CC2D1B

gene
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Also known as KIAA1836Freud-2Lgd1

Summary

CC2D1B (coiled-coil and C2 domain containing 1B, HGNC:29386) is a protein-coding gene on chromosome 1p32.3, encoding Coiled-coil and C2 domain-containing protein 1B (Q5T0F9). Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm.

Source: NCBI Gene 200014 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 209 total
  • MANE Select transcript: NM_001330585

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29386
Approved symbolCC2D1B
Namecoiled-coil and C2 domain containing 1B
Location1p32.3
Locus typegene with protein product
StatusApproved
AliasesKIAA1836, Freud-2, Lgd1
Ensembl geneENSG00000154222
Ensembl biotypeprotein_coding
Entrez200014

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 17 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000284376, ENST00000371586, ENST00000438021, ENST00000450942, ENST00000460261, ENST00000460370, ENST00000470844, ENST00000485966, ENST00000491136, ENST00000492426, ENST00000494789, ENST00000886668, ENST00000886669, ENST00000886670, ENST00000886671, ENST00000886672, ENST00000886673, ENST00000917745, ENST00000917746, ENST00000917747, ENST00000941872, ENST00000941873, ENST00000941874, ENST00000941875

RefSeq mRNA: 2 — MANE Select: NM_001330585 NM_001330585, NM_032449

CCDS: CCDS30714, CCDS81323

Canonical transcript exons

ENST00000284376 — 25 exons

ExonStartEnd
ENSE000014555615236606952366205
ENSE000034855705235902752359157
ENSE000034872085236007452360233
ENSE000034973305235539852355449
ENSE000034995445235833152358461
ENSE000035322265236097452361132
ENSE000035346205235560852355666
ENSE000035440035235778152357898
ENSE000035508655235868652358758
ENSE000035664895236042452360549
ENSE000035910185235577152355844
ENSE000035981425235484052354939
ENSE000035985275235618652356302
ENSE000036011625235700152357126
ENSE000036088465235638452356442
ENSE000036130675235925052359357
ENSE000036402415236151352361616
ENSE000036427395235970552359883
ENSE000036501525235752652357698
ENSE000036551785235945952359534
ENSE000036632045235460852354698
ENSE000036670835236455252364634
ENSE000036691995236260252362746
ENSE000036757465235351852353647
ENSE000039063405235059752353223

Expression profiles

Bgee: expression breadth ubiquitous, 226 present calls, max score 95.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.4628 / max 133.8733, expressed in 1811 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1235712.46281811

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adenohypophysisUBERON:000219695.80gold quality
right lobe of thyroid glandUBERON:000111995.22gold quality
metanephros cortexUBERON:001053394.91gold quality
nerveUBERON:000102194.88gold quality
tibial nerveUBERON:000132394.88gold quality
left lobe of thyroid glandUBERON:000112094.80gold quality
lower esophagus mucosaUBERON:003583494.36gold quality
C1 segment of cervical spinal cordUBERON:000646994.11gold quality
pituitary glandUBERON:000000794.07gold quality
upper lobe of left lungUBERON:000895293.40gold quality
thyroid glandUBERON:000204693.29gold quality
granulocyteCL:000009493.05gold quality
right ovaryUBERON:000211892.67gold quality
left testisUBERON:000453392.54gold quality
left ovaryUBERON:000211992.41gold quality
right testisUBERON:000453492.38gold quality
upper lobe of lungUBERON:000894892.37gold quality
spinal cordUBERON:000224091.99gold quality
right hemisphere of cerebellumUBERON:001489091.90gold quality
minor salivary glandUBERON:000183091.72gold quality
mucosa of transverse colonUBERON:000499191.68gold quality
adrenal tissueUBERON:001830391.68gold quality
body of uterusUBERON:000985391.54gold quality
right uterine tubeUBERON:000130291.32gold quality
right adrenal gland cortexUBERON:003582791.19gold quality
body of pancreasUBERON:000115090.95gold quality
spleenUBERON:000210690.83gold quality
cerebellar hemisphereUBERON:000224590.83gold quality
right lungUBERON:000216790.80gold quality
small intestine Peyer’s patchUBERON:000345490.75gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.04
E-MTAB-6058no99.05

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
HTR1ARepression

miRNA regulators (miRDB)

