MYCL

gene
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Also known as LMYCbHLHe38

Summary

MYCL (MYCL proto-oncogene, bHLH transcription factor, HGNC:7555) is a protein-coding gene on chromosome 1p34.2, encoding Protein L-Myc (P12524). In precision oncology, MYCL EXPRESSION confers sensitivity to I-BET151 + JQ1 in Multiple Myeloma (CIViC Level D).

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 regulation of inner ear auditory receptor cell differentiation. Located in chromosome and nucleoplasm.

Source: NCBI Gene 4610 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 47 total
  • Precision-oncology evidence (CIViC): 1 curated variant–drug association
  • MANE Select transcript: NM_001033081

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7555
Approved symbolMYCL
NameMYCL proto-oncogene, bHLH transcription factor
Location1p34.2
Locus typegene with protein product
StatusApproved
AliasesLMYC, bHLHe38
Ensembl geneENSG00000116990
Ensembl biotypeprotein_coding
OMIM164850
Entrez4610

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000372815, ENST00000372816, ENST00000397332, ENST00000450953

RefSeq mRNA: 3 — MANE Select: NM_001033081 NM_001033081, NM_001033082, NM_005376

CCDS: CCDS30682, CCDS44117, CCDS53300

Canonical transcript exons

ENST00000372816 — 2 exons

ExonStartEnd
ENSE000014587273990093939901917
ENSE000019365183989542839897970

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 90.19.

FANTOM5 (CAGE): breadth broad, TPM avg 4.4829 / max 454.5918, expressed in 899 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
118882.6892752
118891.3620447
118900.3885218
118870.043213

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057690.19gold quality
mononuclear cellCL:000084290.00gold quality
leukocyteCL:000073889.92gold quality
skin of legUBERON:000151188.56gold quality
epithelium of esophagusUBERON:000197688.38gold quality
skin of abdomenUBERON:000141688.27gold quality
esophagus squamous epitheliumUBERON:000692088.10gold quality
upper leg skinUBERON:000426287.58gold quality
zone of skinUBERON:000001487.32gold quality
granulocyteCL:000009485.87gold quality
body of pancreasUBERON:000115085.79gold quality
mucosa of urinary bladderUBERON:000125985.60silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.00gold quality
esophagus mucosaUBERON:000246983.93gold quality
gingivaUBERON:000182883.61gold quality
gingival epitheliumUBERON:000194982.77gold quality
upper arm skinUBERON:000426382.15silver quality
lower esophagus mucosaUBERON:003583481.25gold quality
squamous epitheliumUBERON:000691481.07gold quality
cortical plateUBERON:000534380.84gold quality
skin of hipUBERON:000155480.34gold quality
ganglionic eminenceUBERON:000402379.91gold quality
urinary bladderUBERON:000125579.70gold quality
nasal cavity epitheliumUBERON:000538478.87gold quality
ileal mucosaUBERON:000033178.38gold quality
pancreasUBERON:000126478.35gold quality
oral cavityUBERON:000016777.73gold quality
epithelium of bronchusUBERON:000203177.13gold quality
mucosa of transverse colonUBERON:000499176.83gold quality
bronchial epithelial cellCL:000232876.45gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.97

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
KCNQ4Repression
RLF

Upstream regulators (CollecTRI, top): E2F4, GLI1, MYC, MYF5, MYOD1

miRNA regulators (miRDB)

81 targeting MYCL, 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-6129100.0066.462080
HSA-MIR-6133100.0066.482064
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6130100.0066.692012
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-548AW99.9972.573559
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-548AN99.9770.912817
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-211099.9666.681930
HSA-MIR-391099.9571.132227
HSA-LET-7C-3P99.9573.422862
HSA-MIR-539-5P99.9370.302855
HSA-MIR-338-5P99.9272.342951
HSA-MIR-605-3P99.8869.221833
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-44899.7972.372103
HSA-MIR-548AJ-5P99.7871.123085
HSA-MIR-548F-5P99.7871.023093
HSA-MIR-548G-5P99.7871.123085
HSA-MIR-548X-5P99.7871.123085
HSA-MIR-129999.7771.242389
HSA-MIR-62399.7668.161170
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-366099.6867.331149
HSA-MIR-452699.6867.071136

Literature-anchored findings (GeneRIF, showing 19)

