NUDCD1

gene
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Also known as CML66FLJ14991

Summary

NUDCD1 (NudC domain containing 1, HGNC:24306) is a protein-coding gene on chromosome 8q23.1, encoding NudC domain-containing protein 1 (Q96RS6).

Predicted to be involved in immune system process. Located in cytosol and nucleoplasm.

Source: NCBI Gene 84955 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 99 total
  • MANE Select transcript: NM_032869

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24306
Approved symbolNUDCD1
NameNudC domain containing 1
Location8q23.1
Locus typegene with protein product
StatusApproved
AliasesCML66, FLJ14991
Ensembl geneENSG00000120526
Ensembl biotypeprotein_coding
OMIM606109
Entrez84955

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 10 protein_coding, 4 retained_intron, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000239690, ENST00000427660, ENST00000519607, ENST00000521439, ENST00000676569, ENST00000676990, ENST00000677182, ENST00000677737, ENST00000678094, ENST00000678168, ENST00000679027, ENST00000931096, ENST00000931097, ENST00000931098, ENST00000931099, ENST00000931100, ENST00000931101, ENST00000967053

RefSeq mRNA: 2 — MANE Select: NM_032869 NM_001128211, NM_032869

CCDS: CCDS47910, CCDS6312

Canonical transcript exons

ENST00000239690 — 10 exons

ExonStartEnd
ENSE00000981104109322309109322463
ENSE00000981118109240919109243301
ENSE00002119265109333893109334087
ENSE00003477644109296384109296569
ENSE00003480265109245322109245481
ENSE00003500043109275352109275496
ENSE00003537264109293344109293524
ENSE00003579066109280968109281172
ENSE00003599321109289751109289933
ENSE00003605839109271005109271130

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 99.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.9605 / max 354.6034, expressed in 1796 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
9440823.56601796
944070.3944187

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.09gold quality
oocyteCL:000002393.04gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.54gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.49gold quality
calcaneal tendonUBERON:000370187.91gold quality
germinal epithelium of ovaryUBERON:000130487.89gold quality
cartilage tissueUBERON:000241887.69gold quality
tibialis anteriorUBERON:000138587.54silver quality
cardiac muscle of right atriumUBERON:000337987.31gold quality
ventricular zoneUBERON:000305386.41gold quality
islet of LangerhansUBERON:000000686.30gold quality
myocardiumUBERON:000234986.17silver quality
ganglionic eminenceUBERON:000402385.95gold quality
embryoUBERON:000092285.94gold quality
kidney epitheliumUBERON:000481985.35gold quality
cortical plateUBERON:000534385.35gold quality
spermCL:000001985.33gold quality
deltoidUBERON:000147685.15gold quality
pericardiumUBERON:000240785.05gold quality
smooth muscle tissueUBERON:000113584.74gold quality
omental fat padUBERON:001041484.32gold quality
peritoneumUBERON:000235884.31gold quality
cauda epididymisUBERON:000436084.28gold quality
adrenal tissueUBERON:001830384.07gold quality
placentaUBERON:000198783.63gold quality
ileal mucosaUBERON:000033183.49gold quality
stromal cell of endometriumCL:000225583.47gold quality
adipose tissue of abdominal regionUBERON:000780883.47gold quality
vermiform appendixUBERON:000115483.29gold quality
lymph nodeUBERON:000002983.14gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.04
E-MTAB-6524no116.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting NUDCD1, 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-3134100.0066.43777
HSA-MIR-5193100.0067.261744
HSA-MIR-3163100.0077.238605
HSA-MIR-5692A100.0074.406850
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-118499.9968.191458
HSA-MIR-453499.9966.581907
HSA-MIR-1213699.9872.815713
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-548N99.9871.944170
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-493-5P99.9672.472382
HSA-MIR-211099.9666.681930
HSA-MIR-9-3P99.9670.882068
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-144-3P99.9473.982698
HSA-MIR-498-3P99.9171.271114
HSA-MIR-153-5P99.8973.866317
HSA-MIR-568299.8972.561005
HSA-LET-7A-2-3P99.8770.531921
HSA-MIR-5582-3P99.8672.484221
HSA-LET-7G-3P99.8570.431929
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548F-5P99.7871.023093
HSA-MIR-548AJ-5P99.7871.123085

Literature-anchored findings (GeneRIF, showing 10)