133 targeting CC2D1B, 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-9-5P100.0072.282361
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4692100.0067.322066
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-451499.9967.101870
HSA-MIR-428299.9975.366408
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-806899.9873.852376
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548AN99.9770.912817
HSA-MIR-314899.9775.066478
HSA-MIR-365899.9673.874379
HSA-MIR-211099.9666.681930
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-497-5P99.9271.832674
HSA-MIR-311999.9271.342390
HSA-MIR-454-3P99.9174.011925
HSA-MIR-568099.9169.833421
HSA-MIR-195-5P99.9072.812805
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780

Literature-anchored findings (GeneRIF, showing 5)

  • Paper describes a function of Cc2d1b/Cc2d1a and their Drosophila homologue l(2)gd in D.melanogaster in Notch trafficking. (PMID:17084358)
  • Human Freud-2/CC2D1B binds to the 5-HT1A dual repressor element and represses the human 5-HT1A receptor gene to regulate its expression in non-serotonergic cells and neurons. (PMID:19423080)
  • CC2D1B regulates degradation and signaling of EGFR and TLR4. (PMID:27769858)
  • CC2D1B is essential for ESCRT-III activity during mitotic reformation of the nuclear envelope. (PMID:30513301)
  • Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer. (PMID:33034024)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocc2d1bENSDARG00000099445
mus_musculusCc2d1bENSMUSG00000028582
rattus_norvegicusCc2d1bENSRNOG00000008634
drosophila_melanogasterl(2)gd1FBGN0261983
caenorhabditis_elegansccct-1WBGENE00012578

Paralogs (1): CC2D1A (ENSG00000132024)

Protein

Protein identifiers

Coiled-coil and C2 domain-containing protein 1BQ5T0F9 (reviewed: Q5T0F9)

Alternative names: Five prime repressor element under dual repression-binding protein 2

All UniProt accessions (3): Q5T0F9, H0Y517, H7C1U3

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells.

Subunit / interactions. Interacts with CHMP4B.

Subcellular location. Nucleus.

Tissue specificity. Widely distributed in brain and peripheral tissues.

Similarity. Belongs to the CC2D1 family.

Isoforms (5)

UniProt IDNamesCanonical?
Q5T0F9-11yes
Q5T0F9-22
Q5T0F9-33
Q5T0F9-44
Q5T0F9-55

RefSeq proteins (2): NP_001317514, NP_115825 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR006608CC2D1A/B_DM14Domain
IPR035892C2_domain_sfHomologous_superfamily
IPR037772C2_FreudDomain
IPR039725CC2D1A/BFamily

Pfam: PF00168, PF21528

UniProt features (24 total): splice variant 7, region of interest 5, compositionally biased region 4, modified residue 3, coiled-coil region 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5T0F9-F171.980.32

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 (3): 209, 593, 596

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-9668328Sealing of the nuclear envelope (NE) by ESCRT-III
R-HSA-1640170Cell Cycle
R-HSA-2555396Mitotic Metaphase and Anaphase
R-HSA-2995410Nuclear Envelope (NE) Reassembly
R-HSA-68882Mitotic Anaphase
R-HSA-68886M Phase
R-HSA-69278Cell Cycle, Mitotic

MSigDB gene sets: 109 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GTGCCTT_MIR506, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOCC_NUCLEAR_ENVELOPE, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOCC_ORGANELLE_ENVELOPE, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, REACTOME_MITOTIC_METAPHASE_AND_ANAPHASE, REACTOME_NUCLEAR_ENVELOPE_NE_REASSEMBLY, REACTOME_M_PHASE, STK33_NOMO_UP, STK33_UP, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of transcription by RNA polymerase II (GO:0000122)

GO Molecular Function (4): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nuclear envelope (GO:0005635), nucleoplasm (GO:0005654), cytosol (GO:0005829), endosome membrane (GO:0010008)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Nuclear Envelope (NE) Reassembly1
M Phase1
Mitotic Anaphase1
Mitotic Metaphase and Anaphase1
Cell Cycle, Mitotic1
Cell Cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II2
cellular anatomical structure2
regulation of DNA-templated transcription1
negative regulation of DNA-templated transcription1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
binding1
intracellular membrane-bounded organelle1
nucleus1
endomembrane system1
organelle envelope1
nuclear lumen1
cytoplasm1
endosome1
cytoplasmic vesicle membrane1
bounding membrane of organelle1