  • L-myc polymorphism may affect the induction of lung cancer by smoking (PMID:11802801)
  • L-myc proto oncogene RFLP is associated with lung adenocarcinoma (PMID:11836605)
  • Allelic deletions of L-myc in urine from bladder cancer patients (PMID:11956626)
  • MYCL1, FHIT, SPARC, p16(INK4) and TP53 genes associated to lung cancer in idiopathic pulmoary fibrosis (PMID:12169206)
  • Colorectal tumor patients whose tumors exhibited loss of heterozygosity at MYCL1 at chromosome 1p34 were likely to have a poor prognosis. (PMID:15014029)
  • polymorphisms in the MYCL1 LD region affect lung cancer survival but that the functional element(s) may show population-specific patterns (PMID:17145094)
  • L-myc gene polymorphism may have a role in risk of thyroid cancer (PMID:18566574)
  • The L-myc gene polymorphism may help detect and prevent HNNMSC and LLC in susceptible individuals. It may also contribute to estimation of tumor behavior in patients with HNNMSC. (PMID:18645122)
  • L-Myc may have a role in Merkel cell carcinoma pathogenesis (PMID:19020549)
  • The results demonstrate that MYCL1 rs3134613 is associated with susceptibility to diffuse-type gastric cancer and with differentiation of gastric cancer. (PMID:20874233)
  • MYCL1 is the target of hsa-miR-1827. A rs3134615 G>T SNP in the 3’-UTR altered regulation of MYCL1 expression. This SNP was associated with increased susceptibility to SCLC, possibly resulting from attenuated interaction with the miRNA hsa-miR-1827. (PMID:21676885)
  • The polymorphism of H-ras and L-myc genes is not related to colorectal cancer risk, but there is a synergy between H-ras and L-myc polymorphisms in the development of rectal cancer. (PMID:22490849)
  • Several tagging SNPs and haplotypes in TRIT1, MYCL1 and MFSD2A region are significantly associated with risk and clinicopathological features of gastric cancer in a Chinese population. (PMID:23349019)
  • These results suggest that Mycl1 expression might be useful as a biomarker to predict prognosis and is a promising therapeutic target for patients with gastric cancer. (PMID:25528583)
  • display of the influence of MYCL1 gene on invasion and migration phenotype of gastric cancer cells and a possible explanation from the aspect of structural alteration; results suggested that downregulation of MYCL1 may be a potential therapeutic strategy for gastric cancer (PMID:31025404)
  • MYCL1 Amplification and Expression of L-Myc and c-Myc in Surgically Resected Small-Cell Lung Carcinoma. (PMID:34257619)
  • MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains. (PMID:34930932)
  • MYCL promotes the progression of triplenegative breast cancer by activating the JAK/STAT3 pathway. (PMID:36177900)
  • Comparative study on the mutation spectrum of L-MYC and C-MYC genes of blood cfDNA in patients with ovarian cancer and healthy females. (PMID:37827180)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriomyclaENSDARG00000006003
danio_reriomyclbENSDARG00000034956
mus_musculusMyclENSMUSG00000028654
rattus_norvegicusMyclENSRNOG00000014259

Paralogs (2): MYCN (ENSG00000134323), MYC (ENSG00000136997)

Protein

Protein identifiers

Protein L-MycP12524 (reviewed: P12524)

Alternative names: Class E basic helix-loop-helix protein 38, Protein L-Myc-1, V-myc myelocytomatosis viral oncogene homolog

All UniProt accessions (2): E9PQS5, P12524

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Efficient DNA binding requires dimerization with another bHLH protein. Binds DNA as a heterodimer with MAX.

Subcellular location. Nucleus.

Isoforms (3)

UniProt IDNamesCanonical?
P12524-11yes
P12524-22, Short
P12524-33

RefSeq proteins (3): NP_001028253, NP_001028254, NP_005367 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002418Tscrpt_reg_MycFamily
IPR011598bHLH_domDomain
IPR012682Tscrpt_reg_Myc_NDomain
IPR036638HLH_DNA-bd_sfHomologous_superfamily
IPR050433Myc_transcription_factorsFamily

Pfam: PF00010, PF01056

UniProt features (11 total): region of interest 4, splice variant 3, chain 1, domain 1, sequence variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P12524-F164.820.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 283 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GGTGTGT_MIR329, GOBP_REGULATION_OF_EPIDERMIS_DEVELOPMENT, GOBP_NEUROGENESIS, CTATGCA_MIR153, USF_C, GCM_MYCL1, GOBP_REGULATION_OF_EPITHELIAL_CELL_DIFFERENTIATION, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP, KRASNOSELSKAYA_ILF3_TARGETS_DN, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, TCF4_Q5, RICKMAN_METASTASIS_DN, GOBP_EAR_DEVELOPMENT

