NAB1

gene
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Summary

NAB1 (NGFI-A binding protein 1, HGNC:7626) is a protein-coding gene on chromosome 2q32.2, encoding NGFI-A-binding protein 1 (Q13506). Acts as a transcriptional repressor for zinc finger transcription factors EGR1 and EGR2.

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to act upstream of or within endochondral ossification; nervous system development; and regulation of epidermis development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus.

Source: NCBI Gene 4664 — RefSeq curated summary.

At a glance

  • GWAS associations: 21
  • Clinical variants (ClinVar): 64 total
  • MANE Select transcript: NM_005966

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7626
Approved symbolNAB1
NameNGFI-A binding protein 1
Location2q32.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000138386
Ensembl biotypeprotein_coding
OMIM600800
Entrez4664

Gene structure

Transcript identifiers

Ensembl transcripts: 63 — 62 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000337386, ENST00000409581, ENST00000409641, ENST00000416973, ENST00000423076, ENST00000423376, ENST00000426601, ENST00000434473, ENST00000448811, ENST00000484774, ENST00000903108, ENST00000903109, ENST00000903110, ENST00000903111, ENST00000903112, ENST00000903113, ENST00000903114, ENST00000903115, ENST00000903116, ENST00000903117, ENST00000903118, ENST00000903119, ENST00000903120, ENST00000903121, ENST00000903122, ENST00000903123, ENST00000903124, ENST00000903125, ENST00000903126, ENST00000903127, ENST00000903128, ENST00000903129, ENST00000903130, ENST00000903131, ENST00000903132, ENST00000903133, ENST00000903134, ENST00000903135, ENST00000903136, ENST00000903137, ENST00000903138, ENST00000903139, ENST00000920767, ENST00000920768, ENST00000920769, ENST00000920770, ENST00000920771, ENST00000920772, ENST00000920773, ENST00000920774, ENST00000920775, ENST00000960766, ENST00000960767, ENST00000960768, ENST00000960769, ENST00000960770, ENST00000960771, ENST00000960772, ENST00000960773, ENST00000960774, ENST00000960775, ENST00000960776, ENST00000960777

RefSeq mRNA: 5 — MANE Select: NM_005966 NM_001321312, NM_001321313, NM_001321314, NM_001321315, NM_005966

CCDS: CCDS2307, CCDS82545

Canonical transcript exons

ENST00000337386 — 10 exons

ExonStartEnd
ENSE00000934468190687201190687317
ENSE00000934471190673101190673152
ENSE00000934472190670326190670459
ENSE00000934473190659158190659995
ENSE00001129482190685476190685638
ENSE00001300540190655977190656153
ENSE00001323207190649846190649982
ENSE00001827629190690245190692766
ENSE00001829865190649083190649360
ENSE00003505637190683738190683827

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 96.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9239 / max 82.7082, expressed in 1705 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
243114.85621591
243101.1739684
243120.5933291
243130.3005102

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402396.55gold quality
skin of hipUBERON:000155496.40gold quality
upper leg skinUBERON:000426296.20gold quality
calcaneal tendonUBERON:000370194.88gold quality
endothelial cellCL:000011594.64gold quality
choroid plexus epitheliumUBERON:000391194.59gold quality
cortical plateUBERON:000534394.26gold quality
ventricular zoneUBERON:000305393.54gold quality
colonic epitheliumUBERON:000039793.35gold quality
cranial nerve IIUBERON:000094193.22gold quality
tendon of biceps brachiiUBERON:000818893.19gold quality
tendonUBERON:000004393.17gold quality
gingivaUBERON:000182893.16gold quality
gingival epitheliumUBERON:000194993.12gold quality
right coronary arteryUBERON:000162592.71gold quality
mucosa of paranasal sinusUBERON:000503092.57gold quality
parietal pleuraUBERON:000240092.52gold quality
cerebellar vermisUBERON:000472092.50gold quality
germinal epithelium of ovaryUBERON:000130492.47gold quality
bronchial epithelial cellCL:000232892.30gold quality
skin of abdomenUBERON:000141692.25gold quality
oral cavityUBERON:000016792.21gold quality
hair follicleUBERON:000207392.21gold quality
pleuraUBERON:000097792.11gold quality
embryoUBERON:000092292.00gold quality
descending thoracic aortaUBERON:000234591.85gold quality
zone of skinUBERON:000001491.84gold quality
popliteal arteryUBERON:000225091.76gold quality
tibial arteryUBERON:000761091.76gold quality
sural nerveUBERON:001548891.71gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
MSLNUnknown

Upstream regulators (CollecTRI, top): EGR2

miRNA regulators (miRDB)

