MIER3

gene
On this page

Also known as FLJ35954DKFZp686L09111DKFZp781I1119

Summary

MIER3 (MIER family member 3, HGNC:26678) is a protein-coding gene on chromosome 5q11.2, encoding Mesoderm induction early response protein 3 (Q7Z3K6). Transcriptional repressor.

Predicted to enable histone deacetylase binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of protein-containing complex. Implicated in breast cancer and lung adenocarcinoma. Biomarker of breast cancer; invasive ductal carcinoma; and lung non-small cell carcinoma.

Source: NCBI Gene 166968 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 51 total
  • MANE Select transcript: NM_001297599

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26678
Approved symbolMIER3
NameMIER family member 3
Location5q11.2
Locus typegene with protein product
StatusApproved
AliasesFLJ35954, DKFZp686L09111, DKFZp781I1119
Ensembl geneENSG00000155545
Ensembl biotypeprotein_coding
OMIM620100
Entrez166968

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000336942, ENST00000381199, ENST00000381213, ENST00000381226, ENST00000409421, ENST00000440000, ENST00000451637, ENST00000452157, ENST00000480115, ENST00000497185, ENST00000546593, ENST00000861254

RefSeq mRNA: 3 — MANE Select: NM_001297599 NM_001297598, NM_001297599, NM_152622

CCDS: CCDS3973, CCDS75248, CCDS78011

Canonical transcript exons

ENST00000381199 — 13 exons

ExonStartEnd
ENSE000015514675695209456952123
ENSE000016079175691960356923585
ENSE000034626105694692656947071
ENSE000034630145693066456930745
ENSE000034726955693888356939017
ENSE000035084925692391556924042
ENSE000035256935692876756928861
ENSE000035412905692369156923833
ENSE000035703525695062856950652
ENSE000035915045693542856935500
ENSE000036082415693757856937698
ENSE000036368835693324756933398
ENSE000036402425693566656935751

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 97.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2446 / max 253.7529, expressed in 1583 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
617555.07471576
617560.169959

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033197.13gold quality
jejunal mucosaUBERON:000039995.99gold quality
buccal mucosa cellCL:000233695.92gold quality
colonic mucosaUBERON:000031795.45gold quality
mucosa of sigmoid colonUBERON:000499394.98gold quality
rectumUBERON:000105291.87gold quality
colonic epitheliumUBERON:000039789.72gold quality
duodenumUBERON:000211489.68gold quality
mucosa of transverse colonUBERON:000499189.55gold quality
secondary oocyteCL:000065589.12gold quality
parietal pleuraUBERON:000240088.76gold quality
germinal epithelium of ovaryUBERON:000130488.56gold quality
calcaneal tendonUBERON:000370188.54gold quality
palpebral conjunctivaUBERON:000181288.38gold quality
visceral pleuraUBERON:000240188.28gold quality
transverse colonUBERON:000115787.71gold quality
oviduct epitheliumUBERON:000480487.36gold quality
jejunumUBERON:000211587.34gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.14gold quality
pigmented layer of retinaUBERON:000178286.69gold quality
adrenal tissueUBERON:001830386.63gold quality
endometriumUBERON:000129586.48gold quality
mucosa of paranasal sinusUBERON:000503086.36gold quality
ventricular zoneUBERON:000305386.31gold quality
large intestineUBERON:000005986.19gold quality
colonUBERON:000115585.85gold quality
islet of LangerhansUBERON:000000685.56gold quality
tibiaUBERON:000097985.52gold quality
intestineUBERON:000016085.46gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.45gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

356 targeting MIER3, 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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3646100.0073.565283
HSA-MIR-4262100.0073.263931
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-5692A100.0074.406850
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-9-5P100.0072.282361
HSA-MIR-3924100.0072.092394
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3163100.0077.238605
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-186-5P99.9970.833707
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-607799.9968.042299

Literature-anchored findings (GeneRIF, showing 4)