Protein interactions and networks

STRING

1247 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CC2D1BCHMP4CQ96CF2580
CC2D1BCHMP4AQ9BY43571
CC2D1BGPATCH3Q96I76570
CC2D1BCHMP7Q8WUX9475
CC2D1BPRPF38AQ8NAV1472
CC2D1BAMMECR1LQ6DCA0447
CC2D1BIST1P53990443
CC2D1BCHMP6Q96FZ7440
CC2D1BPURBQ96QR8414
CC2D1BPHGDHO43175410
CC2D1BSPINK8P0C7L1406
CC2D1BFCF1Q9Y324399
CC2D1BZC3H14Q6PJT7398
CC2D1BBCL7CQ8WUZ0398
CC2D1BZKSCAN5Q9Y2L8396

IntAct

22 interactions, top by confidence:

ABTypeScore
SHKBP1CUL3psi-mi:“MI:0914”(association)0.850
CASP7XIAPpsi-mi:“MI:0914”(association)0.840
RFX3RFX1psi-mi:“MI:0914”(association)0.730
TRIM27KPNA1psi-mi:“MI:0914”(association)0.640
MDFICC2D1Bpsi-mi:“MI:0915”(physical association)0.560
CC2D1BMDFIpsi-mi:“MI:0915”(physical association)0.560
BMXARIH2psi-mi:“MI:0914”(association)0.530
CC2D1BH2BC9psi-mi:“MI:0915”(physical association)0.400
CC2D1BH2BC21psi-mi:“MI:0915”(physical association)0.400
CC2D1BH2BC5psi-mi:“MI:0915”(physical association)0.400
CC2D1BH2BC14psi-mi:“MI:0915”(physical association)0.400
CC2D1BCKMpsi-mi:“MI:0915”(physical association)0.400
CHMP4BCC2D1Bpsi-mi:“MI:0914”(association)0.350
SKAP1MYO9Apsi-mi:“MI:0914”(association)0.350
KCNE3PIK3R2psi-mi:“MI:0914”(association)0.350
CC2D1BPCDH7psi-mi:“MI:0914”(association)0.350
BLOC1S5SRGAP2psi-mi:“MI:0914”(association)0.350
CD55CCNB1psi-mi:“MI:0914”(association)0.350
DDX28UBA6psi-mi:“MI:0914”(association)0.350
ZNF843PMPCApsi-mi:“MI:0914”(association)0.350

BioGRID (48): CC2D1B (Two-hybrid), DCTN1 (Co-fractionation), CC2D1B (Affinity Capture-MS), CC2D1B (Affinity Capture-MS), CC2D1B (Affinity Capture-MS), CC2D1B (Affinity Capture-MS), CC2D1B (Affinity Capture-MS), CC2D1B (Affinity Capture-MS), CC2D1B (Protein-RNA), CC2D1B (Two-hybrid), CC2D1B (Proximity Label-MS), CC2D1B (Proximity Label-MS), HIST1H2BM (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), CC2D1B (Proximity Label-MS)

ESM2 similar proteins: A0A0G2JV04, B0V207, D3Z8X7, D3ZFJ3, D3ZND0, F1LM81, G9CGD6, O00499, O08539, O08839, O12940, O60308, O60784, O75674, O88746, P42567, P55194, Q05DH4, Q0GNC1, Q0IHV1, Q27J81, Q3B7M3, Q3UN70, Q4KLN4, Q505K2, Q5FVK6, Q5T0F9, Q5U3K5, Q66HA5, Q68EF0, Q6P1N0, Q6P5E6, Q6P9Q4, Q6P9Q6, Q80V31, Q80V94, Q8BMI3, Q8BRN9, Q8K1A6, Q8R0H9

Diamond homologs: Q29M42, Q5FVK6, Q5T0F9, Q66HA5, Q6P1N0, Q6PF54, Q8BRN9, Q8K1A6, Q9U2M8, Q9VKJ9

SIGNOR signaling

1 interactions.

