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

Gene ID: 4613, updated on 10-Oct-2024

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
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Genomic context

See MYCN in Genome Data Viewer
Location:
2p24.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (15940550..15947004)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (15972182..15978635)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (16080672..16087126)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene MYCN upstream transcript Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:16078668-16079225 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:16080270-16080800 Neighboring gene MYCN opposite strand Neighboring gene RNA, 7SL, cytoplasmic 104, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:16120447-16121234 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:16140957-16141151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:16153570-16154181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:16174407-16174907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:16197762-16198262 Neighboring gene gastric cancer associated transcript 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Feingold syndrome type 1
MedGen: C4551774 OMIM: 164280 GeneReviews: Feingold Syndrome 1
not available
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
Common genes underlying asthma and COPD? Genome-wide analysis on the Dutch hypothesis.
EBI GWAS Catalog
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in 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

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)

NEW Try the new Transcript table

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

  1. NG_007457.2 RefSeqGene

    Range
    5002..11456
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001293228.2NP_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:379438
    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:10372
    Myc_N; Myc amino-terminal region
  2. NM_001293231.2NP_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:167253
    bHLHzip_N-Myc_like; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in N-Myc and similar proteins
    pfam01056
    Location:66161
    Myc_N; Myc amino-terminal region
  3. NM_001293233.2NP_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
  4. NM_005378.6NP_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:379438
    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:10372
    Myc_N; Myc amino-terminal region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    15940550..15947004
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444434.1XP_047300390.1  N-myc proto-oncogene protein isoform X1

    UniProtKB/Swiss-Prot
    P04198, Q53XS5, Q6LDT9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    15972182..15978635
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342160.1XP_054198135.1  N-myc proto-oncogene protein isoform X1

    UniProtKB/Swiss-Prot
    P04198, Q53XS5, Q6LDT9