  • Data suggest that the human 5q11.2 breast cancer risk allele marked by rs889312 is mammary gland autonomous, and MIER3 is a candidate breast cancer susceptibility gene. (PMID:22993404)
  • Histone deacetylase assays confirmed that MIER2, but not MIER3 complexes, have associated deacetylase activity. (PMID:28046085)
  • our data suggested that MIER3 plays a potential tumor suppressor role in CRC progression and may be a potentially valuable clinical prognostic marker of this disease. (PMID:28887525)
  • MIER3 induces epithelial-mesenchymal transition and promotes breast cancer cell aggressiveness via forming a co-repressor complex with HDAC1/HDAC2/Snail. (PMID:34242623)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriomier3aENSDARG00000006253
danio_reriomier3bENSDARG00000021288
mus_musculusMier3ENSMUSG00000032727
rattus_norvegicusMier3ENSRNOG00000013121
drosophila_melanogasterCG1620FBGN0033183
caenorhabditis_elegansWBGENE00017352
caenorhabditis_elegansWBGENE00020320

Paralogs (5): MTA3 (ENSG00000057935), MIER2 (ENSG00000105556), MTA2 (ENSG00000149480), MTA1 (ENSG00000182979), MIER1 (ENSG00000198160)

Protein

Protein identifiers

Mesoderm induction early response protein 3Q7Z3K6 (reviewed: Q7Z3K6)

All UniProt accessions (4): Q7Z3K6, A8MQD4, C9JXP7, H7C1J9

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor.

Subcellular location. Nucleus.

Isoforms (5)

UniProt IDNamesCanonical?
Q7Z3K6-11yes
Q7Z3K6-22
Q7Z3K6-33
Q7Z3K6-44
Q7Z3K6-55

RefSeq proteins (3): NP_001284527, NP_001284528, NP_689835 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000949ELM2_domDomain
IPR001005SANT/MybDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017884SANT_domDomain
IPR040138MIER/MTAFamily
IPR045787MIER1/3_CDomain

Pfam: PF00249, PF01448, PF19426

UniProt features (26 total): modified residue 7, splice variant 5, sequence variant 4, compositionally biased region 4, domain 2, region of interest 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z3K6-F159.100.17

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 (7): 53, 114, 156, 163, 165, 168, 52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 255 (showing top): TGCACTT_MIR519C_MIR519B_MIR519A, AAGCCAT_MIR135A_MIR135B, GCAAGGA_MIR502, ATGCAGT_MIR217, CACCAGC_MIR138, CTATGCA_MIR153, ACTGCAG_MIR173P, FOSTER_TOLERANT_MACROPHAGE_UP, WTGAAAT_UNKNOWN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, ACTTTAT_MIR1425P, CAAGGAT_MIR362, CGTCTTA_MIR208, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, TTTGCAC_MIR19A_MIR19B

GO Biological Process (1): negative regulation of transcription by RNA polymerase II (GO:0000122)

GO Molecular Function (3): transcription corepressor activity (GO:0003714), histone deacetylase binding (GO:0042826), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), protein-containing complex (GO:0032991)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of DNA-templated transcription2
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
transcription coregulator activity1
enzyme binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
cellular_component1

Protein interactions and networks

STRING

872 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MIER3SETD9Q8NE22604
MIER3HDAC1Q13547494
MIER3BAHD1Q8TBE0488
MIER3HDAC2Q92769483
MIER3DYTNA2CJ06441
MIER3MIER1Q8N108405
MIER3TULP4Q9NRJ4374
MIER3MAP3K1Q13233364
MIER3PRMT2P55345359
MIER3SMIM5Q71RC9359
MIER3ZKSCAN8Q15776357
MIER3CTBSQ01459357
MIER3MRPS30Q9NP92351
MIER3ANAPC15P60006345
MIER3LSP1P33241327

IntAct

33 interactions, top by confidence:

ABTypeScore
HDAC2KDM1Apsi-mi:“MI:0914”(association)0.890
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
HDAC1TNRC18psi-mi:“MI:0914”(association)0.790
H2AZ1ZNHIT1psi-mi:“MI:0914”(association)0.770
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
H2AC4PPM1Gpsi-mi:“MI:0914”(association)0.670
H2BC1PPM1Gpsi-mi:“MI:0914”(association)0.640
C16orf87CDC27psi-mi:“MI:0914”(association)0.640
H2BC26PPM1Gpsi-mi:“MI:0914”(association)0.530
H2AC20PPM1Gpsi-mi:“MI:0914”(association)0.530
WIZRPP30psi-mi:“MI:0914”(association)0.350
HDAC1psi-mi:“MI:0914”(association)0.350
HDAC2psi-mi:“MI:0914”(association)0.350
H2AC11U2SURPpsi-mi:“MI:0914”(association)0.350
H2AJWDR46psi-mi:“MI:0914”(association)0.350
MIER3BAHD1psi-mi:“MI:0914”(association)0.350
H2AC11psi-mi:“MI:0914”(association)0.350
H2AC4MPHOSPH10psi-mi:“MI:0914”(association)0.350
H2AZ1PPM1Gpsi-mi:“MI:0914”(association)0.350

