NIBAN1

gene
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Also known as NIBANGIG39

Summary

NIBAN1 (niban apoptosis regulator 1, HGNC:16784) is a protein-coding gene on chromosome 1q25.3, encoding Protein Niban 1 (Q9BZQ8). Regulates phosphorylation of a number of proteins involved in translation regulation including EIF2A, EIF4EBP1 and RPS6KB1.

This gene encodes a member of the family with sequence similarity 129 protein family. This gene is highly expressed in several cancer cells and may serve as a prognostic marker for certain cancers. The encoded protein may play a role in regulating p53-mediated apoptosis.

Source: NCBI Gene 116496 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 185 total
  • MANE Select transcript: NM_052966

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16784
Approved symbolNIBAN1
Nameniban apoptosis regulator 1
Location1q25.3
Locus typegene with protein product
StatusApproved
AliasesNIBAN, GIG39
Ensembl geneENSG00000135842
Ensembl biotypeprotein_coding
OMIM619294
Entrez116496

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000367511, ENST00000417056, ENST00000461167, ENST00000487074, ENST00000496299, ENST00000899938, ENST00000899939, ENST00000899940, ENST00000899941, ENST00000899942, ENST00000899943, ENST00000899944, ENST00000899945, ENST00000899946, ENST00000899947, ENST00000968385, ENST00000968386

RefSeq mRNA: 1 — MANE Select: NM_052966 NM_052966

CCDS: CCDS1364

Canonical transcript exons

ENST00000367511 — 14 exons

ExonStartEnd
ENSE00000822921184823638184823742
ENSE00000822923184884633184884800
ENSE00001128072184890108184890222
ENSE00001128077184894075184894206
ENSE00001152138184899179184899309
ENSE00001444835184974302184974508
ENSE00001908214184791032184796097
ENSE00003507472184808074184808235
ENSE00003562996184818638184818825
ENSE00003580688184798079184798190
ENSE00003597866184831847184831962
ENSE00003650397184823167184823329
ENSE00003692402184803585184803692
ENSE00003693348184805946184806056

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 99.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.9703 / max 3036.4979, expressed in 1657 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1628619.46821478
1628715.21671527
162852.5339834
162880.7515387

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
blood vessel layerUBERON:000479799.49gold quality
saphenous veinUBERON:000731899.40gold quality
parotid glandUBERON:000183199.39gold quality
heart right ventricleUBERON:000208099.38gold quality
vena cavaUBERON:000408799.17gold quality
myocardiumUBERON:000234999.10gold quality
cardiac muscle of right atriumUBERON:000337998.96gold quality
left ventricle myocardiumUBERON:000656698.91gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.68gold quality
seminal vesicleUBERON:000099898.30gold quality
right coronary arteryUBERON:000162598.07gold quality
cauda epididymisUBERON:000436097.92gold quality
urethraUBERON:000005797.88gold quality
superficial temporal arteryUBERON:000161497.87gold quality
mammary ductUBERON:000176597.82gold quality
tracheaUBERON:000312697.67gold quality
nasal cavity epitheliumUBERON:000538497.51gold quality
epithelium of mammary glandUBERON:000324497.50gold quality
calcaneal tendonUBERON:000370197.37gold quality
cartilage tissueUBERON:000241897.20gold quality
skin of hipUBERON:000155497.09gold quality
vastus lateralisUBERON:000137996.90gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450296.89gold quality
palpebral conjunctivaUBERON:000181296.83gold quality
bloodUBERON:000017896.79gold quality
quadriceps femorisUBERON:000137796.78gold quality
biceps brachiiUBERON:000150796.75gold quality
lower esophagus muscularis layerUBERON:003583396.73gold quality
thoracic aortaUBERON:000151596.72gold quality
descending thoracic aortaUBERON:000234596.69gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-MTAB-7381yes677.37
E-MTAB-9221yes20.89
E-GEOD-81547yes20.79
E-MTAB-5061yes19.98
E-ANND-3yes19.53
E-CURD-97no569.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