  • An alternative promoter (CML66-S short isoform) has been identified in combination with alternative splicing as a novel mechanism for regulation of the epitope generation of a self-tumor antigen. (PMID:14688378)
  • CML66 may play an oncogenic role in ways of favoring tumor cells proliferation, invasion and metastasis-associated with multiple pathways. (PMID:18534745)
  • study identified a novel gene, OVA66, which was expressed significantly higher in cancer patients than normal controls; IgG level against OVA66 was significantly elevated in the serum of cancer patients from different histological types of cancer [OVA66] (PMID:18754882)
  • the different NudCD1 isoforms have unique interacting partners, with the first isoform binding to a putative RNA helicase named DHX15 involved in mRNA splicing. (PMID:29021621)
  • NudCD1 significantly increased in renal cell carcinoma and was positively correlated with cell proliferation, migration, and invasion (PMID:29461594)
  • OVA66 overexpression in the cancer cell lines promoted VEGF secretion, tumour growth and angiogenesis in vitro and in vivo (PMID:30833190)
  • NudCD1 Promotes the Proliferation and Metastasis of Non-Small Cell Lung Cancer Cells through the Activation of IGF1R-ERK1/2. (PMID:32634806)
  • Analysis of NudCD1 and NF-kappaBeta in the early detection and course evaluation of renal cancer. (PMID:33336728)
  • NudCD1 as a prognostic marker in colorectal cancer and its role in the upregulation of cellular spindle assembly checkpoint genes and LIS1 pathways. (PMID:36104662)
  • Identifying the role of NUDCD1 in human tumors from clinical and molecular mechanisms: a study based on comprehensive bioinformatics and experimental validation. (PMID:37338527)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionudcd1ENSDARG00000036158
mus_musculusNudcd1ENSMUSG00000038736
rattus_norvegicusNudcd1ENSRNOG00000024929
drosophila_melanogasterCG10347FBGN0030342
caenorhabditis_elegansC44E4.5WBGENE00016654

Protein

Protein identifiers

NudC domain-containing protein 1Q96RS6 (reviewed: Q96RS6)

Alternative names: Chronic myelogenous leukemia tumor antigen 66, Tumor antigen CML66

All UniProt accessions (5): Q96RS6, A0A7I2V457, A0A7I2V4C4, E5RGX7, E5RHQ3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Nucleus Cytoplasm Cytoplasm. Nucleus.

Tissue specificity. Isoform 1 is specifically expressed in leukemias and a variety of solid tumor cell lines and is also detected in testis and heart. Isoform 2 is predominantly expressed in testis and weakly expressed in tumor cells.

Miscellaneous. Isoform 1 is the dominant immunogenic isoform and is capable of eliciting a humoral response in individuals with a variety of solid tumors. Expression of isoform 1 in a wide variety of malignancies as well as the presence of an immunogenic epitope suggest that it may be a suitable target for antigen-specific immunotherapy. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt IDNamesCanonical?
Q96RS6-11, CML66-Lyes
Q96RS6-22, CML66-S
Q96RS6-33

RefSeq proteins (2): NP_001121683, NP_116258* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007052CS_domDomain
IPR008978HSP20-like_chaperoneHomologous_superfamily
IPR037895NUDCD1Family

Pfam: PF04969

UniProt features (13 total): sequence variant 4, splice variant 4, modified residue 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96RS6-F186.410.60

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 (2): 8, 388

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 161 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, COUP_01, WEI_MYCN_TARGETS_WITH_E_BOX, NF1_Q6_01, HNF4_DR1_Q3, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TGGNNNNNNKCCAR_UNKNOWN, DOUGLAS_BMI1_TARGETS_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, NFE2_01, NUYTTEN_EZH2_TARGETS_DN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, STAT1_02

GO Biological Process (1): immune system process (GO:0002376)

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

GO Cellular Component (4): nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
biological_process1
binding1
nuclear lumen1
cytoplasm1
intracellular membrane-bounded organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

1224 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NUDCD1ENY2Q9NPA8706
NUDCD1NUDCD2Q8WVJ2590
NUDCD1EBAG9O00559541
NUDCD1NUDCD3Q8IVD9506
NUDCD1NUDCQ9Y266505
NUDCD1EXOSC5Q9NQT4475
NUDCD1C8orf33Q9H7E9445
NUDCD1TMEM186Q96B77434
NUDCD1ZMAT5Q9UDW3429
NUDCD1ZNF189O75820409
NUDCD1AFTPHQ6ULP2392
NUDCD1RSRC2Q7L4I2378
NUDCD1MRPL50Q8N5N7374
NUDCD1ZNF222Q9UK12370
NUDCD1ZNF623O75123366

IntAct

38 interactions, top by confidence:

