CDC123

gene
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Also known as D123

Summary

CDC123 (cell division cycle 123, HGNC:16827) is a protein-coding gene on chromosome 10p14-p13, encoding Translation initiation factor eIF2 assembly protein (O75794). ATP-dependent protein-folding chaperone for the eIF2 complex. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

Enables ATP binding activity and magnesium ion binding activity. Involved in eukaryotic translation initiation factor 2 complex assembly. Located in cytoplasm.

Source: NCBI Gene 8872 — RefSeq curated summary.

At a glance

  • GWAS associations: 67
  • Clinical variants (ClinVar): 73 total
  • Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_006023

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16827
Approved symbolCDC123
Namecell division cycle 123
Location10p14-p13
Locus typegene with protein product
StatusApproved
AliasesD123
Ensembl geneENSG00000151465
Ensembl biotypeprotein_coding
OMIM617708
Entrez8872

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 19 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000281141, ENST00000378900, ENST00000429258, ENST00000440613, ENST00000442050, ENST00000455773, ENST00000467016, ENST00000497963, ENST00000498747, ENST00000900296, ENST00000900297, ENST00000900298, ENST00000932716, ENST00000932717, ENST00000932718, ENST00000932719, ENST00000932720, ENST00000932721, ENST00000932722, ENST00000932723, ENST00000932724, ENST00000932725, ENST00000932726

RefSeq mRNA: 1 — MANE Select: NM_006023 NM_006023

CCDS: CCDS7090

Canonical transcript exons

ENST00000281141 — 13 exons

ExonStartEnd
ENSE000009997481219618812196319
ENSE000017604771225031112250589
ENSE000034665011220996712210024
ENSE000035051491221029012210322
ENSE000035176601224614912246277
ENSE000035293751223094812230996
ENSE000035295801219870512198776
ENSE000035810741224958112249718
ENSE000035836731223714412237266
ENSE000035969661223845712238485
ENSE000036003981223504812235123
ENSE000036302991221574012215835
ENSE000036516051221736112217467

Expression profiles

Bgee: expression breadth ubiquitous, 296 present calls, max score 96.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 51.6544 / max 598.3145, expressed in 1822 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
10391048.62051822
1039092.28421404
1039120.3872172
1039080.3625190

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
rectumUBERON:000105296.30gold quality
cortical plateUBERON:000534396.11gold quality
secondary oocyteCL:000065596.04gold quality
islet of LangerhansUBERON:000000695.95gold quality
smooth muscle tissueUBERON:000113595.93gold quality
ventricular zoneUBERON:000305395.78gold quality
embryoUBERON:000092295.74gold quality
ganglionic eminenceUBERON:000402395.71gold quality
right atrium auricular regionUBERON:000663195.53gold quality
cardiac atriumUBERON:000208195.42gold quality
monocyteCL:000057695.40gold quality
mucosa of transverse colonUBERON:000499195.22gold quality
mononuclear cellCL:000084295.21gold quality
leukocyteCL:000073895.18gold quality
epithelium of nasopharynxUBERON:000195195.14gold quality
nasopharynxUBERON:000172895.12gold quality
oocyteCL:000002395.00gold quality
stromal cell of endometriumCL:000225594.97gold quality
esophagus mucosaUBERON:000246994.83gold quality
nucleus accumbensUBERON:000188294.82gold quality
lymph nodeUBERON:000002994.79gold quality
caudate nucleusUBERON:000187394.76gold quality
left coronary arteryUBERON:000162694.73gold quality
right coronary arteryUBERON:000162594.72gold quality
descending thoracic aortaUBERON:000234594.61gold quality
heartUBERON:000094894.57gold quality
skin of abdomenUBERON:000141694.56gold quality
vermiform appendixUBERON:000115494.55gold quality
myocardiumUBERON:000234994.55gold quality
skin of legUBERON:000151194.51gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.88
E-CURD-88yes4.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting CDC123, 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-4795-3P100.0074.624024
HSA-MIR-3163100.0077.238605
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-1213699.9872.815713
HSA-MIR-493-5P99.9672.472382
HSA-MIR-589-3P99.9169.622088
HSA-MIR-202-5P99.7867.65991
HSA-MIR-2115-3P99.3169.682026
HSA-MIR-877-3P99.0968.101637
HSA-MIR-376A-3P99.0669.171128
HSA-MIR-376B-3P99.0669.171128
HSA-MIR-361-5P98.9570.161340
HSA-MIR-138-2-3P98.9168.331643
HSA-MIR-374A-3P98.8767.821531
HSA-MIR-2355-5P98.8365.511589
HSA-MIR-147098.1163.53399
HSA-MIR-219B-5P97.9165.80531
HSA-MIR-3156-5P96.9367.36800