143 targeting NIBAN1, 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-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3134100.0066.43777
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-511-3P99.9968.851467
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-806899.9873.852376
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-9-3P99.9670.882068
HSA-MIR-211099.9666.681930
HSA-MIR-365899.9673.874379
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-651-3P99.9473.485177
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-144-3P99.9473.982698
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-311999.9271.342390

Literature-anchored findings (GeneRIF, showing 14)

  • Niban expression is up-regulated in various types of thyroid tumors. (PMID:16949643)
  • The expression of Niban frequently begins in the early stages of head and neck squamous carcinoma and remains upregulated throughout the carcinogenic process. Niban may be a good molecular marker of HNSCC. (PMID:19536772)
  • Gene-expression data suggest a difference in expression between STT3A, Clorf24, and TFF3 in FAs versus carcinomas that may be detected from an FNA sample. Findings must be validated from preoperative FNAs in larger numbers (PMID:21520112)
  • DDIT3, STT3A, ARG2 and FAM129A immunohistochemistry does not appear to be useful in the diagnosis of thyroid follicular neoplasias, as they do not reliably distinguish follicular thyroid carcinoma from follicular thyroid adenoma. (PMID:22157935)
  • Data suggest that decreasing C1orf24 protein levels by restoring microRNA miR-106b function may have therapeutic implications. (PMID:26317551)
  • We have shown that FAM129A is associated with variation in clinical asthma steroid responsiveness and that FAM129A modulates steroid responsiveness in lung epithelial cells. (PMID:29410046)
  • results suggest a conditional regulation of KRT16 gene by ATF4 that may be inhibited in normal cells, but engaged during cancer progression. Potential roles of KRT16, FAM129A and HKDC1 genes upregulation in adaptive stress responses and pathologies are discussed (PMID:29420561)
  • Our data suggest that, in normal thyroid cells, FAM129A induces autophagy in order to maintain cell homeostasis and provide substrates under starvation conditions. Instead, in thyroid cancer cells, decreased autophagy may help the cells to overcome cell death. FAM129A regulates autophagy in a cell- and/or context-dependent manner. (PMID:30400008)
  • Silencing of Niban in HK-2 cells not only increased the AngII- and endoplasmic reticulum stress-induced apoptosis, but also promoted the expression of caspase 8, caspase 9, Bip, and Chop, suggesting that Niban protein is involved in apoptosis regulation in HK-2 cells, and most likely via caspase-dependent pathway. (PMID:31163002)
  • One of the canonical Unfolded protein response branches, through ATF4 and its target gene FAM129A, is required for Prostate cancer growth and thus may serve as a novel therapeutic target. (PMID:31312022)
  • MRNA and protein expression of FAM129A were negatively regulated by miR-135a. (PMID:31729558)
  • MiR-4521 plays a tumor repressive role in growth and metastasis of hepatocarcinoma cells by suppressing phosphorylation of FAK/AKT pathway via targeting FAM129A. (PMID:35127170)
  • The negative feedback loop FAM129A/CXCL14 aggravates the progression of esophageal cancer. (PMID:35776020)
  • FAM129A promotes self-renewal and maintains invasive status via stabilizing the Notch intracellular domain in glioma stem cells. (PMID:37083136)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioniban1bENSDARG00000023053
danio_rerioniban1aENSDARG00000042055
mus_musculusNiban1ENSMUSG00000026483
rattus_norvegicusNiban1ENSRNOG00000002403

Paralogs (2): NIBAN2 (ENSG00000136830), NIBAN3 (ENSG00000167483)

Protein

Protein identifiers

Protein Niban 1Q9BZQ8 (reviewed: Q9BZQ8)

Alternative names: Cell growth-inhibiting gene 39 protein, Protein FAM129A

All UniProt accessions (2): Q9BZQ8, H0Y7M9

UniProt curated annotations — full annotation on UniProt →

Function. Regulates phosphorylation of a number of proteins involved in translation regulation including EIF2A, EIF4EBP1 and RPS6KB1. May be involved in the endoplasmic reticulum stress response.