BioGRID (32): MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-RNA), MIER3 (Affinity Capture-MS), MIER3 (Two-hybrid), MCRS1 (Two-hybrid), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), HDAC2 (Affinity Capture-MS), MIER3 (Affinity Capture-MS), MIER3 (Affinity Capture-MS)

ESM2 similar proteins: A2AKB4, A4D2P6, A5PJX4, D3Z9H7, F5GYI3, G3V9M2, P04198, P07516, P18302, P49796, Q0QWG9, Q0X0E2, Q14DQ1, Q2KI80, Q3SYZ3, Q3TVI4, Q3U3N0, Q3UHF3, Q4R3R9, Q5FVJ4, Q5FVM5, Q5SYB0, Q5T7N3, Q5UEM8, Q60829, Q68CJ9, Q6J4I0, Q6P9J5, Q6UXB0, Q7Z3K6, Q80UZ0, Q8BRJ3, Q8BWU3, Q8C4S8, Q8N344, Q8NC24, Q8NE31, Q8TEY5, Q8VIP2, Q91XE9

Diamond homologs: A5PJX4, O75376, Q3U3N0, Q3UHF3, Q4KKX4, Q4R3R9, Q5REE1, Q5UAK0, Q5ZKT9, Q60974, Q7T105, Q7Z3K6, Q8N108, Q8N344, Q9WU42, Q9Y618, Q4R2Z8, Q62599, Q8K4B0, Q9H0D2, Q8BXJ2, Q96PN7, Q90WN5, Q0GGX2, Q13330, Q62901, Q80TZ9, Q9P2R6, Q18919, Q6PJG2, Q59E36, Q5FWT8, Q5ZJ40, Q6NRZ0, Q6P116, Q6PGA0, Q8C796, Q8CFE3, Q8IZ40, Q8QG78

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 27 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Packaging Of Telomere Ends669.3×2e-09
NuRD complex assembly966.8×5e-13
Recognition and association of DNA glycosylase with site containing an affected purine664.4×3e-09
Cleavage of the damaged purine664.4×3e-09
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression864.1×6e-12
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3761.9×2e-10
Interaction of NuRD complexes with transcription factors960.1×6e-13
Recognition and association of DNA glycosylase with site containing an affected pyrimidine658.2×4e-09

GO biological processes:

GO termPartnersFoldFDR
heterochromatin formation991.9×4e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2370 predictions. Top by Δscore:

VariantEffectΔscore
5:56923581:CAAAG:Cacceptor_gain1.0000
5:56923582:AAAG:Aacceptor_gain1.0000
5:56923583:AAG:Aacceptor_gain1.0000
5:56923584:AG:Aacceptor_gain1.0000
5:56923586:C:CCacceptor_gain1.0000
5:56923586:CTA:Cacceptor_loss1.0000
5:56923587:T:Cacceptor_loss1.0000
5:56923685:TTTTA:Tdonor_loss1.0000
5:56923686:TTTAC:Tdonor_loss1.0000
5:56923687:TTAC:Tdonor_loss1.0000
5:56923688:TACCT:Tdonor_loss1.0000
5:56923689:ACC:Adonor_loss1.0000
5:56923690:CCT:Cdonor_loss1.0000
5:56923832:CC:Cacceptor_gain1.0000
5:56923833:CC:Cacceptor_gain1.0000
5:56923913:A:ACdonor_gain1.0000
5:56923914:C:CCdonor_gain1.0000
5:56923914:CGTAA:Cdonor_gain1.0000
5:56930658:TCTTA:Tdonor_loss1.0000
5:56930659:CTTA:Cdonor_loss1.0000
5:56930660:TTA:Tdonor_loss1.0000
5:56930661:TA:Tdonor_loss1.0000
5:56930662:ACCT:Adonor_loss1.0000
5:56933395:TATA:Tacceptor_gain1.0000
5:56933396:ATA:Aacceptor_gain1.0000
5:56933397:TA:Tacceptor_gain1.0000
5:56933399:C:CCacceptor_gain1.0000
5:56935422:CCTTA:Cdonor_loss1.0000
5:56935423:CTTA:Cdonor_loss1.0000
5:56935424:TTAC:Tdonor_loss1.0000