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 7)

  • A significant association of rs10906115 in CDC123/CAMK1D and rs1359790 near SPRY2 was identified with type 2 diabetes in a Japanese population. (PMID:21909839)
  • Association to type 2 diabetes was found for rs13266634 (SLC30A8), rs7923837 (HHEX), rs10811661 (CDKN2A/2B), rs4402960 (IGF2BP2), rs12779790 (CDC123/CAMK1D), and rs2237892 (KCNQ1). (PMID:22923468)
  • CDC123 may have a role in novel protein modifications (PMID:25976611)
  • There were no statistically significant differences in the distribution of CDC123/CAMK1D rs12779790 genotypes and alleles between women with gestational diabetes mellitus and healthy pregnant women. (PMID:28079868)
  • USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. (PMID:37314216)
  • Binding of human Cdc123 to eIF2gamma. (PMID:37507029)
  • CDC123 promotes Hepatocellular Carcinoma malignant progression by regulating CDKAL1. (PMID:38237400)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocdc123ENSDARG00000075025
mus_musculusCdc123ENSMUSG00000039128
rattus_norvegicusCdc123ENSRNOG00000017770

Protein

Protein identifiers

Translation initiation factor eIF2 assembly proteinO75794 (reviewed: O75794)

Alternative names: Cell division cycle protein 123 homolog, HT-1080, PZ32

All UniProt accessions (5): O75794, H7BZW7, X6RA30, X6RF82, X6RKY7

UniProt curated annotations — full annotation on UniProt →

Function. ATP-dependent protein-folding chaperone for the eIF2 complex. Binds to the gamma subunit of the eIF2 complex which allows the subunit to assemble with the alpha and beta subunits.

Subunit / interactions. Interacts with the eIF2 complex gamma subunit EIF2S3 (via C-terminus); the interaction is direct. Interacts with the eIF2 complex alpha subunit EIF2S1. Interacts with the eIF2 complex beta subunit EIF2S2.

Subcellular location. Cytoplasm.

Tissue specificity. Widely expressed. Expressed in spleen, thymus, prostate, testis, ovary, small intestine, colon and leukocytes with the highest expression in testis.

Similarity. Belongs to the CDC123 family.

RefSeq proteins (1): NP_006014* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009772CDC123Family

Pfam: PF07065

UniProt features (49 total): binding site 16, helix 14, strand 10, turn 3, mutagenesis site 2, sequence conflict 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8PHVX-RAY DIFFRACTION1.97
8PHDX-RAY DIFFRACTION2.08

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75794-F184.820.64

Functional residue map

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

Ligand- & substrate-binding residues (16): 104; 179; 193; 233; 246; 246; 248; 248; 107; 109; 111; 167

Post-translational modifications (1): 60

Mutagenesis-validated functional residues (2):

PositionPhenotype
233severely disrupts assembly factor activity.
246severely disrupts assembly factor activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 175 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, MORF_HDAC1, MORF_UBE2N, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, MISSIAGLIA_REGULATED_BY_METHYLATION_UP, MORF_SKP1A, GOBP_PROTEIN_MATURATION, GOBP_PROTEIN_FOLDING, SCHLOSSER_SERUM_RESPONSE_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP

