MNDA

gene
On this page

Also known as PYHIN3

Summary

MNDA (myeloid cell nuclear differentiation antigen, HGNC:7183) is a protein-coding gene on chromosome 1q23.1, encoding Myeloid cell nuclear differentiation antigen (P41218). May act as a transcriptional activator/repressor in the myeloid lineage.

The myeloid cell nuclear differentiation antigen (MNDA) is detected only in nuclei of cells of the granulocyte-monocyte lineage. A 200-amino acid region of human MNDA is strikingly similar to a region in the proteins encoded by a family of interferon-inducible mouse genes, designated Ifi-201, Ifi-202, and Ifi-203, that are not regulated in a cell- or tissue-specific fashion. The 1.8-kb MNDA mRNA, which contains an interferon-stimulated response element in the 5-prime untranslated region, was significantly upregulated in human monocytes exposed to interferon alpha. MNDA is located within 2,200 kb of FCER1A, APCS, CRP, and SPTA1. In its pattern of expression and/or regulation, MNDA resembles IFI16, suggesting that these genes participate in blood cell-specific responses to interferons.

Source: NCBI Gene 4332 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 640 total — 1 pathogenic
  • MANE Select transcript: NM_002432

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7183
Approved symbolMNDA
Namemyeloid cell nuclear differentiation antigen
Location1q23.1
Locus typegene with protein product
StatusApproved
AliasesPYHIN3
Ensembl geneENSG00000163563
Ensembl biotypeprotein_coding
OMIM159553
Entrez4332

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000368141, ENST00000438394, ENST00000491210, ENST00000867925, ENST00000867926, ENST00000963510, ENST00000963511

RefSeq mRNA: 1 — MANE Select: NM_002432 NM_002432

CCDS: CCDS1177

Canonical transcript exons

ENST00000368141 — 7 exons

ExonStartEnd
ENSE00001075996158843955158844122
ENSE00001075997158845587158846003
ENSE00001075998158843279158843415
ENSE00001075999158847728158847916
ENSE00001446406158849190158849502
ENSE00001446407158842134158842418
ENSE00001446408158831351158831557

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 99.69.

FANTOM5 (CAGE): breadth broad, TPM avg 47.6526 / max 10342.7847, expressed in 454 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
589545.6028452
58960.374392
58980.3668117
59000.3208103
59100.248968
58970.201081
59090.193958
59080.148255
58990.105847
59070.090033

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057699.69gold quality
mononuclear cellCL:000084299.66gold quality
leukocyteCL:000073899.64gold quality
trabecular bone tissueUBERON:000248399.59gold quality
bloodUBERON:000017899.45gold quality
granulocyteCL:000009499.29gold quality
bone marrowUBERON:000237198.77gold quality
periodontal ligamentUBERON:000826698.62gold quality
germinal epithelium of ovaryUBERON:000130498.29gold quality
bone marrow cellCL:000209298.21gold quality
spleenUBERON:000210696.12gold quality
palpebral conjunctivaUBERON:000181294.07gold quality
right lungUBERON:000216792.67gold quality
vermiform appendixUBERON:000115492.43gold quality
lower lobe of lungUBERON:000894990.91gold quality
upper lobe of left lungUBERON:000895289.16gold quality
upper lobe of lungUBERON:000894888.99gold quality
gall bladderUBERON:000211088.81gold quality
lungUBERON:000204888.57gold quality
deciduaUBERON:000245087.54gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.12silver quality
caecumUBERON:000115386.13gold quality
visceral pleuraUBERON:000240185.47gold quality
calcaneal tendonUBERON:000370185.15gold quality
pleuraUBERON:000097785.04gold quality
parietal pleuraUBERON:000240084.13gold quality
amniotic fluidUBERON:000017382.84gold quality
right adrenal gland cortexUBERON:003582782.68gold quality
lymph nodeUBERON:000002982.52gold quality
layer of synovial tissueUBERON:000761681.39gold quality

Single-cell (SCXA)

Detected in 29 experiment(s), a significant marker in 29.

