleb assembly1
lipid droplet organization1
organelle fusion1
lipid transport1
membrane organization1
protein binding1
molecular_function1
phospholipid binding1
anion binding1
transporter activity1
lipid carrier activity1
intermembrane lipid transfer1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
intracellular membraneless organelle1
ER to Golgi transport vesicle membrane1
vesicle coat1

Protein interactions and networks

STRING

943 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CIDEBDFFAO00273937
CIDEBDFFBO76075904
CIDEBLAMP1P11279871
CIDEBAPOBP04114789
CIDEBPLIN1O60240729
CIDEBFASP25445629
CIDEBCASP3P42574601
CIDEBAOC3Q16853599
CIDEBMTTPP55157551
CIDEBLAMP2P13473545
CIDEBEEA1Q15075544
CIDEBKLRG1Q96E93540
CIDEBPTPRCP08575528
CIDEBIFNGP01579526
CIDEBPLIN2Q99541521

IntAct

225 interactions, top by confidence:

ABTypeScore
CIDEBCIDEBpsi-mi:“MI:0915”(physical association)0.700
CIDEBMVB12Apsi-mi:“MI:0915”(physical association)0.560
TBX2CIDEBpsi-mi:“MI:0915”(physical association)0.560
FUNDC2CIDEBpsi-mi:“MI:0915”(physical association)0.560
SMARCC1CIDEBpsi-mi:“MI:0915”(physical association)0.560
NFU1CIDEBpsi-mi:“MI:0915”(physical association)0.560
CIDEBRHBDD2psi-mi:“MI:0915”(physical association)0.560
COL10A1CIDEBpsi-mi:“MI:0915”(physical association)0.560
SCO2CIDEBpsi-mi:“MI:0915”(physical association)0.560
MESTCIDEBpsi-mi:“MI:0915”(physical association)0.560
SPG21CIDEBpsi-mi:“MI:0915”(physical association)0.560
TEX44CIDEBpsi-mi:“MI:0915”(physical association)0.560
TIMM17BCIDEBpsi-mi:“MI:0915”(physical association)0.560
ABHD16ACIDEBpsi-mi:“MI:0915”(physical association)0.560
CLCN1CIDEBpsi-mi:“MI:0915”(physical association)0.560
PPIFCIDEBpsi-mi:“MI:0915”(physical association)0.560
DHRSXCIDEBpsi-mi:“MI:0915”(physical association)0.560
TSR1CIDEBpsi-mi:“MI:0915”(physical association)0.560
PBX3CIDEBpsi-mi:“MI:0915”(physical association)0.560
PDHXCIDEBpsi-mi:“MI:0915”(physical association)0.560
PISDCIDEBpsi-mi:“MI:0915”(physical association)0.560
CAND2CIDEBpsi-mi:“MI:0915”(physical association)0.560
SCO1CIDEBpsi-mi:“MI:0915”(physical association)0.560
FKBP8CIDEBpsi-mi:“MI:0915”(physical association)0.560

BioGRID (81): MVB12A (Affinity Capture-MS), MVB12A (Affinity Capture-MS), CIDEB (Affinity Capture-RNA), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid), CIDEB (Two-hybrid)

ESM2 similar proteins: A0A8M9QN10, A1BPI0, A2ARM1, A2CI97, A2CI98, A2CJ06, C9JE40, O15055, O43147, O54943, O70173, O70303, O70361, O95238, P0C2N6, P0C6P5, P56645, P59025, P59729, P97433, Q0P4K8, Q3TD16, Q5EB20, Q5PQS0, Q5SSZ5, Q5VUB5, Q6IRN0, Q6P4K6, Q76I79, Q7TSI1, Q80TQ5, Q80UW3, Q810F8, Q8C8C1, Q8CCC3, Q8CJE2, Q8N1W1, Q8ND61, Q8TB24, Q8WWF5