Subcellular location. Cytoplasm. Membrane.

Tissue specificity. Expressed in various types of thyroid tumor such as papillary thyroid carcinomas and oxyphilic thyroid tumors but not in normal thyroid tissue (at protein level). Strongly expressed in heart, skeletal muscle, pancreas, white blood cells and prostate with moderate expression in colon and spleen. Expressed in renal carcinoma cells but not in normal kidney.

Miscellaneous. ‘Niban’ means ‘second’ in Japanese.

Similarity. Belongs to the Niban family.

RefSeq proteins (1): NP_443198* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026088Niban-likeFamily
IPR059060Niban_1/2/3_domDomain

Pfam: PF26086, PF26089

UniProt features (31 total): modified residue 7, compositionally biased region 6, sequence conflict 6, region of interest 5, sequence variant 4, initiator methionine 1, chain 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BZQ8-F170.110.49

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 (8): 579, 582, 596, 602, 646, 708, 926, 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 357 (showing top): VERHAAK_AML_WITH_NPM1_MUTATED_DN, KOBAYASHI_EGFR_SIGNALING_24HR_UP, BENPORATH_ES_WITH_H3K27ME3, GOBP_REGULATION_OF_PHOSPHORYLATION, XU_GH1_AUTOCRINE_TARGETS_UP, AAGTCCA_MIR422B_MIR422A, PEREZ_TP63_TARGETS, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, FOSTER_TOLERANT_MACROPHAGE_UP, GOBP_POSITIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS

GO Biological Process (5): negative regulation of protein phosphorylation (GO:0001933), positive regulation of protein phosphorylation (GO:0001934), response to endoplasmic reticulum stress (GO:0034976), positive regulation of translation (GO:0045727), regulation of translation (GO:0006417)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
regulation of protein phosphorylation2
protein phosphorylation2
translation2
negative regulation of protein modification process1
negative regulation of phosphorylation1
positive regulation of protein modification process1
positive regulation of phosphorylation1
cellular response to stress1
regulation of translation1
positive regulation of gene expression1
positive regulation of protein metabolic process1
post-transcriptional regulation of gene expression1
regulation of protein metabolic process1
binding1
intracellular anatomical structure1
cytoplasm1
membrane1
cell periphery1
extracellular vesicle1

Protein interactions and networks

STRING

1702 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NIBAN1STT3AP46977505
NIBAN1OSBPL10Q9BXB5479
NIBAN1CCDC179H3BU77477
NIBAN1EPHA2P29317380
NIBAN1TMEM100Q9NV29361
NIBAN1CFAP92Q9ULG3351
NIBAN1ACTC1P04270350
NIBAN1SYNPO2Q9UMS6329
NIBAN1CLMNQ96JQ2315
NIBAN1EFL1Q7Z2Z2294
NIBAN1ZNF777Q9ULD5290
NIBAN1CHAC1Q9BUX1290
NIBAN1RHOFQ9HBH0282
NIBAN1HES2Q9Y543263
NIBAN1CRISPLD2Q9H0B8258

IntAct

22 interactions, top by confidence:

ABTypeScore
NIBAN1FHL2psi-mi:“MI:0915”(physical association)0.720
FHL2NIBAN1psi-mi:“MI:0915”(physical association)0.720
NPM1NIBAN1psi-mi:“MI:0915”(physical association)0.600
NIBAN1NPM1psi-mi:“MI:0407”(direct interaction)0.600
NPM1NIBAN1psi-mi:“MI:0407”(direct interaction)0.600
NIBAN1DDIT4Lpsi-mi:“MI:0915”(physical association)0.560
DDIT4LNIBAN1psi-mi:“MI:0915”(physical association)0.560
AKT1NIBAN1psi-mi:“MI:0915”(physical association)0.540
AKT1NIBAN1psi-mi:“MI:0217”(phosphorylation reaction)0.540
ECE1NIBAN1psi-mi:“MI:0915”(physical association)0.370
ESYT2psi-mi:“MI:0914”(association)0.350
NIBAN1FHL2psi-mi:“MI:0915”(physical association)0.000