ExperimentMarker?Max mean expression
E-CURD-112yes4826.20
E-GEOD-149689yes3848.26
E-MTAB-9801yes3584.86
E-GEOD-150728yes3127.81
E-MTAB-10042yes2795.47
E-HCAD-32yes2019.12
E-HCAD-10yes1428.75
E-CURD-55yes1351.29
E-MTAB-9067yes914.22
E-MTAB-6678yes840.45
E-GEOD-130473yes819.99
E-MTAB-9906yes797.01
E-CURD-79yes704.63
E-ANND-5yes675.08
E-HCAD-4yes216.76

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1, SPI1

miRNA regulators (miRDB)

20 targeting MNDA, 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-607799.9968.042299
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-806899.9873.852376
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-806399.9169.763146
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-380-3P99.8970.181978
HSA-MIR-469899.8471.414303
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-494-3P99.7071.452795
HSA-MIR-1213299.4768.901341
HSA-MIR-889-3P99.4069.762103
HSA-MIR-314698.8566.77601
HSA-MIR-6796-3P98.6865.49689
HSA-MIR-3152-5P96.9866.88819

Literature-anchored findings (GeneRIF, showing 13)

  • Retroviral mediated expression of the human myeloid nuclear antigen in a null cell line upregulates Dlk1 expression (PMID:12112016)
  • variation in MNDA expression appeared to change with phenotypic specialization of monocytes in atherosclerosis consistent with its association with inflammation and suspected roles in regulating gene expression or in mediating cell death (PMID:15778972)
  • MNDA has a role regulating programmed cell death in myeloid progenitor cells, and that its down-regulation in myelodysplastic syndromes is related to granulocyte-macrophage progenitor cell sensitivity to TRAIL-induced programmed cell death. (PMID:16651415)
  • MNDA expression is a useful tool for the recognition of nodal marginal zone lymphoma (PMID:19474799)
  • Myeloid antigen expression is a predictor of a poor response to chemotherapy, and an adverse prognostic factor in adult T-lymphoblastic lymphoma, but not in children with T-LBL. (PMID:20193116)
  • Studied the HIN domain of recombinant myeloid nuclear differentiation antigen (MNDA). (PMID:24557068)
  • these data support the inclusion of MNDA in the diagnostic evaluation of extramedullary B-cell lymphomas, particularly those in which the differential diagnosis is between low-grade follicular lymphoma and marginal zone lymphoma. (PMID:24925224)
  • MFC adds significant information on dyspoiesis in the diagnostic work up for MDS and provides prognostic information. MNDA expression can be assessed by MFC and may facilitate evaluation of dyspoiesis when added to MDS MFC panels. (PMID:26184452)
  • MNDA expression is an independent marker for the evaluation of dyspoiesis and may be added to the standard panel for quantitative assessment by FCM. (PMID:26822549)
  • IRTA1 and MNDA are useful markers in the differential diagnosis of marginal zone lymphomas (MZLs). (PMID:30346478)
  • MNDA controls the expression of MCL-1 and BCL-2 in chronic lymphocytic leukemia cells. (PMID:32682001)
  • MNDA, a PYHIN factor involved in transcriptional regulation and apoptosis control in leukocytes. (PMID:38680493)
  • Myeloid cell-expressed MNDA enhances M2 polarization to facilitate the metastasis of hepatocellular carcinoma. (PMID:38904028)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
mus_musculusIfi202bENSMUSG00000026535
mus_musculusIfi211ENSMUSG00000026536
mus_musculusIfi205ENSMUSG00000054203
mus_musculusMndalENSMUSG00000090272
rattus_norvegicusMndaENSRNOG00000003486

Paralogs (3): PYHIN1 (ENSG00000163564), IFI16 (ENSG00000163565), AIM2 (ENSG00000163568)

Protein

Protein identifiers

Myeloid cell nuclear differentiation antigenP41218 (reviewed: P41218)

All UniProt accessions (3): P41218, H0Y6P3, Q5VUU6

UniProt curated annotations — full annotation on UniProt →

Function. May act as a transcriptional activator/repressor in the myeloid lineage. Plays a role in the granulocyte/monocyte cell-specific response to interferon. Stimulates the DNA binding of the transcriptional repressor protein YY1.

