MYCN MYCN proto-oncogene, bHLH transcription factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: MYCNprovided by HGNC
Official Full Name: MYCN proto-oncogene, bHLH transcription factorprovided by HGNC
Primary source: HGNC:HGNC:7559
See related: Ensembl:ENSG00000134323 MIM:164840; AllianceGenome:HGNC:7559
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NMYC; ODED; MODED; MPAPA; N-myc; FGLDS1; bHLHe37; MYCNsORF; MYCNsPEP
Summary: This gene is a member of the MYC family and encodes a protein with a basic helix-loop-helix (bHLH) domain. This protein is located in the nucleus and must dimerize with another bHLH protein in order to bind DNA. Amplification of this gene is associated with a variety of tumors, most notably neuroblastomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
Expression: Broad expression in placenta (RPKM 4.0), ovary (RPKM 2.1) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p24.3

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (15940550..15947004)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (15972182..15978635)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (16080672..16087126)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness.
Title: CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness.
MTHFD1 regulates the NADPH redox homeostasis in MYCN-amplified neuroblastoma.
Title: MTHFD1 regulates the NADPH redox homeostasis in MYCN-amplified neuroblastoma.
MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression.
Title: MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression.
Computational completion of the Aurora interaction region of N-Myc in the Aurora a kinase complex.
Title: Computational completion of the Aurora interaction region of N-Myc in the Aurora a kinase complex.
Prediction of MYCN Gene Amplification in Pediatric Neuroblastomas: Development of a Deep Learning-Based Tool for Automatic Tumor Segmentation and Comparative Analysis of Computed Tomography-Based Radiomics Features Harmonization.
Title: Prediction of MYCN Gene Amplification in Pediatric Neuroblastomas: Development of a Deep Learning-Based Tool for Automatic Tumor Segmentation and Comparative Analysis of Computed Tomography-Based Radiomics Features Harmonization.
MYCN amplification, TERT rearrangements and ATRX mutations in neuroblastoma: clinicopathological correlates- an Indian perspective.
Title: MYCN amplification, TERT rearrangements and ATRX mutations in neuroblastoma: clinicopathological correlates- an Indian perspective.
LncRNA AC142119.1 facilitates the progression of neuroblastoma by epigenetically initiating the transcription of MYCN.
Title: LncRNA AC142119.1 facilitates the progression of neuroblastoma by epigenetically initiating the transcription of MYCN.
USP7 Inhibition Suppresses Neuroblastoma Growth via Induction of p53-Mediated Apoptosis and EZH2 and N-Myc Downregulation.
Title: USP7 Inhibition Suppresses Neuroblastoma Growth via Induction of p53-Mediated Apoptosis and EZH2 and N-Myc Downregulation.
A novel MYCN-YTHDF1 cascade contributes to retinoblastoma tumor growth by eliciting m[6]A -dependent activation of multiple oncogenes.
Title: A novel MYCN-YTHDF1 cascade contributes to retinoblastoma tumor growth by eliciting m(6)A -dependent activation of multiple oncogenes.
MYCN amplification and International Neuroblastoma Risk Group stratification on fine-needle aspiration biopsy and their correlation to survival in neuroblastoma.
Title: MYCN amplification and International Neuroblastoma Risk Group stratification on fine-needle aspiration biopsy and their correlation to survival in neuroblastoma.

Submit: New GeneRIF Correction See all GeneRIFs (433)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Feingold syndrome type 1 MedGen: C4551774 OMIM: 164280 GeneReviews: Feingold Syndrome 1	Compare labs
Megalencephaly-polydactyly syndrome MedGen: CN377205 OMIM: 620748 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2017-07-12) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2017-07-12) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study identifies susceptibility loci for Wilms tumor. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genes underlying asthma and COPD? Genome-wide analysis on the Dutch hypothesis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MYCN_953 (e-PCR)
- UniSTS:277517

MYCN_V227 (e-PCR)
- UniSTS:277517

D2S2719 (e-PCR)
- UniSTS:52755

MYCN (e-PCR)
- UniSTS:266043

RH69067 (e-PCR)
- UniSTS:82532

RH17899 (e-PCR)
- UniSTS:32360

MARC_10471-10472:999704936:1 (e-PCR)
- UniSTS:267151

D2S390 (e-PCR), detects polymorphism
- UniSTS:31440

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of miRNA transcription	IC Inferred by Curator more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: N-myc proto-oncogene protein

Names: class E basic helix-loop-helix protein 37; neuroblastoma MYC oncogene; neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene; oncogene NMYC; v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007457.2 RefSeqGene

Range

5002..11456

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001293228.2 → NP_001280157.1 N-myc proto-oncogene protein isoform 1

See identical proteins and their annotated locations for NP_001280157.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the full-length transcript. Its exon 1 includes segments 1a and 1b (also known as exon 1a and exon 1b, PMID: 20017904). This variant encodes isoform 1.

Source sequence(s)

AC010145, BC002712

Consensus CDS

CCDS1687.1

UniProtKB/Swiss-Prot

P04198, Q53XS5, Q6LDT9

UniProtKB/TrEMBL

B4DRZ1

Conserved Domains (2) summary

cd00083
Location:379 → 438

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam01056
Location:10 → 372

Myc_N; Myc amino-terminal region
NM_001293231.2 → NP_001280160.1 N-myc proto-oncogene protein isoform 2

See identical proteins and their annotated locations for NP_001280160.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks segment 1b and exon 2, which results in an upstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC010145, BC002712

Consensus CDS

CCDS86823.1

UniProtKB/TrEMBL

A0A1W2PPD9

Related

ENSP00000491476.1, ENST00000638417.1

Conserved Domains (2) summary

cd11456
Location:167 → 253

bHLHzip_N-Myc_like; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in N-Myc and similar proteins

pfam01056
Location:66 → 161

Myc_N; Myc amino-terminal region
NM_001293233.2 → NP_001280162.1 N-myc proto-oncogene protein isoform 3

See identical proteins and their annotated locations for NP_001280162.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks segment 1b in the 5' region, compared to variant 1. This variant includes two open reading frames; the isoform (3, also known as MYCNOT, see PMID: 20017904) represented by this Refseq is translated from the upstream open reading frame. The isoform 3 has an identical N-terminus to that of the isoform 2, and the function of the isoform 3 is currently unknown.

Source sequence(s)

AC010145, BC002712

UniProtKB/TrEMBL

Q9H224
NM_005378.6 → NP_005369.2 N-myc proto-oncogene protein isoform 1

See identical proteins and their annotated locations for NP_005369.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks segment 1b in the 5' region, compared to variant 1. This variant includes two open reading frames; the isoform 1 represented by this RefSeq is translated from the downstream open reading frame. This transcript and variant 1 encode the same isoform 1.

Source sequence(s)

AC010145, BC002712

Consensus CDS

CCDS1687.1

UniProtKB/Swiss-Prot

P04198, Q53XS5, Q6LDT9

UniProtKB/TrEMBL

B4DRZ1

Related

ENSP00000281043.3, ENST00000281043.4

Conserved Domains (2) summary

cd00083
Location:379 → 438

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam01056
Location:10 → 372

Myc_N; Myc amino-terminal region