NLE1

gene
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Also known as FLJ10458Rsa4

Summary

NLE1 (notchless homolog 1, HGNC:19889) is a protein-coding gene on chromosome 17q12, encoding Notchless protein homolog 1 (Q9NVX2). Plays a role in regulating Notch activity. It is a common-essential gene (DepMap: required in 98.3% of cancer cell lines).

Predicted to be involved in regulation of Notch signaling pathway. Predicted to act upstream of or within several processes, including chordate embryonic development; hematopoietic stem cell homeostasis; and positive regulation of canonical Wnt signaling pathway. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 54475 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 83 total
  • Cancer dependency (DepMap): dependent in 98.3% of screened cell lines (common-essential)
  • MANE Select transcript: NM_018096

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19889
Approved symbolNLE1
Namenotchless homolog 1
Location17q12
Locus typegene with protein product
StatusApproved
AliasesFLJ10458, Rsa4
Ensembl geneENSG00000073536
Ensembl biotypeprotein_coding
OMIM620924
Entrez54475

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000360831, ENST00000442241, ENST00000586869, ENST00000588019, ENST00000588642, ENST00000589367, ENST00000593176, ENST00000932057

RefSeq mRNA: 2 — MANE Select: NM_018096 NM_001014445, NM_018096

CCDS: CCDS11291, CCDS45647

Canonical transcript exons

ENST00000442241 — 13 exons

ExonStartEnd
ENSE000007141913513333935133498
ENSE000007141943513524935135451
ENSE000007141963513616935136215
ENSE000008876213513317135133241
ENSE000011875383514225835142303
ENSE000016231343512873035132449
ENSE000023472873514197935142122
ENSE000035059293513700135137193
ENSE000035141983513984935140066
ENSE000035369423513781435137890
ENSE000035424943513923535139314
ENSE000036500483513754335137640
ENSE000036540213513636235136497

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 90.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.3112 / max 116.2935, expressed in 1685 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1653439.31121685

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.83gold quality
body of pancreasUBERON:000115088.57gold quality
cortical plateUBERON:000534384.96gold quality
ganglionic eminenceUBERON:000402382.72gold quality
pancreasUBERON:000126482.48gold quality
ventricular zoneUBERON:000305381.27gold quality
stromal cell of endometriumCL:000225581.20gold quality
left ovaryUBERON:000211981.08gold quality
prefrontal cortexUBERON:000045180.90gold quality
hindlimb stylopod muscleUBERON:000425280.73gold quality
embryoUBERON:000092280.66gold quality
gastrocnemiusUBERON:000138880.14gold quality
right ovaryUBERON:000211879.78gold quality
body of stomachUBERON:000116179.70gold quality
mucosa of transverse colonUBERON:000499179.43gold quality
muscle of legUBERON:000138379.25gold quality
left adrenal glandUBERON:000123479.13gold quality
left adrenal gland cortexUBERON:003582579.13gold quality
right adrenal glandUBERON:000123379.12gold quality
esophagus mucosaUBERON:000246978.79gold quality
right adrenal gland cortexUBERON:003582778.67gold quality
body of uterusUBERON:000985377.95gold quality
omental fat padUBERON:001041477.93gold quality
peritoneumUBERON:000235877.86gold quality
ovaryUBERON:000099277.80gold quality
granulocyteCL:000009477.75gold quality
left uterine tubeUBERON:000130377.56gold quality
left coronary arteryUBERON:000162677.28gold quality
stomachUBERON:000094577.24gold quality
adrenal glandUBERON:000236977.21gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting NLE1, 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-1193100.0065.93529
HSA-MIR-8485100.0077.574731
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-430299.8967.941187
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-182599.7268.111089
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-149-5P99.2567.161315
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-66199.0965.942062
HSA-MIR-6868-5P99.0665.691284
HSA-MIR-4725-5P98.6765.42628
HSA-MIR-504-5P98.6765.40631
HSA-MIR-4722-5P98.4666.341611
HSA-MIR-313898.4167.53744
HSA-MIR-445098.2668.35725
HSA-MIR-4768-3P98.1666.022330
HSA-MIR-430398.0168.132304
HSA-MIR-6787-5P97.5463.85457
HSA-MIR-3127-5P97.5265.24786
HSA-MIR-3200-5P97.3465.97826
HSA-MIR-148B-5P97.2966.30992
HSA-MIR-6874-3P97.2966.34975
HSA-MIR-6856-3P96.4766.27781
HSA-MIR-808196.4267.75738
HSA-MIR-24-1-5P95.5765.85492
HSA-MIR-24-2-5P95.5766.16484
HSA-MIR-31-3P95.1769.82575