Subunit / interactions. Participates in a ternary complex with YY1 and the YY1 target DNA element. Binds nucleolin and nucleophosmin/NPM/B23.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed constitutively in cells of the myeloid lineage. Found in promyelocyte stage cells as well as in all other stage cells including peripheral blood monocytes and granulocytes. Also appears in myeloblast cells in some cases of acute myeloid Leukemia.

Domain organisation. Its N-terminal half (200 amino acids) is sufficient for maximum enhancement of YY1 DNA binding and a portion of this sequence is responsible for binding YY1.

Induction. Strongly induced by alpha interferon which selectively affects expression in late stage cells in the monocytic but not the granulocytic lineage. Induced in vitro by dimethylsulfoxide and 1,25 dihydroxyvitamin D3.

RefSeq proteins (1): NP_002423* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004020DAPINDomain
IPR004021HIN200/IF120xDomain
IPR011029DEATH-like_dom_sfHomologous_superfamily
IPR012340NA-bd_OB-foldHomologous_superfamily
IPR040205HIN-200Family

Pfam: PF02758, PF02760

UniProt features (38 total): strand 14, helix 13, sequence variant 3, domain 2, compositionally biased region 2, chain 1, turn 1, region of interest 1, short sequence motif 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
5H7QX-RAY DIFFRACTION1.45
5WPZX-RAY DIFFRACTION2
8I6KX-RAY DIFFRACTION2.4
2DBGSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P41218-F178.600.62

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation
R-HSA-168249Innate Immune System
R-HSA-168256Immune System

MSigDB gene sets: 268 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, REACTOME_INNATE_IMMUNE_SYSTEM, MCLACHLAN_DENTAL_CARIES_UP, GOBP_RESPONSE_TO_PEPTIDE, GOBP_B_CELL_ACTIVATION, GOCC_SECRETORY_GRANULE, GOBP_NEGATIVE_REGULATION_OF_LEUKOCYTE_PROLIFERATION, MODULE_151, CHUNG_BLISTER_CYTOTOXICITY_DN, MODULE_45, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP

GO Biological Process (7): activation of innate immune response (GO:0002218), cellular defense response (GO:0006968), DNA damage response (GO:0006974), negative regulation of B cell proliferation (GO:0030889), cellular response to interferon-beta (GO:0035458), positive regulation of apoptotic process (GO:0043065), B cell receptor signaling pathway (GO:0050853)

GO Molecular Function (3): double-stranded DNA binding (GO:0003690), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (9): extracellular region (GO:0005576), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), azurophil granule lumen (GO:0035578), extracellular exosome (GO:0070062), ficolin-1-rich granule lumen (GO:1904813), nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Innate Immune System1
Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
nuclear lumen2
activation of immune response1
positive regulation of innate immune response1
defense response1
cellular response to stress1
regulation of B cell proliferation1
B cell proliferation1
negative regulation of lymphocyte proliferation1
negative regulation of B cell activation1
response to interferon-beta1
cellular response to cytokine stimulus1
apoptotic process1
regulation of apoptotic process1
positive regulation of programmed cell death1
antigen receptor-mediated signaling pathway1
DNA binding1
nucleic acid binding1
binding1
intracellular membraneless organelle1
cytoplasm1
vacuolar lumen1
secretory granule lumen1
azurophil granule1
extracellular vesicle1
intracellular organelle lumen1
ficolin-1-rich granule1
intracellular membrane-bounded organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

1552 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MNDAMEFVO15553727
MNDASPTA1P02549542
MNDAFCER1AP12319528
MNDAPYCARDQ9ULZ3518
MNDACD53P19397517
MNDAIFNA16P05015514
MNDAIFNA8P01565511
MNDAIFNA7P01567507
MNDAIFNA21P01568507
MNDAFPR1P21462507
MNDAIFNA5P01569506
MNDAIFNA14P01570505
MNDATLR8Q9NR97504
MNDALYZP00695494
MNDAIFNA6P05013492