GO Biological Process (2): eukaryotic translation initiation factor 2 complex assembly (GO:1905143), protein folding (GO:0006457)

GO Molecular Function (6): magnesium ion binding (GO:0000287), ATP binding (GO:0005524), protein folding chaperone (GO:0044183), nucleotide binding (GO:0000166), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein-containing complex assembly1
cellular process1
protein maturation1
metal ion binding1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
molecular_function1
protein folding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
cation binding1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1448 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CDC123CAMK1DQ8IU85873
CDC123JAZF1Q86VZ6820
CDC123CDKAL1Q5VV42780
CDC123TSPAN8P19075720
CDC123HHEXQ03014720
CDC123ADAMTS9Q9P2N4720
CDC123SLC30A8Q8IWU4719
CDC123EIF2S3P41091705
CDC123IGF2BP2Q9Y6M1670
CDC123WFS1O76024668
CDC123MTNR1BP49286668
CDC123TCF7L2Q9NQB0659
CDC123KCNQ1P51787644
CDC123KCNJ11Q14654644
CDC123C2CD4AQ8NCU7621

IntAct

45 interactions, top by confidence:

ABTypeScore
MED17MED19psi-mi:“MI:0914”(association)0.840
EIF2S3CDC123psi-mi:“MI:0407”(direct interaction)0.760
CDC123EIF2S3psi-mi:“MI:0407”(direct interaction)0.760
EIF2S2CDC123psi-mi:“MI:0914”(association)0.710
CDC123EIF2S2psi-mi:“MI:0914”(association)0.710
CDC123EIF2S2psi-mi:“MI:0915”(physical association)0.710
TGIF2LYPGPpsi-mi:“MI:0914”(association)0.640
HLA-DRAENTPD6psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
OIP5CYTH3psi-mi:“MI:0914”(association)0.530
SUI2CDC123psi-mi:“MI:0915”(physical association)0.500
CDC123psi-mi:“MI:0407”(direct interaction)0.440
CDC123FXR1psi-mi:“MI:0915”(physical association)0.370
EIF2S1CDC123psi-mi:“MI:0915”(physical association)0.370
HSPB1CDC123psi-mi:“MI:0915”(physical association)0.370
CDC123ZNF512Bpsi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
EIF2S3EIF3CLpsi-mi:“MI:0914”(association)0.350
EIF5EIF3CLpsi-mi:“MI:0914”(association)0.350
EIF2S2TOR1Bpsi-mi:“MI:0914”(association)0.350
CDC123CLTCL1psi-mi:“MI:0914”(association)0.350
FCGRTWBP4psi-mi:“MI:0914”(association)0.350
CDC123SUI3psi-mi:“MI:0914”(association)0.350
FAM111ADFFApsi-mi:“MI:0914”(association)0.350
GJA1CDC123psi-mi:“MI:0914”(association)0.350

BioGRID (1869): GCD11 (Two-hybrid), CDC123 (Affinity Capture-MS), CDC123 (Two-hybrid), CDC123 (Proximity Label-MS), CDC123 (Proximity Label-MS), CDC123 (Proximity Label-MS), CDC123 (Proximity Label-MS), CDC123 (Proximity Label-MS), CDC123 (Affinity Capture-MS), CDC123 (Affinity Capture-MS), CDC123 (Affinity Capture-RNA), CDC123 (Affinity Capture-MS), CDC123 (Affinity Capture-MS), CDC123 (Affinity Capture-MS), CDC123 (Reconstituted Complex)

ESM2 similar proteins: A2Z4C5, A7X672, A7X680, B0K012, B8AJL9, B8AR41, B9SQI7, E0CSI1, O08848, O75794, O81770, O82730, P0C0T1, P10155, P42694, P57060, P93115, Q0J035, Q10PL5, Q13572, Q1PET6, Q28559, Q2PG37, Q2R483, Q2YDG3, Q33BI9, Q3U2J5, Q5F477, Q5F480, Q5R9U9, Q62834, Q69QJ7, Q6AY91, Q6DFV5, Q75GI4, Q7SY78, Q80YV4, Q8BYN3, Q8CII2, Q8LB01