185 targeting NAB1, 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-3646100.0073.565283
HSA-MIR-8485100.0077.574731
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-656-3P100.0072.152788
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4262100.0073.263931
HSA-MIR-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692A100.0074.406850
HSA-MIR-126-5P100.0072.713180
HSA-MIR-366299.9973.825684
HSA-MIR-453499.9966.581907
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AJ-3P99.9673.385345

Literature-anchored findings (GeneRIF, showing 5)

  • mutations in the human NABI gene are most likely not involved in the pathogenesis of peripheral neuropathies. (PMID:12030330)
  • Methylation pattern of the corresponding NGFI-A binding site in the human glucocorticoid receptor exon 1-F specific promoter in post mortem hippocampal tissue. (PMID:17853270)
  • Data show that the suppressive effect of valproic acid on chondrocytes is not due to reduced expression or recruitment of Egr-1 to the mPGES-1 promoter and involves upregulation of NAB1. (PMID:21239760)
  • These data suggest that type I IFN stimulation induces a rapid recruitment of a repressive Egr3/Nab1 complex that silences transcription from the ifngr1 promoter. (PMID:23935197)
  • N6-Methyladenosine modified circ-NAB1 modulates cell cycle and epithelial-mesenchymal transition via CDKN3 in endometrial cancer. (PMID:38814199)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerionab1bENSDARG00000040700
danio_rerionab1aENSDARG00000042940
mus_musculusNab1ENSMUSG00000002881
rattus_norvegicusNab1ENSRNOG00000012959
drosophila_melanogasternabFBGN0259986
caenorhabditis_elegansWBGENE00003107

Paralogs (1): NAB2 (ENSG00000166886)

Protein

Protein identifiers

NGFI-A-binding protein 1Q13506 (reviewed: Q13506)

Alternative names: EGR-1-binding protein 1, Transcriptional regulatory protein p54

All UniProt accessions (8): Q13506, B8ZZS2, C9J3V0, C9JFF6, C9JID4, C9JJ42, C9JL92, H0Y4C5

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor for zinc finger transcription factors EGR1 and EGR2.

Subunit / interactions. Homomultimers may associate with EGR1 bound to DNA.

Subcellular location. Nucleus.

Tissue specificity. Isoform Short is found in myeloid leukemia cell line KG-1.

Domain organisation. The NAB conserved domain 1 (NCD1) interacts with EGR1 inhibitory domain and mediates multimerization. The NAB conserved domain 2 (NCD2) is necessary for transcriptional repression.

Similarity. Belongs to the NAB family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13506-1Longyes
Q13506-2Short

RefSeq proteins (5): NP_001308241, NP_001308242, NP_001308243, NP_001308244, NP_005957* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006986Nab1_CDomain
IPR006988Nab_NDomain
IPR006989NAB_co-repressor_domDomain
IPR038398NCD2_sfHomologous_superfamily
IPR039040NAB_famFamily

Pfam: PF04902, PF04904, PF04905

UniProt features (37 total): cross-link 14, helix 8, region of interest 5, modified residue 4, sequence conflict 2, chain 1, splice variant 1, strand 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2YUFSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13506-F164.900.32

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (18): 407, 126, 129, 143, 212, 333, 333, 355, 369, 373, 454, 465, 477, 480, 480, 172, 183, 328

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

IDPathway
R-HSA-9031628NGF-stimulated transcription
R-HSA-9619665EGR2 and SOX10-mediated initiation of Schwann cell myelination
R-HSA-1266738Developmental Biology
R-HSA-162582Signal Transduction
R-HSA-166520Signaling by NTRKs
R-HSA-187037Signaling by NTRK1 (TRKA)
R-HSA-198725Nuclear Events (kinase and transcription factor activation)
R-HSA-9006934Signaling by Receptor Tyrosine Kinases
R-HSA-9675108Nervous system development

MSigDB gene sets: 326 (showing top): GGGACCA_MIR133A_MIR133B, JI_RESPONSE_TO_FSH_UP, GCM_GSPT1, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_EPIDERMIS_DEVELOPMENT, GOZGIT_ESR1_TARGETS_DN, GCM_ZNF198, GOBP_NEUROGENESIS, HEIDENBLAD_AMPLICON_8Q24_DN, GOBP_REPLACEMENT_OSSIFICATION, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_BONE_DEVELOPMENT, WANG_RESPONSE_TO_BEXAROTENE_DN, GOBP_ENSHEATHMENT_OF_NEURONS, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP

GO Biological Process (6): endochondral ossification (GO:0001958), regulation of DNA-templated transcription (GO:0006355), Schwann cell differentiation (GO:0014037), myelination (GO:0042552), regulation of epidermis development (GO:0045682), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (1): transcription coregulator activity (GO:0003712)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-7 pathways:

CategoryPathways
Nuclear Events (kinase and transcription factor activation)1
Nervous system development1
Signaling by Receptor Tyrosine Kinases1
Signaling by NTRKs1
Signaling by NTRK1 (TRKA)1
Signal Transduction1
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA-templated transcription2
replacement ossification1
endochondral bone morphogenesis1
regulation of gene expression1
regulation of RNA biosynthetic process1
peripheral nervous system development1
glial cell differentiation1
axon ensheathment1
epidermis development1
regulation of developmental process1
regulation of DNA-templated transcription1
negative regulation of RNA biosynthetic process1
transcription regulator activity1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

626 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NAB1EGR2P11161957
NAB1EGR3Q06889950
NAB1EGR1P18146941
NAB1EGR4Q05215880
NAB1STAT2P52630584
NAB1STAT4Q14765569
NAB1STAT6P42226518
NAB1STAT1P42224478
NAB1NGFP01138472
NAB1ANKRD36A6QL64444
NAB1FKBP14Q9NWM8425
NAB1PPRC1Q5VV67424
NAB1NEMP2A6NFY4413
NAB1TCF3P15883408
NAB1MFSD6Q6ZSS7399

IntAct

14 interactions, top by confidence:

ABTypeScore
NAB1SDHApsi-mi:“MI:0915”(physical association)0.400
NAB1POU2AF1psi-mi:“MI:0915”(physical association)0.370
Ppp2r1aCCHCR1psi-mi:“MI:0914”(association)0.350
Racgap1DDX3Xpsi-mi:“MI:0914”(association)0.350
Mkln1NNTpsi-mi:“MI:0914”(association)0.350
CPAPCCP110psi-mi:“MI:0914”(association)0.350
NAB2GLSpsi-mi:“MI:0914”(association)0.350
AKTIPPGGT1Bpsi-mi:“MI:0914”(association)0.350
EGR1NAB1psi-mi:“MI:0914”(association)0.350
EEF1AKMT3SMCHD1psi-mi:“MI:0914”(association)0.350
PRICKLE4USO1psi-mi:“MI:0914”(association)0.350
MVKNAB1psi-mi:“MI:0914”(association)0.350
NAB1gptBpsi-mi:“MI:0915”(physical association)0.000

BioGRID (43): NAB1 (Affinity Capture-RNA), NAB1 (Affinity Capture-RNA), NAB1 (Affinity Capture-RNA), NAB1 (Affinity Capture-RNA), NAB1 (Affinity Capture-MS), NAB1 (Synthetic Growth Defect), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-MS), NAB1 (Affinity Capture-RNA), NAB1 (Affinity Capture-MS)

ESM2 similar proteins: A0FIN4, A2VD01, A9ZLX4, D2HNW6, D4A7U2, O88974, O94988, P10914, P14316, P15314, P16236, P17433, P17947, P23570, P23906, P49140, Q00IB7, Q13506, Q13905, Q15047, Q1LY51, Q3B7M3, Q3SZP0, Q3TTA7, Q3UWM4, Q4V7W5, Q5HYC2, Q5RJA1, Q5XJV7, Q61122, Q62722, Q6A098, Q6AI12, Q6BDS1, Q6DFR2, Q6GQL0, Q6PKU1, Q6ZMT4, Q6ZNC4, Q80TJ7

Diamond homologs: O35589, Q13506, Q15742, Q59E55, Q61122, Q61127, Q62722, Q22002

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1155 predictions. Top by Δscore:

VariantEffectΔscore
2:190670306:ACTCT:Aacceptor_gain1.0000
2:190670310:T:TAacceptor_gain1.0000
2:190670315:T:TAacceptor_gain1.0000
2:190670316:G:Aacceptor_gain1.0000
2:190670320:A:AGacceptor_gain1.0000
2:190670321:T:Gacceptor_gain1.0000
2:190670321:TCCA:Tacceptor_loss1.0000
2:190670323:CA:Cacceptor_loss1.0000
2:190670324:A:AGacceptor_gain1.0000
2:190670324:AGCT:Aacceptor_loss1.0000
2:190670325:G:GGacceptor_gain1.0000
2:190670325:GC:Gacceptor_gain1.0000
2:190670325:GCT:Gacceptor_gain1.0000
2:190670325:GCTC:Gacceptor_gain1.0000
2:190670325:GCTCA:Gacceptor_gain1.0000
2:190670455:ACCAA:Adonor_gain1.0000
2:190670456:CCAA:Cdonor_gain1.0000
2:190670457:CAA:Cdonor_gain1.0000
2:190670458:AA:Adonor_gain1.0000
2:190670459:AGTA:Adonor_loss1.0000
2:190670460:G:GGdonor_gain1.0000
2:190670460:GT:Gdonor_loss1.0000
2:190670464:G:GGdonor_gain1.0000
2:190685467:A:AGacceptor_gain1.0000
2:190685470:TACTA:Tacceptor_loss1.0000
2:190685471:ACTAG:Aacceptor_loss1.0000
2:190685472:CTAGC:Cacceptor_loss1.0000
2:190685473:TAGC:Tacceptor_loss1.0000
2:190685473:TAGCA:Tacceptor_gain1.0000
2:190685474:A:AGacceptor_gain1.0000