Diamond homologs: F1MN90, O00273, O54786, O60543, O70302, O70303, P56198, Q3T191, Q5XI33, Q96AQ7, Q9UHD4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 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
Aerobic respiration and respiratory electron transport614.8×5e-04
Respiratory electron transport513.2×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance98
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

667 predictions. Top by Δscore:

VariantEffectΔscore
14:24306134:CACT:Cacceptor_gain1.0000
14:24306136:CT:Cacceptor_gain1.0000
14:24306370:TTACC:Tdonor_loss1.0000
14:24306371:TACC:Tdonor_loss1.0000
14:24306372:A:ACdonor_gain1.0000
14:24306372:AC:Adonor_gain1.0000
14:24306372:ACC:Adonor_gain1.0000
14:24306372:ACCC:Adonor_loss1.0000
14:24306373:C:CCdonor_gain1.0000
14:24306373:CC:Cdonor_gain1.0000
14:24306373:CCC:Cdonor_gain1.0000
14:24306402:TGCAA:Tdonor_gain1.0000
14:24306519:AATGC:Aacceptor_gain1.0000
14:24306520:ATGC:Aacceptor_gain1.0000
14:24306521:TGC:Tacceptor_gain1.0000
14:24306522:GC:Gacceptor_gain1.0000
14:24306523:CC:Cacceptor_gain1.0000
14:24306523:CCT:Cacceptor_loss1.0000
14:24306524:C:CCacceptor_gain1.0000
14:24306528:CCAA:Cacceptor_gain1.0000
14:24306529:C:CTacceptor_gain1.0000
14:24306529:C:Tacceptor_gain1.0000
14:24306530:A:Tacceptor_gain1.0000
14:24306531:A:ACacceptor_gain1.0000
14:24306531:A:Cacceptor_gain1.0000
14:24306535:C:CTacceptor_gain1.0000
14:24306536:A:Tacceptor_gain1.0000
14:24307365:A:ACdonor_gain1.0000
14:24307366:C:CCdonor_gain1.0000
14:24307366:CTTA:Cdonor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000076387 (14:24308808 C>A), RS1000519268 (14:24309126 A>C), RS1000657788 (14:24313263 G>A), RS1001512399 (14:24310053 C>T), RS1001777583 (14:24312013 T>A,C), RS1001807949 (14:24308372 A>G), RS1002566053 (14:24313250 C>T), RS1003131748 (14:24307754 G>A), RS1003612742 (14:24308066 C>T), RS1003777466 (14:24304905 G>A), RS1003797456 (14:24305241 A>C,G), RS1003920918 (14:24305611 G>A,C,T), RS1004174576 (14:24304827 A>C), RS1004288668 (14:24310888 C>T), RS1004397389 (14:24305083 A>C,G)

Disease associations

OMIM: gene MIM:604441 | 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
GCST002371_1Parent of origin effect on language impairment (paternal)4.000000e-08
GCST008163_14Height4.000000e-06
GCST010206_7Anorectal malformation4.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression, increases expression3
Cyclosporinedecreases expression3
sodium arsenitedecreases expression, increases expression2
Arsenic Trioxidedecreases expression, increases expression2
Fluorouracilincreases expression2
Silicon Dioxidedecreases expression2
Aflatoxin B1decreases expression, affects expression2
methyleugenoldecreases expression1
propionaldehydedecreases expression1
VX-agentincreases expression1
cobaltous chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
2,3-dimethoxy-1,4-naphthoquinonedecreases expression1
usnic acidincreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
pinostrobinincreases expression1
Bortezomibdecreases expression1
Rosiglitazonedecreases expression1
Troglitazonedecreases expression1
Acetaminophendecreases expression1
Arsenicaffects cotreatment, decreases expression1
Benzo(a)pyrenedecreases expression1
Cadmiumdecreases expression1
Cisplatinincreases expression1
Dimethylnitrosaminedecreases expression1
Endosulfandecreases expression, affects cotreatment1
Estradioldecreases expression1
Fluoridesaffects cotreatment, decreases expression1
Folic Acidaffects expression1

Clinical trials (associated diseases)

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