BioGRID (36): FAM129A (Two-hybrid), FAM129A (Affinity Capture-MS), FAM129A (Affinity Capture-RNA), FAM129A (Two-hybrid), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), FAM129A (Proximity Label-MS), AKT1 (Affinity Capture-Western), NPM1 (Affinity Capture-Western)

ESM2 similar proteins: A1A4V9, A4IFI1, A8E4X8, B0BMZ6, G5E8P0, O75161, P18302, P59017, P59240, P85299, P97432, Q14596, Q2HJA5, Q2T9R2, Q3B7M3, Q3MHU5, Q3U0L2, Q3ZBK7, Q3ZK22, Q499E4, Q501R9, Q53GS7, Q569K6, Q58DT5, Q5FVG6, Q5RAS2, Q5SPX1, Q5T7N3, Q5XI52, Q60698, Q60943, Q6NZQ0, Q6P9J5, Q80U62, Q812A5, Q8C0R7, Q8CC12, Q8IWY9, Q8IYY4, Q8N6L0

Diamond homologs: B4F7E8, Q3UW53, Q8R1F1, Q96TA1, Q9BZQ8, Q9ESN0

SIGNOR signaling

2 interactions.

AEffectBMechanism
AKTunknownNIBAN1phosphorylation
AKT1unknownNIBAN1phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance157
Likely benign13
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3578 predictions. Top by Δscore:

VariantEffectΔscore
1:184798073:TCTTA:Tdonor_loss1.0000
1:184798074:CTTA:Cdonor_loss1.0000
1:184798075:TTA:Tdonor_loss1.0000
1:184798076:TA:Tdonor_loss1.0000
1:184798078:CCTTT:Cdonor_gain1.0000
1:184798206:T:TCacceptor_gain1.0000
1:184803575:ATCC:Adonor_gain1.0000
1:184803583:A:ACdonor_gain1.0000
1:184803584:C:CCdonor_gain1.0000
1:184806053:TTAG:Tacceptor_gain1.0000
1:184806057:C:CCacceptor_gain1.0000
1:184806065:C:CTacceptor_gain1.0000
1:184808069:CCCA:Cdonor_loss1.0000
1:184808070:CCA:Cdonor_loss1.0000
1:184808072:A:ATdonor_loss1.0000
1:184808072:ACCT:Adonor_gain1.0000
1:184808073:C:CTdonor_loss1.0000
1:184808073:CCTC:Cdonor_gain1.0000
1:184808075:T:TAdonor_gain1.0000
1:184808103:C:CTdonor_gain1.0000
1:184808234:TG:Tacceptor_gain1.0000
1:184808243:T:Cacceptor_gain1.0000
1:184808246:G:Cacceptor_gain1.0000
1:184808246:G:GCacceptor_gain1.0000
1:184823163:TGA:Tdonor_loss1.0000
1:184823164:GA:Gdonor_loss1.0000
1:184823165:A:AGdonor_loss1.0000
1:184823330:C:CCacceptor_gain1.0000
1:184823649:T:TAdonor_gain1.0000
1:184831841:TATTA:Tdonor_loss1.0000