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • SMAD4 Loss Induces c-MYC-Mediated NLE1 Upregulation to Support Protein Biosynthesis, Colorectal Cancer Growth, and Metastasis. (PMID:36219392)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionle1ENSDARG00000057105
mus_musculusNle1ENSMUSG00000020692
rattus_norvegicusNle1ENSRNOG00000008287
drosophila_melanogasterNleFBGN0021874
caenorhabditis_elegansWBGENE00021074

Protein

Protein identifiers

Notchless protein homolog 1Q9NVX2 (reviewed: Q9NVX2)

All UniProt accessions (5): Q9NVX2, A0A0A0MRH0, K7EK23, K7EN33, K7ERN7

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in regulating Notch activity. Plays a role in regulating the expression of CDKN1A and several members of the Wnt pathway, probably via its effects on Notch activity. Required during embryogenesis for inner mass cell survival.

Subunit / interactions. Associates with the pre-60S ribosomal particle. Interacts (via WD repeats) with uL18. Interacts (via UBL domain) with MDN1 (via VWFA/MIDAS domain).

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the NLE1/RSA4 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NVX2-11yes
Q9NVX2-22

RefSeq proteins (2): NP_001014445, NP_060566* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001632WD40_G-protein_beta-likeDomain
IPR001680WD40_rptRepeat
IPR012972NLEDomain
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR020472WD40_PAC1Repeat
IPR036322WD40_repeat_dom_sfHomologous_superfamily

Pfam: PF00400, PF08154

UniProt features (26 total): repeat 8, sequence variant 5, strand 4, modified residue 2, helix 2, initiator methionine 1, chain 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

14 structures.

PDBMethodResolution (Å)
6WAJX-RAY DIFFRACTION1.9
8QL1X-RAY DIFFRACTION2.3
8FL3ELECTRON MICROSCOPY2.53
8FL2ELECTRON MICROSCOPY2.67
8RL2ELECTRON MICROSCOPY2.84
8FL4ELECTRON MICROSCOPY2.89
8FL0ELECTRON MICROSCOPY2.91
9QIWELECTRON MICROSCOPY3.04
8INKELECTRON MICROSCOPY3.2
8IPDELECTRON MICROSCOPY3.2
8IPYELECTRON MICROSCOPY3.2
8IR1ELECTRON MICROSCOPY3.3
8IR3ELECTRON MICROSCOPY3.5
8IPXELECTRON MICROSCOPY4.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NVX2-F193.940.86

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): 2, 79

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 166 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_BLASTOCYST_FORMATION, MUELLER_PLURINET, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_SOMITOGENESIS, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (11): mitotic cell cycle (GO:0000278), somitogenesis (GO:0001756), kidney development (GO:0001822), inner cell mass cell differentiation (GO:0001826), Notch signaling pathway (GO:0007219), regulation of Notch signaling pathway (GO:0008593), ribosomal large subunit biogenesis (GO:0042273), negative regulation of mitotic cell cycle (GO:0045930), skeletal system morphogenesis (GO:0048705), hematopoietic stem cell homeostasis (GO:0061484), positive regulation of canonical Wnt signaling pathway (GO:0090263)

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

GO Cellular Component (3): nucleoplasm (GO:0005654), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nuclear lumen2
cell cycle1
mitotic nuclear division1
anterior/posterior pattern specification1
segmentation1
chordate embryonic development1
anatomical structure formation involved in morphogenesis1
somite development1
animal organ development1
renal system development1
blastocyst formation1
cell differentiation1
cell surface receptor signaling pathway1
Notch signaling pathway1
regulation of signal transduction1
ribonucleoprotein complex biogenesis1
ribosome biogenesis1
mitotic cell cycle1
regulation of mitotic cell cycle1
negative regulation of cell cycle1
skeletal system development1
animal organ morphogenesis1
homeostasis of number of cells1
positive regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
binding1
cellular anatomical structure1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2156 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NLE1NOP56O00567551
NLE1MDN1Q9NU22509
NLE1RSL24D1Q9UHA3476
NLE1ZNF529Q6P280466
NLE1GNL3LQ9NVN8457
NLE1GNL3Q9BVP2453
NLE1BOP1Q14137443
NLE1WDR18Q9BV38437
NLE1WDR12Q9GZL7430
NLE1NOP53Q9NZM5429
NLE1SRPRBQ9Y5M8425
NLE1NIP7Q9Y221412
NLE1TAAR1Q96RJ0406
NLE1NMD3Q96D46405
NLE1NVLO15381403