Diamond homologs: A1CMB9, A1DLP3, A2R4R1, A5E3J7, A6R687, A6SDA8, A7A1A3, A7EUE6, A7RFT2, A7TPB3, O75794, Q05791, Q0CH08, Q0V340, Q2PG37, Q2U988, Q2YDG3, Q4WDA4, Q5AFX2, Q5AYN6, Q5BKN5, Q62834, Q641C9, Q6C101, Q6CL84, Q6FNU7, Q6PC40, Q75A37, Q75JF9, Q8CII2, Q9P7N5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign2
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2453 predictions. Top by Δscore:

VariantEffectΔscore
10:12198703:A:AGacceptor_gain1.0000
10:12198704:G:GCacceptor_gain1.0000
10:12198704:GT:Gacceptor_gain1.0000
10:12198704:GTGT:Gacceptor_gain1.0000
10:12198704:GTGTC:Gacceptor_gain1.0000
10:12198772:GGAAG:Gdonor_gain1.0000
10:12198773:G:GTdonor_gain1.0000
10:12198774:A:Tdonor_gain1.0000
10:12209965:A:AGacceptor_gain1.0000
10:12209965:AG:Aacceptor_gain1.0000
10:12209966:G:GGacceptor_gain1.0000
10:12209966:GG:Gacceptor_gain1.0000
10:12215776:G:GTdonor_gain1.0000
10:12215834:GG:Gdonor_gain1.0000
10:12215835:GG:Gdonor_gain1.0000
10:12215846:A:AGdonor_gain1.0000
10:12215846:A:Gdonor_gain1.0000
10:12215850:G:GGdonor_gain1.0000
10:12217002:A:Tdonor_gain1.0000
10:12217463:CAGCC:Cdonor_gain1.0000
10:12217464:AGCC:Adonor_gain1.0000
10:12217465:GCC:Gdonor_gain1.0000
10:12217465:GCCG:Gdonor_gain1.0000
10:12217466:CC:Cdonor_gain1.0000
10:12217466:CCGTA:Cdonor_loss1.0000
10:12217467:CGTA:Cdonor_loss1.0000
10:12217468:G:GGdonor_gain1.0000
10:12217469:TAA:Tdonor_loss1.0000
10:12235039:T:TAacceptor_gain1.0000
10:12235042:TTACA:Tacceptor_loss1.0000

AlphaMissense

2271 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:12217370:T:AW115R1.000
10:12217370:T:CW115R1.000
10:12217437:C:TS137F1.000
10:12217364:G:CA113P0.999
10:12217365:C:AA113E0.999
10:12217433:A:CS136R0.999
10:12217435:T:AS136R0.999
10:12217435:T:GS136R0.999
10:12217437:C:AS137Y0.999
10:12235058:G:CR167P0.999
10:12235094:G:CR179P0.999
10:12235103:T:AV182D0.999
10:12196285:T:AW14R0.998
10:12196285:T:CW14R0.998
10:12196318:A:CS25R0.998
10:12198705:T:AS25R0.998
10:12198705:T:GS25R0.998
10:12215771:T:AV90D0.998
10:12215810:C:AP103H0.998
10:12215814:G:CK104N0.998
10:12215814:G:TK104N0.998
10:12215816:T:CL105P0.998
10:12215821:T:AW107R0.998
10:12215821:T:CW107R0.998
10:12215831:C:AP110Q0.998
10:12215831:C:GP110R0.998
10:12217361:G:CD112H0.998
10:12217372:G:CW115C0.998
10:12217372:G:TW115C0.998
10:12217374:T:AI116K0.998

dbSNP variants (sampled 300 via entrez): RS1000007864 (10:12233967 TAGTG>T), RS1000094391 (10:12217055 C>T), RS1000114906 (10:12227817 A>C), RS1000126099 (10:12230843 T>A,C,G), RS1000167002 (10:12239118 G>A), RS1000234817 (10:12194378 T>C), RS1000276893 (10:12196593 T>C), RS1000289386 (10:12248465 T>C), RS1000291019 (10:12222967 C>T), RS1000331269 (10:12201460 T>A), RS1000344504 (10:12236598 C>T), RS1000427151 (10:12238947 G>A,T), RS1000444045 (10:12242473 TTG>T), RS1000576619 (10:12221310 C>T), RS1000587352 (10:12244629 T>G)