AEffectBMechanism
CC2D1B“down-regulates quantity by repression”HTR1A“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 30 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
Assembly of the ORC complex at the origin of replication536.0×4e-05
Condensation of Prophase Chromosomes534.0×4e-05
G2/M DNA damage checkpoint526.1×9e-05
HCMV Late Events521.4×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance167
Likely benign11
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

4095 predictions. Top by Δscore:

VariantEffectΔscore
1:52353646:ACCT:Aacceptor_loss1.0000
1:52353648:C:Aacceptor_loss1.0000
1:52353649:T:Aacceptor_loss1.0000
1:52354629:A:ACdonor_gain1.0000
1:52354630:C:CCdonor_gain1.0000
1:52354630:CA:Cdonor_gain1.0000
1:52354630:CACT:Cdonor_gain1.0000
1:52354834:CCTCA:Cdonor_loss1.0000
1:52354835:CTCA:Cdonor_loss1.0000
1:52354836:TCA:Tdonor_loss1.0000
1:52354837:CACCC:Cdonor_loss1.0000
1:52354838:A:ACdonor_gain1.0000
1:52354838:A:ATdonor_loss1.0000
1:52354838:AC:Adonor_gain1.0000
1:52354839:C:CCdonor_gain1.0000
1:52354839:CC:Cdonor_gain1.0000
1:52354935:AAATT:Aacceptor_gain1.0000
1:52354936:AATT:Aacceptor_gain1.0000
1:52354937:ATT:Aacceptor_gain1.0000
1:52354938:TT:Tacceptor_gain1.0000
1:52354940:C:CCacceptor_gain1.0000
1:52354940:CT:Cacceptor_loss1.0000
1:52354941:T:Aacceptor_loss1.0000
1:52354944:C:CTacceptor_gain1.0000
1:52354945:A:Tacceptor_gain1.0000
1:52355853:A:Tacceptor_gain1.0000
1:52356190:CAGT:Cdonor_gain1.0000
1:52356298:CAAAT:Cacceptor_gain1.0000
1:52356299:AAAT:Aacceptor_gain1.0000
1:52356300:AAT:Aacceptor_gain1.0000

AlphaMissense

5495 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:52353613:A:GL828P0.998
1:52355809:A:GL703P0.998
1:52357029:A:GL623P0.997
1:52358755:A:CY421D0.997
1:52353595:A:GL834P0.996
1:52355636:A:TV726E0.996
1:52355648:A:GL722P0.996
1:52353548:A:GW850R0.995
1:52353548:A:TW850R0.995
1:52354918:A:GL760P0.995
1:52355785:A:GL711P0.995
1:52359037:C:GR416P0.995
1:52359766:G:TA294D0.995
1:52360509:C:GR173P0.995
1:52354670:C:GG796R0.994
1:52358700:A:GL439S0.994
1:52358746:C:GA424P0.994
1:52358754:T:GY421S0.994
1:52359779:A:CY290D0.994
1:52354669:C:TG796D0.993
1:52354690:A:GF789S0.993
1:52356258:A:GL667P0.993
1:52357017:A:GL627P0.993
1:52359038:G:TR416S0.993
1:52360498:A:CY177D0.993
1:52353613:A:CL828R0.992
1:52355785:A:CL711R0.992
1:52355794:C:TG708E0.992
1:52355795:C:GG708R0.992
1:52355795:C:TG708R0.992

dbSNP variants (sampled 300 via entrez): RS1000283233 (1:52358521 C>T), RS1000300011 (1:52364203 C>G), RS1000635840 (1:52365770 G>A,C), RS1000659872 (1:52353750 C>T), RS1000688113 (1:52365532 C>T), RS1000927185 (1:52359622 C>T), RS1001306228 (1:52362992 C>A), RS1001482401 (1:52357642 G>A), RS1001695280 (1:52357402 G>A), RS1001731691 (1:52352333 C>G,T), RS1001784048 (1:52352321 T>TC), RS1001805315 (1:52351838 C>T), RS1001864969 (1:52367428 C>T), RS1001944253 (1:52357392 C>T), RS1002068795 (1:52353470 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
mercuric bromideincreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
tetrahydropalmatinedecreases expression1
beta-lapachoneincreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangincreases expression1
Sunitinibincreases expression1
Vehicle Emissionsaffects expression, increases abundance1
Benzo(a)pyreneaffects methylation, decreases methylation1
Cadmiumincreases expression, increases abundance1
Methapyrileneincreases methylation1
Phthalic Acidsincreases expression1
Quercetinincreases expression1
Smokedecreases expression1
Cadmium Chlorideincreases abundance, increases expression1
Particulate Matterincreases abundance, affects 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.