MYCBP2 MYC binding protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: MYCBP2provided by HGNC
Official Full Name: MYC binding protein 2provided by HGNC
Primary source: HGNC:HGNC:23386
See related: Ensembl:ENSG00000005810 MIM:610392; AllianceGenome:HGNC:23386
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: PAM; Phr; PHR1; Myc-bp2
Summary: This gene encodes an E3 ubiquitin-protein ligase and member of the PHR (Phr1/MYCBP2, highwire and RPM-1) family of proteins. The encoded protein plays a role in axon guidance and synapse formation in the developing nervous system. In mammalian cells, this protein regulates the cAMP and mTOR signaling pathways, and may additionally regulate autophagy. Reduced expression of this gene has been observed in acute lymphoblastic leukemia patients and a mutation in this gene has been identified in patients with a rare inherited vision defect. [provided by RefSeq, Mar 2017]
Expression: Ubiquitous expression in skin (RPKM 12.3), brain (RPKM 10.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q22.3

Exon count:: 83

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (77044657..77327094, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (76268292..76550942, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (77618792..77901229, complement)

Chromosome 13 - NC_000013.11 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 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?

Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function.
Title: Ubiquitin ligase and signalling hub MYCBP2 is required for efficient EPHB2 tyrosine kinase receptor function.
Loss-of-function variants in MYCBP2 cause neurobehavioural phenotypes and corpus callosum defects.
Title: Loss-of-function variants in MYCBP2 cause neurobehavioural phenotypes and corpus callosum defects.
MYCBP2 expression correlated with inflammatory cell infiltration and prognosis immunotherapy in thyroid cancer patients.
Title: MYCBP2 expression correlated with inflammatory cell infiltration and prognosis immunotherapy in thyroid cancer patients.
FBXO45-MYCBP2 regulates mitotic cell fate by targeting FBXW7 for degradation.
Title: FBXO45-MYCBP2 regulates mitotic cell fate by targeting FBXW7 for degradation.
MYCBP2, a member of the c-myc oncogene family, is a direct functional target of miR-1247. Furthermore, in colorectal cancer patients, MYCBP2 protein levels are associated with miR-1247 levels and survival
Title: Epigenetically regulated miR-1247 functions as a novel tumour suppressor via MYCBP2 in methylator colon cancers.
identification of the neuron-associated E3 ligase MYCBP2 (also known as PHR1) as the apparent single member of a class of RING-linked E3 ligase with esterification activity and intrinsic selectivity for threonine over serine
Title: Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity.
Data indicate an oncogenic role for an Ikaros protein/MYCBP2 protein/proto-oncogene protein c-MYC axis in adult acute lymphoblastic leukemia (ALL), providing a mechanism of target therapies that activate Ikaros in ALL.
Title: Clinical significance of high c-MYC and low MYCBP2 expression and their association with Ikaros dysfunction in adult acute lymphoblastic leukemia.
Arf-bp1 and Pam are novel regulators of circadian gene expression that target Rev-erb alpha for degradation
Title: E3 ligases Arf-bp1 and Pam mediate lithium-stimulated degradation of the circadian heme receptor Rev-erb alpha.
Data show that epithelial-mesenchymal transition (EMT)-transcription factors can be dynamically degraded by an atypical ubiquitin E3 ligase complex Skp1-Pam-Fbxo45 (SPFFbxo45).
Title: Atypical ubiquitin E3 ligase complex Skp1-Pam-Fbxo45 controls the core epithelial-to-mesenchymal transition-inducing transcription factors.
In castration resistant prostate cancer, MYCBP2 is down-regulated at the mRNA and protein levels.
Title: MiR-1247-5p is overexpressed in castration resistant prostate cancer and targets MYCBP2.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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

EBI GWAS Catalog

Description
Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of pre-eclampsia detects novel maternal single nucleotide polymorphisms and copy-number variants in subsets of the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study cohort. 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

SHGC-108010 (e-PCR)
- UniSTS:170498

D13S1306 (e-PCR), detects polymorphism
- UniSTS:14177

SHGC-150891 (e-PCR)
- UniSTS:173430

STS-Z40889 (e-PCR)
- UniSTS:73883

WI-21663 (e-PCR)
- UniSTS:74414

RH79670 (e-PCR)
- UniSTS:85231

Clone Names

FLJ10106, FLJ13826, FLJ21597, FLJ21646, KIAA0916, DKFZp686M08244

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in branchiomotor neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in central nervous system projection neuron axonogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K48-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein localization	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic assembly at neuromuscular junction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IC Inferred by Curator more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
located_in microtubule cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase MYCBP2

Names: Highwire; MYC binding protein 2, E3 ubiquitin protein ligase; PAM/Highwire/RPM-1 protein 1; RING-type E3 ubiquitin transferase MYCBP2; myc-binding protein 2; protein associated with Myc

NP_055872.4

EC 2.3.2.33

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_053031.1 RefSeqGene

Range

4949..287386

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_015057.5 → NP_055872.4 E3 ubiquitin-protein ligase MYCBP2

Status: REVIEWED

Source sequence(s)

AC001226, AF075587, AL159154, AL159158, AL359257

UniProtKB/Swiss-Prot

A6NJC6, O75592, Q5JSX8, Q5VZN6, Q6PIB6, Q9UQ11, Q9Y6E4

UniProtKB/TrEMBL

A0A804HIR9

Related

ENSP00000444596.2, ENST00000544440.7

Conserved Domains (9) summary

pfam00415
Location:958 → 1006

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam08005
Location:1727 → 1882

PHR; PHR domain

pfam11702
Location:2880 → 3023

DUF3295; Protein of unknown function (DUF3295)

pfam13540
Location:943 → 971

RCC1_2; Regulator of chromosome condensation (RCC1) repeat

cd16463
Location:4425 → 4479

RING-H2_PHR; RING finger, H2 subclass, found in the PHR protein family

cl02148
Location:3748 → 3840

APC10-like; APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination

cl25836
Location:2725 → 2930

Retinal; Retinal protein

cl27659
Location:2394 → 2445

Filamin; Filamin/ABP280 repeat

cl27697
Location:527 → 716

RCC1; Regulator of chromosome condensation (RCC1) repeat