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of inner ear auditory receptor cell differentiation (GO:0045607), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): 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 (GO:0003677), protein dimerization activity (GO:0046983), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
cellular anatomical structure2
transcription by RNA polymerase II1
inner ear auditory receptor cell differentiation1
regulation of epidermal cell differentiation1
regulation of inner ear receptor cell differentiation1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
nucleic acid binding1
protein binding1
transcription cis-regulatory region binding1
transcription regulator activity1
binding1
chromosome1
nuclear lumen1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1338 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MYCLMAXP25912851
MYCLEP400Q96L91829
MYCLRLFQ13129804
MYCLLIN28AQ9H9Z2763
MYCLPPIEQ9UNP9729
MYCLKLF4P78338714
MYCLSOX2P48431696
MYCLGLIS1Q8NBF1678
MYCLTP53P04637635
MYCLPOU5F1P31359618
MYCLCOL9A2Q14055604
MYCLREEP5Q00765580
MYCLWDR12Q9GZL7573
MYCLMNTQ99583549
MYCLNANOGQ9H9S0547

IntAct

20 interactions, top by confidence:

ABTypeScore
MAXE2F6psi-mi:“MI:0914”(association)0.710
MYCLCASKpsi-mi:“MI:0914”(association)0.350
MYCLKIF5Cpsi-mi:“MI:0914”(association)0.350
AKT1MYCLpsi-mi:“MI:2364”(proximity)0.270
BRAFMYCLpsi-mi:“MI:2364”(proximity)0.270
FBXW7MYCLpsi-mi:“MI:2364”(proximity)0.270
SMAD4MYCLpsi-mi:“MI:2364”(proximity)0.270
MYCLSMARCA4psi-mi:“MI:2364”(proximity)0.270
SMARCA4MYCLpsi-mi:“MI:2364”(proximity)0.270
MYCLSPOPpsi-mi:“MI:2364”(proximity)0.270
SPOPMYCLpsi-mi:“MI:2364”(proximity)0.270
PTPN11MYCLpsi-mi:“MI:2364”(proximity)0.270
MYCLPTENpsi-mi:“MI:2364”(proximity)0.270
MYCLEGFRpsi-mi:“MI:2364”(proximity)0.270

BioGRID (87): KLC3 (Affinity Capture-MS), KLC4 (Affinity Capture-MS), KAT5 (Affinity Capture-MS), EPC1 (Affinity Capture-MS), ING3 (Affinity Capture-MS), EPC2 (Affinity Capture-MS), EP400 (Affinity Capture-MS), KIF5A (Affinity Capture-MS), TRRAP (Affinity Capture-MS), KLC2 (Affinity Capture-MS), MBTD1 (Affinity Capture-MS), VPS72 (Affinity Capture-MS), MEAF6 (Affinity Capture-MS), JAZF1 (Affinity Capture-MS), KIF5B (Affinity Capture-MS)

ESM2 similar proteins: A2RU30, D3YN49, D3ZDX9, D6RGH6, E9PV82, F1QN48, F1SLM8, F7BHS0, G3N1S4, H2M146, O35451, O94983, P10166, P12524, P12525, P20389, P23999, Q08B36, Q14140, Q14153, Q1HGE8, Q3UZ45, Q5JXC2, Q5M9G5, Q5R815, Q61817, Q64210, Q68DK7, Q6NSI3, Q6P1D7, Q6PB51, Q6PDM1, Q7TNY7, Q80Y50, Q8BP99, Q8BXQ8, Q8IY92, Q8K3I4, Q8K589, Q8R0W1

Diamond homologs: A1YG22, A2T7L5, B8XIA5, P01106, P01108, P01109, P01110, P03966, P04198, P06171, P06295, P06646, P09416, P0C0N8, P0C0N9, P10166, P10395, P12523, P12524, P15063, P15171, P18444, P20389, P21438, P22555, P23583, P23999, P24793, P26014, P28574, P49032, P49033, P49709, P52160, P52161, P52162, P52164, P61244, P61245, P68271

SIGNOR signaling

2 interactions.

AEffectBMechanism
MYCLup-regulatesProliferation
MYCLup-regulatesDifferentiation

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

302 predictions. Top by Δscore:

VariantEffectΔscore
1:39897967:TTCT:Tacceptor_gain1.0000
1:39897969:CT:Cacceptor_gain1.0000
1:39897971:C:CCacceptor_gain1.0000
1:39897976:C:CTacceptor_gain1.0000
1:39897976:C:Tacceptor_gain1.0000
1:39897977:G:Tacceptor_gain1.0000
1:39897989:C:CTacceptor_gain1.0000
1:39897990:A:Tacceptor_gain1.0000
1:39897966:ATTCT:Aacceptor_gain0.9900
1:39897970:TC:Tacceptor_loss0.9900
1:39897971:C:CAacceptor_loss0.9900
1:39897972:T:Cacceptor_loss0.9900
1:39900933:CCTTA:Cdonor_loss0.9900
1:39900934:CTTA:Cdonor_loss0.9900
1:39900935:TTACC:Tdonor_loss0.9900
1:39900936:TACCC:Tdonor_loss0.9900
1:39900937:A:ACdonor_gain0.9900
1:39900937:A:Cdonor_loss0.9900
1:39900937:AC:Adonor_gain0.9900
1:39900938:C:CCdonor_gain0.9900
1:39900938:CC:Cdonor_gain0.9900
1:39897967:TTCTC:Tacceptor_gain0.9800
1:39897968:TCTC:Tacceptor_gain0.9800
1:39897969:CTCT:Cacceptor_gain0.9800
1:39901803:CTCAC:Cdonor_loss0.9700
1:39901804:TCACC:Tdonor_loss0.9700
1:39901344:T:TAdonor_gain0.9600
1:39901440:CTCC:Cacceptor_gain0.9600
1:39901825:C:CTdonor_gain0.9500
1:39901441:TCCC:Tacceptor_loss0.9400

AlphaMissense

2371 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:39897499:A:GL323P1.000
1:39897510:T:AK319N1.000
1:39897510:T:GK319N1.000
1:39897556:A:GL304P1.000
1:39897565:A:GF301S1.000
1:39897577:A:GL297P1.000
1:39897586:C:GR294P1.000
1:39897588:C:AR293S1.000
1:39897588:C:GR293S1.000
1:39897589:C:AR293M1.000
1:39897589:C:GR293T1.000
1:39897595:C:GR291P1.000
1:39897596:G:TR291S1.000
1:39897597:C:AE290D1.000
1:39897597:C:GE290D1.000
1:39897598:T:AE290V1.000
1:39897599:C:TE290K1.000
1:39897611:G:CH286D1.000
1:39901336:G:CF33L1.000
1:39901336:G:TF33L1.000
1:39901338:A:GF33L1.000
1:39901347:A:GW30R1.000
1:39901347:A:TW30R1.000
1:39897490:G:TA326D0.999
1:39897491:C:GA326P0.999
1:39897499:A:TL323Q0.999
1:39897502:A:TI322N0.999
1:39897511:T:AK319I0.999
1:39897512:T:CK319E0.999
1:39897552:C:AR305S0.999

dbSNP variants (sampled 300 via entrez): RS1000383217 (1:39900118 T>C), RS1000703940 (1:39898441 A>G), RS1001412518 (1:39899831 T>C), RS1001763850 (1:39899081 A>C,G), RS1002173108 (1:39901270 G>C), RS1002780086 (1:39899689 G>A), RS1002931163 (1:39899364 G>A), RS1003359409 (1:39903910 T>A), RS1003519625 (1:39897923 C>A,T), RS1004024765 (1:39899048 G>A), RS1004140693 (1:39898784 A>G), RS1004187969 (1:39898260 T>C), RS1004200986 (1:39895050 C>A,G), RS1005055787 (1:39902493 G>A), RS1005129214 (1:39902307 A>G,T)

Disease associations

OMIM: gene MIM:164850 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010002_380Refractive error4.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

Clinical evidence (CIViC)

Drug × variant × indication: 1 predictive associations from 1 curated evidence items.

VariantTherapyIndicationEffectLevelCIViC
MYCL EXPRESSIONI-BET151 + JQ1Multiple MyelomaSensitivity/ResponseCIViC DEID1706

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, increases expression, affects cotreatment5
trichostatin Aaffects cotreatment, decreases expression, affects expression, increases expression4
sodium arsenitedecreases expression, increases expression4
mercuric bromidedecreases expression, affects cotreatment2
Air Pollutantsdecreases expression2
Benzo(a)pyrenedecreases expression, increases methylation2
Calcitriolincreases expression, affects cotreatment2
Estradioldecreases expression, affects cotreatment2
Lipopolysaccharidesincreases expression, affects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Testosteroneaffects cotreatment, increases expression, decreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
bisphenol Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
perfluorooctanoic acidincreases expression1
nickel sulfatedecreases expression1
hydroquinonedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
seocalcitolincreases expression1
monomethylarsonous aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphindecreases expression, affects cotreatment1
licochalcone Bincreases expression1
GSK1210151Adecreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Endosulfanincreases expression1
Formaldehydedecreases expression1
Methotrexatedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 somatic stem cell

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

CellosaurusNameCategorySex
CVCL_LJ42LM-NSC008Somatic stem cellFemale

Clinical trials (associated diseases)

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

  • Associated diseases: plasma cell myeloma
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): plasma cell myeloma