ABTypeScore
DHX38PPP4Cpsi-mi:“MI:0914”(association)0.730
DHX38NUDCD1psi-mi:“MI:0915”(physical association)0.710
COPG1NUDCD1psi-mi:“MI:0915”(physical association)0.710
DHX8AHCYL1psi-mi:“MI:0914”(association)0.640
COPG1COPEpsi-mi:“MI:0914”(association)0.640
DHX38PPP4R3Apsi-mi:“MI:0914”(association)0.640
DHX38DHX16psi-mi:“MI:0914”(association)0.630
NUDCD1COPB1psi-mi:“MI:0915”(physical association)0.620
DHX32POLRMTpsi-mi:“MI:0914”(association)0.530
ABCF2AHCYL1psi-mi:“MI:0914”(association)0.530
NUDCD1psi-mi:“MI:0915”(physical association)0.400
NUDCD1DHX8psi-mi:“MI:0915”(physical association)0.400
NUDCD1DHX16psi-mi:“MI:0915”(physical association)0.400
ARAFNUDCD1psi-mi:“MI:0915”(physical association)0.400
NUDCD1COPG2psi-mi:“MI:0915”(physical association)0.400
NUDCD1AKT3psi-mi:“MI:0915”(physical association)0.400
NXF1NUDCD1psi-mi:“MI:0915”(physical association)0.400
NUDCD1TUBAL3psi-mi:“MI:0914”(association)0.350
DHX15BBXpsi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
USP36STK25psi-mi:“MI:0914”(association)0.350
COPAESYT2psi-mi:“MI:0914”(association)0.350
COPB2ESYT2psi-mi:“MI:0914”(association)0.350
COPEESYT2psi-mi:“MI:0914”(association)0.350
COPG1ATL3psi-mi:“MI:0914”(association)0.350
COPG2ILVBLpsi-mi:“MI:0914”(association)0.350
COPZ1ATL3psi-mi:“MI:0914”(association)0.350

BioGRID (110): NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Affinity Capture-MS), NUDCD1 (Proximity Label-MS), NUDCD1 (Proximity Label-MS), NUDCD1 (Proximity Label-MS), NUDCD1 (Proximity Label-MS)

ESM2 similar proteins: A1KXW8, A6QL50, E1BGQ2, H0Y354, O94955, P47224, Q08326, Q0IIH8, Q1JQA1, Q1RMS8, Q1RMZ1, Q2TBU5, Q3T1H6, Q4R372, Q4R528, Q4R9C4, Q5F480, Q5F4A1, Q5I0G3, Q5RCQ0, Q5RFG8, Q5TFE4, Q5TYM5, Q641X7, Q6L9T8, Q6PIP5, Q7L622, Q7Z6J8, Q7ZX59, Q86X60, Q8BFZ8, Q8BKW4, Q8BM85, Q8BX13, Q8CEL2, Q8N5C7, Q8N635, Q8NHU2, Q8TCF1, Q8TCJ0

Diamond homologs: Q28IB1, Q503C8, Q6PIP5, Q7T0S2, Q96RS6, Q54M64, Q9VVA6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 38 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
COPI-dependent Golgi-to-ER retrograde traffic834.1×6e-09
COPI-mediated anterograde transport833.8×6e-09

GO biological processes:

GO termPartnersFoldFDR
intra-Golgi vesicle-mediated transport7111.7×4e-11
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum551.1×4e-06
endoplasmic reticulum to Golgi vesicle-mediated transport624.7×9e-06
mRNA splicing, via spliceosome513.9×1e-03
intracellular protein transport611.8×5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2390 predictions. Top by Δscore:

VariantEffectΔscore
8:109245324:AAAG:Adonor_gain1.0000
8:109264095:TAAAG:Tdonor_gain1.0000
8:109271138:C:CTacceptor_gain1.0000
8:109275347:CTTA:Cdonor_loss1.0000
8:109275348:TTACC:Tdonor_loss1.0000
8:109275349:TACCA:Tdonor_loss1.0000
8:109275350:A:ACdonor_gain1.0000
8:109275350:A:ATdonor_loss1.0000
8:109275350:AC:Adonor_gain1.0000
8:109275351:C:CTdonor_gain1.0000
8:109275351:CC:Cdonor_gain1.0000
8:109275351:CCA:Cdonor_gain1.0000
8:109275351:CCAG:Cdonor_gain1.0000
8:109275351:CCAGT:Cdonor_gain1.0000
8:109275492:CCAAG:Cacceptor_gain1.0000
8:109275493:CAAGC:Cacceptor_gain1.0000
8:109275494:AAG:Aacceptor_gain1.0000
8:109275495:AG:Aacceptor_gain1.0000
8:109275496:GC:Gacceptor_loss1.0000
8:109275497:C:CCacceptor_gain1.0000
8:109275503:G:Cacceptor_gain1.0000
8:109275503:G:GCacceptor_gain1.0000
8:109275504:T:Cacceptor_gain1.0000
8:109275504:T:TCacceptor_gain1.0000
8:109275505:T:Cacceptor_gain1.0000
8:109275505:T:TCacceptor_gain1.0000
8:109275509:A:ACacceptor_gain1.0000
8:109275509:A:Cacceptor_gain1.0000
8:109280964:ATAC:Adonor_loss1.0000
8:109280966:AC:Adonor_loss1.0000