IntAct

70 interactions, top by confidence:

ABTypeScore
CCT2TXNDC9psi-mi:“MI:0914”(association)0.730
NOL12RRP8psi-mi:“MI:0914”(association)0.640
MECP2KPNA3psi-mi:“MI:0914”(association)0.640
NSA2GNL2psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
PLEKHO1UBA6psi-mi:“MI:0914”(association)0.530
NSA2TYW5psi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
IGHMBP2THAP12psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
RBM4NVLpsi-mi:“MI:0914”(association)0.530
NIFKRSL1D1psi-mi:“MI:0914”(association)0.530
THAP7RPS27Apsi-mi:“MI:0914”(association)0.530
GNL3NLE1psi-mi:“MI:0915”(physical association)0.500
NLE1CHRM5psi-mi:“MI:0915”(physical association)0.370
EWSR1NLE1psi-mi:“MI:0915”(physical association)0.370
Spire2KLF4psi-mi:“MI:0914”(association)0.350
NOP9ENDOVpsi-mi:“MI:0914”(association)0.350
CHMP4Bpsi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350

BioGRID (578): NLE1 (Affinity Capture-MS), NLE1 (Affinity Capture-MS), NLE1 (Affinity Capture-MS), NLE1 (Affinity Capture-MS), NLE1 (Affinity Capture-MS), NLE1 (Two-hybrid), GBE1 (Co-fractionation), HNRNPH3 (Co-fractionation), MTHFD1 (Co-fractionation), NLE1 (Co-fractionation), NLE1 (Co-fractionation), SPAG7 (Co-fractionation), NLE1 (Affinity Capture-MS), NLE1 (Affinity Capture-Western), NLE1 (Affinity Capture-MS)

ESM2 similar proteins: A0AUS0, A4R2Q6, A5DL92, A5WVX1, A7RHG8, A8IR43, A8IRK7, A8QB65, A8XL02, A9UP22, B2B5V0, B3MJV8, B3N534, B3RQN1, B4GT01, B4JPT9, B4KKN1, B4LS78, B4P116, B5DG67, B7PY76, G0SFB5, P49177, P61480, P91343, Q0CLJ4, Q0VC24, Q29KQ0, Q2GXT0, Q58D20, Q5BJ90, Q5FVN8, Q5REE6, Q5RFF8, Q6CEW7, Q6NX08, Q756D0, Q7QJ33, Q8H594, Q8VEJ4

Diamond homologs: A0A223GEB2, A1L271, A2QPZ4, A4R3M4, A6H603, A6RRD4, B2VWG7, B3MHX6, B3MJV8, B4GT01, B4JPT9, B5DG67, B8N9H4, C0S902, C1GB49, C4R6H3, C4YPI7, C5GVJ9, C5JD40, E3LB80, G0S8H7, G1SJB4, G4MQX3, O14775, O18640, O24076, O24456, O42248, O42249, O94527, P0CS34, P0CS35, P25382, P25387, P38011, P40968, P46800, P49026, P49027, P52287

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 79 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
Peptide chain elongation718.1×1e-05
Viral mRNA Translation718.1×1e-05
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA717.9×1e-05
Selenocysteine synthesis717.2×1e-05
Eukaryotic Translation Termination717.2×1e-05
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)716.8×1e-05
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA716.8×1e-05
Formation of a pool of free 40S subunits716.0×2e-05

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation717.5×3e-05
rRNA processing815.3×2e-05
translation79.7×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1668 predictions. Top by Δscore:

VariantEffectΔscore
17:35129569:C:Gdonor_gain1.0000
17:35129575:GAGC:Gdonor_gain1.0000
17:35129578:C:Gdonor_gain1.0000
17:35129606:GT:Gdonor_gain1.0000
17:35129659:G:GGdonor_gain1.0000
17:35130278:TCA:Tacceptor_loss1.0000
17:35130279:CAGT:Cacceptor_loss1.0000
17:35130280:A:AGacceptor_gain1.0000
17:35130280:AGT:Aacceptor_loss1.0000
17:35130281:G:Aacceptor_loss1.0000
17:35130281:G:GAacceptor_gain1.0000
17:35130281:GTTT:Gacceptor_gain1.0000
17:35133169:A:ACdonor_gain1.0000
17:35133169:ACAT:Adonor_gain1.0000
17:35133170:C:CCdonor_gain1.0000
17:35133170:CAT:Cdonor_gain1.0000
17:35133170:CATC:Cdonor_gain1.0000
17:35133334:CCTA:Cdonor_loss1.0000
17:35133336:TACC:Tdonor_loss1.0000
17:35133337:A:ACdonor_gain1.0000
17:35133337:A:Tdonor_loss1.0000
17:35133338:C:CCdonor_gain1.0000
17:35133338:CCT:Cdonor_gain1.0000
17:35133496:TAC:Tacceptor_gain1.0000
17:35133497:ACCTG:Aacceptor_loss1.0000
17:35133499:C:CCacceptor_gain1.0000
17:35133505:C:CTacceptor_gain1.0000
17:35133505:C:Tacceptor_gain1.0000
17:35133506:A:Tacceptor_gain1.0000
17:35134970:TGA:Tdonor_gain1.0000

AlphaMissense

3153 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:35133197:A:CS473R1.000
17:35133197:A:TS473R1.000
17:35133199:T:GS473R1.000
17:35133226:A:GW464R1.000
17:35133226:A:TW464R1.000
17:35133420:G:CS431R1.000
17:35133420:G:TS431R1.000
17:35133422:T:GS431R1.000
17:35135296:A:CS389R1.000
17:35135296:A:TS389R1.000
17:35135298:T:GS389R1.000
17:35135420:G:AS348F1.000
17:35137166:G:CS221R1.000
17:35137166:G:TS221R1.000
17:35137168:T:GS221R1.000
17:35139302:A:CS131R1.000
17:35139302:A:TS131R1.000
17:35139304:T:GS131R1.000
17:35132448:A:GW483R0.999
17:35132448:A:TW483R0.999
17:35133192:C:TG475E0.999
17:35133195:C:TG474D0.999
17:35133221:A:CS465R0.999
17:35133221:A:TS465R0.999
17:35133223:T:GS465R0.999
17:35133358:A:GL452P0.999
17:35133392:A:GW441R0.999
17:35133392:A:TW441R0.999
17:35133396:C:AK439N0.999
17:35133396:C:GK439N0.999

dbSNP variants (sampled 300 via entrez): RS1000163855 (17:35130645 G>A), RS1000190657 (17:35141190 A>G), RS1000318372 (17:35136458 C>T), RS1000365527 (17:35134995 T>C), RS1000425693 (17:35130934 C>G,T), RS1000649241 (17:35136717 G>A), RS1000679543 (17:35133874 C>T), RS1000822510 (17:35140085 G>A), RS1000896574 (17:35141490 G>A), RS1000919481 (17:35139814 A>C), RS1001054646 (17:35135077 A>G), RS1001423057 (17:35139851 T>C), RS1001455680 (17:35139559 TC>T), RS1001649997 (17:35134123 A>T), RS1001985352 (17:35132960 G>A)

Disease associations

OMIM: gene MIM:620924 | 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

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, affects cotreatment, increases expression2
sodium arsenitedecreases expression, increases expression2
Estradiolincreases expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
trichostatin Aaffects expression1
potassium chromate(VI)increases expression1
nivalenolincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
nutlin 3affects cotreatment, increases secretion1
enzalutamideaffects expression1
LDN 193189affects cotreatment, decreases expression1
Temozolomideincreases expression1
Cisplatindecreases expression, decreases reaction1
Dactinomycinaffects cotreatment, increases secretion1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Phenobarbitalaffects expression1
Piroxicamdecreases expression, decreases reaction1
Quercetinincreases expression1
Ribonucleotidesaffects binding1
Silicon Dioxideincreases 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.