IntAct

96 interactions, top by confidence:

ABTypeScore
HEMGNNPM1psi-mi:“MI:0914”(association)0.600
MNDAA2Mpsi-mi:“MI:0915”(physical association)0.560
MNDADNM2psi-mi:“MI:0915”(physical association)0.560
TOR1AMNDApsi-mi:“MI:0915”(physical association)0.560
MNDApsi-mi:“MI:0915”(physical association)0.560
GRNMNDApsi-mi:“MI:0915”(physical association)0.560
MNDAMETpsi-mi:“MI:0915”(physical association)0.560
MNDANDUFV1psi-mi:“MI:0915”(physical association)0.560
MNDAPEX1psi-mi:“MI:0915”(physical association)0.560
PSEN2MNDApsi-mi:“MI:0915”(physical association)0.560
MNDATTRpsi-mi:“MI:0915”(physical association)0.560
YWHAGMNDApsi-mi:“MI:0915”(physical association)0.560
SETDB1MNDApsi-mi:“MI:0915”(physical association)0.560
KAT5MNDApsi-mi:“MI:0915”(physical association)0.560
LMO3MNDApsi-mi:“MI:0915”(physical association)0.560
MNDAHTTpsi-mi:“MI:0915”(physical association)0.560

BioGRID (189): MNDA (Synthetic Lethality), MNDA (Two-hybrid), MNDA (Two-hybrid), MNDA (Two-hybrid), MNDA (Biochemical Activity), MNDA (Proximity Label-MS), AATF (Affinity Capture-MS), ATXN2 (Affinity Capture-MS), ATXN2L (Affinity Capture-MS), BMS1 (Affinity Capture-MS), BOP1 (Affinity Capture-MS), BRIX1 (Affinity Capture-MS), BYSL (Affinity Capture-MS), KNOP1 (Affinity Capture-MS), C7orf50 (Affinity Capture-MS)

ESM2 similar proteins: A6H5X4, B1AUS7, D0QMC3, O35368, O60224, O60225, P0C6Y7, P0DOV1, P0DOV2, P23497, P41218, Q15361, Q16384, Q16385, Q16666, Q2KIN0, Q3U827, Q3ZCI6, Q4R7Q1, Q504N7, Q5H9L4, Q5I0E2, Q5I0J8, Q5RAK3, Q5RCZ8, Q5RD14, Q5W0A0, Q62187, Q6K0P9, Q71F23, Q7RTT3, Q7RTT4, Q7RTT5, Q7RTT6, Q86T96, Q8BV49, Q8BVM9, Q8C0V1, Q8C6C7, Q8CGE8

Diamond homologs: D0QMC3, O14862, O35368, P0DOV1, P0DOV2, P41218, Q16666, Q3V3Q4, Q504N7, Q5RD14, Q6K0P9, Q8BV49, Q8CGE8, Q8SPH9, Q91VJ1, Q9R002, W6CW81

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance409
Likely benign225
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3247947NC_000001.10:g.(?158581054)(158819027_?)delPathogenic

SpliceAI

924 predictions. Top by Δscore:

VariantEffectΔscore
1:158831556:AGGTG:Adonor_loss1.0000
1:158831558:GTGAG:Gdonor_loss1.0000
1:158843273:T:TAacceptor_gain1.0000
1:158843274:GTCA:Gacceptor_loss1.0000
1:158843275:TCAGT:Tacceptor_loss1.0000
1:158843277:A:AGacceptor_gain1.0000
1:158843277:A:Cacceptor_loss1.0000
1:158843277:AGTT:Aacceptor_gain1.0000
1:158843278:G:Aacceptor_loss1.0000
1:158843278:G:GCacceptor_gain1.0000
1:158843278:GT:Gacceptor_gain1.0000
1:158843278:GTT:Gacceptor_gain1.0000
1:158843278:GTTG:Gacceptor_gain1.0000
1:158843278:GTTGC:Gacceptor_gain1.0000
1:158844524:A:Gdonor_gain1.0000
1:158847727:GA:Gacceptor_gain1.0000
1:158847727:GAAAA:Gacceptor_gain1.0000
1:158847934:GAGAA:Gdonor_gain1.0000
1:158832452:ATTTT:Adonor_gain0.9900
1:158842132:A:AGacceptor_gain0.9900
1:158842133:G:GGacceptor_gain0.9900
1:158843280:T:Aacceptor_gain0.9900
1:158843411:CTCAG:Cdonor_loss0.9900
1:158843412:TCAG:Tdonor_loss0.9900
1:158843413:CAGGT:Cdonor_loss0.9900
1:158843416:G:Tdonor_loss0.9900
1:158843417:T:Gdonor_loss0.9900
1:158844514:GACA:Gdonor_gain0.9900
1:158845802:G:GTdonor_gain0.9900
1:158847724:GCAG:Gacceptor_loss0.9900

AlphaMissense

2694 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:158845794:T:CF260L0.988
1:158845796:T:AF260L0.988
1:158845796:T:GF260L0.988
1:158845989:T:CF325L0.987
1:158845991:T:AF325L0.987
1:158845991:T:GF325L0.987
1:158845722:T:CF236L0.986
1:158845724:T:AF236L0.986
1:158845724:T:GF236L0.986
1:158845728:G:CA238P0.985
1:158847905:A:CS389R0.983
1:158847907:C:AS389R0.983
1:158847907:C:GS389R0.983
1:158845738:C:AA241D0.982
1:158845795:T:CF260S0.979
1:158845723:T:CF236S0.978
1:158845729:C:AA238D0.976
1:158845795:T:GF260C0.975
1:158845737:G:CA241P0.971
1:158847767:G:CD343H0.970
1:158842319:T:CF56L0.969
1:158842321:C:AF56L0.969
1:158842321:C:GF56L0.969
1:158845990:T:CF325S0.968
1:158847762:T:AI341K0.966
1:158845983:G:TG323W0.965
1:158845735:T:AV240E0.961
1:158845666:T:CL217P0.959
1:158847848:T:CF370L0.959
1:158847850:C:AF370L0.959

dbSNP variants (sampled 300 via entrez): RS1000020171 (1:158831854 G>A), RS1000041657 (1:158845366 T>C), RS1000104626 (1:158847583 T>A), RS1000140086 (1:158838491 T>C), RS1000261373 (1:158838779 A>G), RS1000386485 (1:158844495 C>A,T), RS1000634142 (1:158833985 CT>C), RS1000849837 (1:158839713 A>G,T), RS1000963958 (1:158833622 C>T), RS1001318188 (1:158846433 A>C), RS1001477663 (1:158833312 T>C), RS1001547798 (1:158833585 G>C), RS1001663143 (1:158846796 C>T), RS1001689962 (1:158830327 C>A,T), RS1001963614 (1:158836325 G>T)

Disease associations

OMIM: gene MIM:159553 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST001762_657Obesity-related traits1.000000e-06
GCST008765_1Perceived intensity of aspartame3.000000e-06
GCST009391_61Metabolite levels5.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0003939energy intake
EFO:0010352diacylglycerol 34:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — Absent in melanoma (AIM)-like receptors (ALRs)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Nickeldecreases expression, increases expression3
Tretinoinincreases expression2
triphenyl phosphateaffects expression1
sulforaphaneincreases expression1
tetrathiomolybdateincreases expression1
4-hydroxy-2-nonenaldecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
Air Pollutantsaffects expression, increases abundance1
Air Pollutants, Occupationaldecreases expression1
Benzo(a)pyrenedecreases expression1
Cadmiumdecreases expression, increases abundance1
Caffeineincreases phosphorylation1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment, decreases expression1
Ozoneaffects expression, increases abundance1
Zidovudineaffects cotreatment, increases expression1
Asbestos, Serpentinedecreases expression1
Uranium Compoundsincreases expression1
Antirheumatic Agentsdecreases expression1
Cadmium Chloridedecreases expression, increases abundance1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.