AlphaMissense

3859 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:109243295:A:TV489D1.000
8:109243088:C:TG558E0.999
8:109243203:A:CY520D0.999
8:109243282:C:AK493N0.999
8:109243282:C:GK493N0.999
8:109243301:C:TG487D0.999
8:109245322:C:GG487R0.999
8:109245385:A:GW466R0.999
8:109245385:A:TW466R0.999
8:109333944:A:GY23H0.999
8:109333951:G:CF20L0.999
8:109333951:G:TF20L0.999
8:109333953:A:GF20L0.999
8:109243055:A:GL569P0.998
8:109243058:A:TV568D0.998
8:109243089:C:GG558R0.998
8:109243089:C:TG558R0.998
8:109243133:G:TA543D0.998
8:109243162:T:AR533S0.998
8:109243162:T:GR533S0.998
8:109243163:C:GR533T0.998
8:109243299:A:GY488H0.998
8:109245327:G:TA485D0.998
8:109245352:A:GW477R0.998
8:109245352:A:TW477R0.998
8:109333937:A:GL25P0.998
8:109333944:A:CY23D0.998
8:109243126:C:AQ545H0.997
8:109243126:C:GQ545H0.997
8:109243235:G:TA509D0.997

dbSNP variants (sampled 300 via entrez): RS1000042395 (8:109309448 A>G), RS1000061467 (8:109264797 T>C), RS1000086586 (8:109320520 T>A,C), RS1000133580 (8:109258719 A>T), RS1000207530 (8:109273953 T>C), RS1000219899 (8:109265310 G>A), RS1000242247 (8:109311406 C>T), RS1000253954 (8:109265021 G>A), RS1000292040 (8:109271823 A>C,G), RS1000304063 (8:109294943 T>A,C), RS1000320738 (8:109324922 T>C), RS1000368340 (8:109276721 ATC>A), RS1000423130 (8:109318020 TA>T), RS1000449364 (8:109271511 A>C), RS1000494974 (8:109330179 G>A)

Disease associations

OMIM: gene MIM:606109 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST003518_76Daytime sleep phenotypes2.000000e-06
GCST003542_207Night sleep phenotypes5.000000e-06
GCST008595_200Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)7.000000e-09
GCST009391_2140Metabolite levels3.000000e-06

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007828daytime rest measurement
EFO:0004337intelligence
EFO:0004784self reported educational attainment
EFO:0010384phosphatidylcholine 38:2 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression4
methylmercuric chloridedecreases expression3
Nickelincreases expression, decreases expression3
trichostatin Aaffects cotreatment, decreases expression2
sodium arseniteincreases abundance, increases expression, decreases expression, affects cotreatment2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression2
Arsenicaffects methylation, affects cotreatment, increases abundance, increases expression2
Benzo(a)pyrenedecreases expression, decreases methylation2
Valproic Acidaffects expression, increases expression2
Cadmium Chloridedecreases expression2
Particulate Matterincreases abundance, decreases expression2
FR900359increases phosphorylation1
dicrotophosdecreases expression1
2,4,6-tribromophenolincreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
decabromobiphenyl etherincreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
potassium chromate(VI)affects cotreatment, decreases expression1
coumarinincreases phosphorylation1
epigallocatechin gallatedecreases expression, affects cotreatment1
nutlin 3affects cotreatment, increases secretion1
dorsomorphindecreases expression, affects cotreatment1
jinfukangaffects cotreatment, decreases expression1
LDN 193189affects cotreatment, decreases expression1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Air Pollutants, Occupationaldecreases expression1
Vehicle Emissionsdecreases expression, increases abundance1
Carbamazepineaffects expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_KT84HeLa SilenciX NUDCD1Cancer cell lineFemale

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.