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NAB2 NGFI-A binding protein 2 [ Homo sapiens (human) ]

Gene ID: 4665, updated on 2-Nov-2024

Summary

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Official Symbol
NAB2provided by HGNC
Official Full Name
NGFI-A binding protein 2provided by HGNC
Primary source
HGNC:HGNC:7627
See related
Ensembl:ENSG00000166886 MIM:602381; AllianceGenome:HGNC:7627
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
MADER
Summary
This gene encodes a member of the family of NGFI-A binding (NAB) proteins, which function in the nucleus to repress transcription induced by some members of the EGR (early growth response) family of transactivators. NAB proteins can homo- or hetero-multimerize with other EGR or NAB proteins through a conserved N-terminal domain, and repress transcription through two partially redundant C-terminal domains. Transcriptional repression by the encoded protein is mediated in part by interactions with the nucleosome remodeling and deactylase (NuRD) complex. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in endometrium (RPKM 17.8), ovary (RPKM 17.7) and 25 other tissues See more
Orthologs
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Genomic context

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See NAB2 in Genome Data Viewer
Location:
12q13.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57089114..57095476)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57056986..57063348)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57482897..57489259)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57423222-57424059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6521 Neighboring gene myosin IA Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:57440635-57441834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6522 Neighboring gene nuclear envelope integral membrane protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4571 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57485501-57485781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4572 Neighboring gene Sharpr-MPRA regulatory region 4597 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57488515-57489045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57489590-57490426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57493803-57494325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57495608-57496108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57496109-57496609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57504271-57505218 Neighboring gene uncharacterized LOC124902946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57505219-57506164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4574 Neighboring gene signal transducer and activator of transcription 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57521273-57521926 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57527325-57528080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57540016-57540944 Neighboring gene LDL receptor related protein 1 Neighboring gene LRP1 antisense RNA

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Mader: a novel nuclear protein over expressed in human melanomas. Kirsch KH, et al. Oncogene, 1996 Mar 7. PMID 8649813
  2. The transcriptional corepressor NAB2 inhibits NGF-induced differentiation of PC12 cells. Qu Z, et al. J Cell Biol, 1998 Aug 24. PMID 9722618, Free PMC Article
  3. Frequent and early loss of the EGR1 corepressor NAB2 in human prostate carcinoma. Abdulkadir SA, et al. Hum Pathol, 2001 Sep. PMID 11567222
  4. The impact of histopathology and NAB2-STAT6 fusion subtype in classification and grading of meningeal solitary fibrous tumor/hemangiopericytoma. Fritchie K, et al. Acta Neuropathol, 2019 Feb. PMID 30584643, Free PMC Article
  5. 'Papillary' solitary fibrous tumor/hemangiopericytoma with nuclear STAT6 expression and NAB2-STAT6 fusion. Ishizawa K, et al. Brain Tumor Pathol, 2016 Apr. PMID 26746203