AlphaMissense

6120 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:184894137:A:GW86R0.998
1:184894137:A:TW86R0.998
1:184798161:A:CF528L0.997
1:184798161:A:TF528L0.997
1:184798163:A:GF528L0.997
1:184823304:A:TV283D0.996
1:184823646:A:GW272R0.996
1:184823646:A:TW272R0.996
1:184823714:A:GL249P0.996
1:184831918:C:GA216P0.996
1:184823653:C:AK269N0.995
1:184823653:C:GK269N0.995
1:184899271:A:CY32D0.995
1:184803664:C:GR492P0.994
1:184803675:G:CS488R0.994
1:184803675:G:TS488R0.994
1:184803677:T:GS488R0.994
1:184899282:A:GF28S0.994
1:184796061:A:GL568S0.993
1:184823656:T:AR268S0.993
1:184823656:T:GR268S0.993
1:184805946:C:AK482N0.992
1:184805946:C:GK482N0.992
1:184818750:A:GL354P0.992
1:184823702:A:GL253P0.992
1:184798186:A:GL520P0.991
1:184805953:A:TV480D0.991
1:184805956:C:GR479P0.990
1:184806044:C:GA450P0.990
1:184818734:G:CS359R0.990

dbSNP variants (sampled 300 via entrez): RS1000011072 (1:184943978 T>C), RS1000014237 (1:184948293 T>G), RS1000042745 (1:184915313 T>C), RS1000046788 (1:184947909 T>C), RS1000060424 (1:184902899 A>G), RS1000086643 (1:184814054 A>T), RS1000109076 (1:184878681 A>T), RS1000119292 (1:184802913 G>A,C), RS1000136654 (1:184861434 C>T), RS1000146962 (1:184812755 C>T), RS1000188227 (1:184792996 T>G), RS1000205849 (1:184894441 A>G), RS1000289521 (1:184855443 A>G), RS1000305736 (1:184820562 C>T), RS1000313111 (1:184897772 A>G)

Disease associations

OMIM: gene MIM:619294 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST001762_684Obesity-related traits4.000000e-06
GCST004049_12Cough in response to angiotensin-converting enzyme inhibitor drugs4.000000e-07
GCST004735_20Epstein-Barr virus copy number in lymphoblastoid cell lines9.000000e-06
GCST008521_3Bitter beverage consumption1.000000e-06
GCST008745_89Estimated glomerular filtration rate in non-diabetics5.000000e-09
GCST008747_3Estimated glomerular filtration rate1.000000e-11
GCST008747_54Estimated glomerular filtration rate4.000000e-12
GCST009997_4Thyroid volume in Hashimoto’s thyroiditis1.000000e-07
GCST010145_7Cerebrospinal fluid immune biomarker levels1.000000e-08
GCST010396_266Gut microbiota (bacterial taxa, hurdle binary method)3.000000e-07
GCST90000025_837Appendicular lean mass4.000000e-12
GCST90002395_546Mean platelet volume1.000000e-10

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0005325response to angiotensin-converting enzyme inhibitor
EFO:0010089bitter beverage consumption measurement
EFO:0010596monocyte chemotactic protein 1 measurement
EFO:0007874gut microbiome measurement
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, increases expression, increases methylation5
Valproic Acidincreases expression5
Cyclosporineincreases expression4
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression3
Tretinoindecreases expression, increases expression3
perfluorooctanoic acidincreases expression2
mercuric bromideincreases expression, affects cotreatment2
entinostatincreases expression, affects cotreatment2
bisphenol Sincreases expression, affects cotreatment2
bisphenol AFdecreases expression, increases expression2
Cisplatinincreases expression, affects response to substance2
Copperaffects binding, increases expression2
Dexamethasoneincreases expression, decreases expression, affects cotreatment2
Estradiolaffects cotreatment, increases expression, decreases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
FR900359affects phosphorylation1
bisphenol Fincreases expression1
methylmercuric chlorideincreases expression1
propionaldehydeincreases expression1
pirinixic acidincreases activity, increases expression, affects binding1
sodium arsenatedecreases expression1
titanium dioxidedecreases expression1
ethyl-p-hydroxybenzoateincreases expression1
hydroxyhydroquinoneincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
o,p’-DDTincreases expression1
afimoxifeneincreases expression1
cobaltous chlorideincreases expression1
butyraldehydeincreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Epstein-Barr virus infection