Disease associations

OMIM: gene MIM:617708 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

67 associations (top):

StudyTraitp-value
GCST000167_2Type 2 diabetes1.000000e-10
GCST000796_1Type 2 diabetes1.000000e-08
GCST001248_9Pulmonary function6.000000e-13
GCST001251_9Pulmonary function3.000000e-12
GCST001666_5Type 2 diabetes7.000000e-09
GCST001784_5Pulmonary function (smoking interaction)2.000000e-11
GCST002352_8Type 2 diabetes3.000000e-09
GCST003400_48Type 2 diabetes1.000000e-12
GCST004183_23Lung function (FEV1)1.000000e-11
GCST004184_19Lung function (FVC)5.000000e-06
GCST004185_42Lung function (FEV1/FVC)2.000000e-16
GCST004894_101Type 2 diabetes3.000000e-29
GCST004894_72Type 2 diabetes3.000000e-10
GCST004904_158Body mass index1.000000e-09
GCST004904_49Body mass index7.000000e-09
GCST005047_11Type 2 diabetes2.000000e-06
GCST005413_13Type 2 diabetes4.000000e-10
GCST006001_26Hemoglobin A1c levels1.000000e-11
GCST006801_10Type 2 diabetes5.000000e-06
GCST006867_114Type 2 diabetes2.000000e-17
GCST007096_172Pulse pressure5.000000e-08
GCST007099_34Systolic blood pressure7.000000e-07
GCST007429_138Lung function (FVC)7.000000e-11
GCST007430_81Peak expiratory flow9.000000e-36
GCST007431_155Lung function (FEV1/FVC)4.000000e-67
GCST007432_185FEV11.000000e-47
GCST007692_64Chronic obstructive pulmonary disease6.000000e-23
GCST007847_39Type 2 diabetes8.000000e-27
GCST007847_62Type 2 diabetes3.000000e-07
GCST008662_7Lung function in never smokers (low FEV1 vs high FEV1)2.000000e-10

EFO canonical traits (12, from GWAS)

EFO IDTrait name
EFO:0003892pulmonary function measurement
EFO:0004713FEV/FVC ratio
EFO:0004314forced expiratory volume
EFO:0004312vital capacity
EFO:0004340body mass index
EFO:0004541HbA1c measurement
EFO:0005763pulse pressure measurement
EFO:0006335systolic blood pressure
EFO:0009718peak expiratory flow
EFO:0005000leptin measurement
EFO:0004327electrocardiography
EFO:0007800body fat percentage

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression2
Air Pollutantsaffects cotreatment, decreases expression, increases abundance2
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases abundance, affects cotreatment, decreases expression1
salinomycindecreases expression1
beta-lapachonedecreases expression1
sodium arsenitedecreases expression1
benzo(e)pyreneincreases methylation1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
K 7174decreases expression1
7-(benzylamino)-1,3,4,8-tetrahydropyrrolo(4,3,2-de)quinolin-8(1H)-onedecreases expression1
Resveratroldecreases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Doxorubicinincreases expression1
Ivermectindecreases expression1
Methapyrileneincreases methylation1
Ozonedecreases expression, increases abundance, affects cotreatment1
Rotenonedecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Cyclosporinedecreases methylation1
Aflatoxin B1increases methylation1
Particulate Matterdecreases expression, increases abundance1
Volatile Organic Compoundsaffects cotreatment, decreases 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): myocardial infarction