See all (76) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NAB2::STAT6 fusions and genome-wide DNA methylation profiling: Predictors of patient outcomes in meningeal solitary fibrous tumors.
    Title: NAB2::STAT6 fusions and genome-wide DNA methylation profiling: Predictors of patient outcomes in meningeal solitary fibrous tumors.
  2. Analysis of clinicopathological features and NAB2-STAT6 fusion variants of meningeal solitary fibrous tumor with ectopic salivary gland components in the cerebellopontine angle.
    Title: Analysis of clinicopathological features and NAB2-STAT6 fusion variants of meningeal solitary fibrous tumor with ectopic salivary gland components in the cerebellopontine angle.
  3. Teratocarcinosarcoma-Like and Adamantinoma-Like Head and Neck Neoplasms Harboring NAB2::STAT6: Unusual Variants of Solitary Fibrous Tumor or Novel Tumor Entities?
    Title: Teratocarcinosarcoma-Like and Adamantinoma-Like Head and Neck Neoplasms Harboring NAB2::STAT6: Unusual Variants of Solitary Fibrous Tumor or Novel Tumor Entities?
  4. Clinical and molecular implications of NAB2-STAT6 fusion variants in solitary fibrous tumour.
    Title: Clinical and molecular implications of NAB2-STAT6 fusion variants in solitary fibrous tumour.
  5. Lipomatous Solitary Fibrous Tumors Harbor Rare NAB2-STAT6 Fusion Variants and Show Up-Regulation of the Gene PPARG, Encoding for a Regulator of Adipocyte Differentiation.
    Title: Lipomatous Solitary Fibrous Tumors Harbor Rare NAB2-STAT6 Fusion Variants and Show Up-Regulation of the Gene PPARG, Encoding for a Regulator of Adipocyte Differentiation.
  6. NAB2-STAT6 fusion protein mediates cell proliferation and oncogenic progression via EGR-1 regulation.
    Title: NAB2-STAT6 fusion protein mediates cell proliferation and oncogenic progression via EGR-1 regulation.
  7. Gene Expression in Solitary Fibrous Tumors (SFTs) Correlates with Anatomic Localization and NAB2-STAT6 Gene Fusion Variants.
    Title: Gene Expression in Solitary Fibrous Tumors (SFTs) Correlates with Anatomic Localization and NAB2-STAT6 Gene Fusion Variants.
  8. NAB2-STAT6 fusion type was not significantly associated with recurrence-free or overall survival, but was associated with phenotype
    Title: The impact of histopathology and NAB2-STAT6 fusion subtype in classification and grading of meningeal solitary fibrous tumor/hemangiopericytoma.
  9. Study characterized sequences in NAB2 that mediate its nuclear localization and determined that the KKXK motif that aligns with the NAB1 KRXK motif is necessary for NAB2 nuclear localization, while the K(X2)R motif situated 11 residues upstream is not.
    Title: Refining the nuclear localization signal within the Egr transcriptional coregulator NAB2.
  10. Here, we demonstrate that pulmonary adenofibromas are neoplastic lesions harbouring NAB2-STAT6 fusion genes ,the molecular hallmark of solitary fibrous tumours.
    Title: Recurrent NAB2-STAT6 gene fusions and oestrogen receptor-α expression in pulmonary adenofibromas.
Submit: New GeneRIF Correction See all GeneRIFs (38)

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
A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study.
EBI GWAS Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association study of sensory disturbances in the inferior alveolar nerve after bilateral sagittal split ramus osteotomy.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of NGFI-A binding protein 2 (NAB2; EGR1 binding protein 2; MADER) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC75085

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription corepressor activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in Schwann cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in endochondral ossification IEA
Inferred from Electronic Annotation
more info
  
involved_in myelination IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase III IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of epidermis development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
NGFI-A-binding protein 2
Names
EGR1 binding protein 2
melanoma-associated delayed early response protein

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.

mRNA and Protein(s)

  1. NM_001330305.2 → NP_001317234.1  NGFI-A-binding protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter, but has the same N- and C-termini as isoform 1.
    Source sequence(s)
    BC065931, BQ956141
    Consensus CDS
    CCDS81701.1
    UniProtKB/Swiss-Prot
    Q15742
    Related
    ENSP00000341491.6, ENST00000342556.6
    Conserved Domains (2) summary
    pfam04905
    Location:237 → 363
    NCD2; NAB conserved region 2 (NCD2)
    pfam04904
    Location:37 → 114
    NCD1; NAB conserved region 1 (NCD1)

  2. NM_005967.4 → NP_005958.1  NGFI-A-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_005958.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC065931
    Consensus CDS
    CCDS8930.1
    UniProtKB/Swiss-Prot
    B2RAK3, O76006, Q14797, Q15742
    Related
    ENSP00000300131.3, ENST00000300131.8
    Conserved Domains (2) summary
    pfam04904
    Location:36 → 114
    NCD1; NAB conserved region 1 (NCD1)
    pfam04905
    Location:237 → 363
    NCD2; NAB conserved region 2 (NCD2)

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57089114..57095476
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57056986..57063348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15742.1 GenPept UniProtKB/Swiss-Prot:Q15742

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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