AlphaMissense

3194 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:190659204:G:AG10R1.000
2:190659204:G:CG10R1.000
2:190659217:T:AL14Q1.000
2:190659217:T:CL14P1.000
2:190659226:T:AI17K1.000
2:190659226:T:GI17R1.000
2:190659229:T:CL18S1.000
2:190659244:T:AL23Q1.000
2:190659244:T:CL23P1.000
2:190659265:T:CF30S1.000
2:190659276:G:AG34S1.000
2:190659276:G:CG34R1.000
2:190659276:G:TG34C1.000
2:190659277:G:AG34D1.000
2:190659277:G:TG34V1.000
2:190659279:G:CG35R1.000
2:190659279:G:TG35C1.000
2:190659280:G:AG35D1.000
2:190659280:G:TG35V1.000
2:190659282:G:CD36H1.000
2:190659282:G:TD36Y1.000
2:190659283:A:CD36A1.000
2:190659283:A:GD36G1.000
2:190659283:A:TD36V1.000
2:190659284:T:AD36E1.000
2:190659284:T:GD36E1.000
2:190659285:G:CD37H1.000
2:190659286:A:CD37A1.000
2:190659286:A:GD37G1.000
2:190659286:A:TD37V1.000

dbSNP variants (sampled 300 via entrez): RS1000001698 (2:190676069 T>A), RS1000037170 (2:190676458 G>A), RS1000067459 (2:190647508 CTT>C), RS1000088218 (2:190662474 A>T), RS1000093194 (2:190647805 C>T), RS1000095308 (2:190683513 G>A), RS1000360898 (2:190667222 A>G), RS1000485622 (2:190672528 C>T), RS1000633112 (2:190678007 G>A), RS1000687189 (2:190664232 G>A,T), RS1000724138 (2:190664841 C>G), RS1000745785 (2:190665954 C>G), RS1000789156 (2:190650076 A>G), RS1000973373 (2:190688435 T>C), RS1001032137 (2:190679940 G>A)

Disease associations

OMIM: gene MIM:600800 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

StudyTraitp-value
GCST003129_7Primary biliary cholangitis2.000000e-14
GCST003518_14Daytime sleep phenotypes3.000000e-06
GCST003654_5Bone mineral density (Ward’s triangle area)7.000000e-07
GCST006052_5Polymyositis4.000000e-06
GCST006979_50Heel bone mineral density5.000000e-14
GCST007094_193Diastolic blood pressure2.000000e-06
GCST007095_1Systolic blood pressure9.000000e-06
GCST007095_94Systolic blood pressure3.000000e-07
GCST007096_38Pulse pressure1.000000e-10
GCST007097_55Pulse pressure3.000000e-06
GCST007097_56Pulse pressure1.000000e-06
GCST007099_203Systolic blood pressure5.000000e-13
GCST007267_293Systolic blood pressure3.000000e-09
GCST007278_7Systemic seropositive rheumatic diseases (Systemic sclerosis or systemic lupus erythematosus or rheumatoid arthritis or idiopathic inflammatory myopathies)7.000000e-11
GCST009131_4Systemic sclerosis5.000000e-09
GCST009597_200Multiple sclerosis6.000000e-06
GCST009873_29Autoimmune traits (pleiotropy)2.000000e-08
GCST009877_13Rheumatoid arthritis1.000000e-08
GCST011096_35Systemic lupus erythematosus1.000000e-13
GCST011097_1Systemic lupus erythematosus7.000000e-09
GCST90011866_10Systemic lupus erythematosus3.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0007828daytime rest measurement
EFO:0007785femoral neck bone mineral density
EFO:0009270heel bone mineral density
EFO:0006336diastolic blood pressure
EFO:0006335systolic blood pressure
EFO:0005763pulse pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, decreases expression, affects cotreatment3
entinostatdecreases expression, affects cotreatment2
Arsenicaffects cotreatment, decreases expression, increases abundance2
Tamoxifenaffects expression, affects cotreatment, increases expression2
Cadmium Chloridedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases expression1
TAK-243decreases sumoylation1
dicrotophosdecreases expression1
methylmercuric chlorideincreases expression1
cobaltous chloridedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
coumarinincreases phosphorylation1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Sunitinibincreases expression1
Zoledronic Acidincreases expression1
Air Pollutantsincreases abundance, decreases expression1
Benzeneincreases expression1
Benzo(a)pyrenedecreases methylation1
Caffeineaffects phosphorylation1
Cisplatinaffects response to substance1
Coumestrolincreases expression, affects cotreatment1
Demecolcinedecreases expression1

Clinical trials (associated diseases)

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