AlphaMissense

3682 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:56923992:C:AK325N1.000
5:56923992:C:GK325N1.000
5:56923995:C:AW324C1.000
5:56923995:C:GW324C1.000
5:56923997:A:GW324R1.000
5:56923997:A:TW324R1.000
5:56924006:A:CY321D1.000
5:56924016:A:CC317W1.000
5:56924031:C:AR312S1.000
5:56924031:C:GR312S1.000
5:56928780:A:TI304K1.000
5:56928788:A:CF301L1.000
5:56928788:A:TF301L1.000
5:56928789:A:GF301S1.000
5:56928790:A:GF301L1.000
5:56928795:T:AK299I1.000
5:56928822:A:GF290S1.000
5:56928845:C:AW282C1.000
5:56928845:C:GW282C1.000
5:56928847:A:GW282R1.000
5:56928847:A:TW282R1.000
5:56930732:A:GL254P1.000
5:56937679:A:GL112P1.000
5:56937691:A:TI108K1.000
5:56923982:G:TR329S0.999
5:56923988:A:GS327P0.999
5:56923993:T:AK325M0.999
5:56923993:T:GK325T0.999
5:56923994:T:CK325E0.999
5:56923996:C:GW324S0.999

dbSNP variants (sampled 300 via entrez): RS1000028732 (5:56946599 AG>A), RS1000029254 (5:56924297 G>A,C), RS1000060002 (5:56946743 G>A), RS1000094389 (5:56952271 C>A,T), RS1000103388 (5:56952774 G>A,C), RS1000215380 (5:56946372 T>C), RS1000307436 (5:56941128 A>G), RS1000355473 (5:56940420 A>T), RS1000388445 (5:56940725 G>C,T), RS1000389311 (5:56933010 T>C), RS1000516037 (5:56947722 T>G), RS1000588712 (5:56946092 A>G), RS1000699130 (5:56942008 G>A,T), RS1000704966 (5:56927202 G>A), RS1000729749 (5:56942405 T>A)

Disease associations

OMIM: gene MIM:620100 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST005956_55Waist-to-hip ratio adjusted for BMI9.000000e-06
GCST005957_9Waist-to-hip ratio adjusted for BMI (age <50)2.000000e-07
GCST005962_24Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)3.000000e-08
GCST008151_101Waist circumference2.000000e-06
GCST008160_103Waist circumference2.000000e-06
GCST009665_14Breast cancer8.000000e-07
GCST010701_111Cortical surface area (MOSTest)8.000000e-12
GCST010702_47Subcortical volume (MOSTest)6.000000e-10
GCST010703_329Brain morphology (MOSTest)2.000000e-10
GCST011154_4Fasting plasma glucose1.000000e-06

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression7
trichostatin Adecreases expression, affects cotreatment3
sodium arsenitedecreases expression, increases expression3
Tobacco Smoke Pollutionincreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359decreases phosphorylation1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, affects expression, increases abundance1
coumarinaffects phosphorylation1
methacrylaldehydeaffects cotreatment, affects expression, increases abundance1
perfluoro-n-nonanoic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
perfluorohexanesulfonic acidincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Acroleinaffects cotreatment, affects expression, increases abundance1
Air Pollutantsaffects cotreatment, affects expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Doxorubicindecreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydedecreases expression1
Methyl Methanesulfonateincreases expression1
Ozoneincreases abundance, affects cotreatment, affects expression1
Thimerosalincreases expression1
Tretinoindecreases expression1
Triiodothyroninedecreases expression1
Cyclosporineincreases methylation1
Acrylamideincreases expression1

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.