MIXL1

gene
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Also known as MILD1MIXL

Summary

MIXL1 (Mix paired-like homeobox, HGNC:13363) is a protein-coding gene on chromosome 1q42.12, encoding Homeobox protein MIXL1 (Q9H2W2). Transcription factor that play a central role in proper axial mesendoderm morphogenesis and endoderm formation.

Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including endodermal cell differentiation; negative regulation of hematopoietic progenitor cell differentiation; and positive regulation of mesoderm development. Predicted to act upstream of or within cell migration involved in gastrulation and hemopoiesis. Located in nucleoplasm.

Source: NCBI Gene 83881 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 39 total
  • MANE Select transcript: NM_031944

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13363
Approved symbolMIXL1
NameMix paired-like homeobox
Location1q42.12
Locus typegene with protein product
StatusApproved
AliasesMILD1, MIXL
Ensembl geneENSG00000185155
Ensembl biotypeprotein_coding
OMIM609852
Entrez83881

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000366810, ENST00000542034, ENST00000557734

RefSeq mRNA: 2 — MANE Select: NM_031944 NM_001282402, NM_031944

CCDS: CCDS1552, CCDS60432

Canonical transcript exons

ENST00000366810 — 2 exons

ExonStartEnd
ENSE00002485896226225507226227060
ENSE00003902013226223664226224074

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 88.12.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.7337 / max 189.8406, expressed in 156 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
88641.463994
88630.098246
88650.087346
88660.084337

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002388.12gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.91gold quality
secondary oocyteCL:000065580.74gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.84silver quality
bone marrow cellCL:000209276.44gold quality
lymph nodeUBERON:000002967.51gold quality
gingival epitheliumUBERON:000194967.46gold quality
gingivaUBERON:000182864.02gold quality
vermiform appendixUBERON:000115462.27gold quality
parotid glandUBERON:000183161.29gold quality
caecumUBERON:000115360.01gold quality
epithelium of nasopharynxUBERON:000195159.88gold quality
tonsilUBERON:000237259.09gold quality
esophagus squamous epitheliumUBERON:000692058.75gold quality
biceps brachiiUBERON:000150758.42gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450257.88gold quality
colonic epitheliumUBERON:000039757.87silver quality
upper leg skinUBERON:000426257.80silver quality
amniotic fluidUBERON:000017357.63gold quality
pigmented layer of retinaUBERON:000178257.53gold quality
oral cavityUBERON:000016757.26gold quality
cerebellar cortexUBERON:000212957.00gold quality
duodenumUBERON:000211456.97gold quality
nasal cavity epitheliumUBERON:000538456.80gold quality
cerebellumUBERON:000203756.75gold quality
cerebellar hemisphereUBERON:000224556.69gold quality
Brodmann (1909) area 23UBERON:001355456.25gold quality
mucosa of transverse colonUBERON:000499156.07gold quality
rectumUBERON:000105255.93gold quality
superficial temporal arteryUBERON:000161455.89gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-MTAB-5061yes1819.12
E-GEOD-109979yes1035.13
E-MTAB-7052yes152.98
E-CURD-6yes39.16
E-MTAB-9067yes9.08
E-ANND-3yes5.86
E-CURD-97no95.71
E-MTAB-7303no28.50
E-MTAB-7249no18.51

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

7 targets.

TargetRegulation
CXCR4Activation
GSCActivation
HBA1Activation
KDRActivation
MIXL1
PDGFRAActivation
TBXTActivation

JASPAR motifs

MotifNameFamily
MA0662.1MIXL1Paired-related HD factors
MA0662.2MIXL1Paired-related HD factors

JASPAR matrix evidence (PMIDs): PMID:19711456

Upstream regulators (CollecTRI, top): FOXH1, GLI3, GSC, KDM6B, MIXL1

miRNA regulators (miRDB)

61 targeting MIXL1, 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-150-5P99.9966.691976
HSA-MIR-1213699.9872.815713
HSA-MIR-302E99.9670.742669
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
HSA-MIR-659-3P99.8570.691620
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-373-3P99.8470.681668
HSA-MIR-520E-3P99.8470.551698
HSA-MIR-372-3P99.8370.581691
HSA-MIR-520A-3P99.8370.591687
HSA-MIR-520B-3P99.8370.561699
HSA-MIR-520C-3P99.8370.561699
HSA-MIR-520D-3P99.8370.781676
HSA-MIR-132399.8369.892471
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-205299.7969.372031
HSA-MIR-548AJ-5P99.7871.123085
HSA-MIR-548F-5P99.7871.023093
HSA-MIR-548G-5P99.7871.123085
HSA-MIR-548X-5P99.7871.123085
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-430699.7270.503630
HSA-MIR-149-3P99.7268.223963

Literature-anchored findings (GeneRIF, showing 7)

  • shows functional similarity to Xenopus Mix.1 (PMID:12070013)
  • These results demonstrate for a functional role for TGF-beta ligands in regulation of mammalian Mixl1, identify FoxH1 as an essential co-activator, and implicate Nodal as the embryonic regulator of Mixl1 in mesendoderm morphogenesis. (PMID:15982639)
  • MIXL1 protein is differentially expressed in non-Hodgkin lymphoma and Hodgkin lymphoma; findings suggest that MIXL1 overexpression may play a role in driving proliferatin or blocking differentiation in lymphoma oncogenesis (PMID:17303500)
  • Targeted insertion in human embryonic stem cells of sequences encoding green fluorescent protein (GFP) into the locus of MIXL1, a gene transiently expressed in the primitive streak during embryogenesis. (PMID:18032708)
  • Brachyury and related Tbx proteins interact with the Mixl1 homeodomain protein and negatively regulate Mixl1 transcriptional activity (PMID:22164283)
  • results demonstrate that Mixl1 and Flk1 play roles…during dimethyl sulfoxide-induced mesodermal specification in P19 cells. (PMID:25521758)
  • Findings support the existence of a novel MIXL1-c REL mediated survival axis in AML that can be targeted by BMPR1 inhibitors. (MIXL1- human gene, Mixl1- mouse ortholog, MIXL1- protein). (PMID:25544748)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriomixl1ENSDARG00000069252
mus_musculusMixl1ENSMUSG00000026497
rattus_norvegicusMixl1ENSRNOG00000003176

Paralogs (50): ARX (ENSG00000004848), PAX6 (ENSG00000007372), PAX7 (ENSG00000009709), ALX4 (ENSG00000052850), GSC2 (ENSG00000063515), PITX1 (ENSG00000069011), PAX2 (ENSG00000075891), RHOXF1 (ENSG00000101883), CRX (ENSG00000105392), EVX1 (ENSG00000106038), PAX4 (ENSG00000106331), NOBOX (ENSG00000106410), PITX3 (ENSG00000107859), PHOX2B (ENSG00000109132), OTX1 (ENSG00000115507), PRRX1 (ENSG00000116132), VSX2 (ENSG00000119614), ESX1 (ENSG00000123576), PAX8 (ENSG00000125618), PAX1 (ENSG00000125813), RHOXF2 (ENSG00000131721), GSC (ENSG00000133937), RAX (ENSG00000134438), PAX3 (ENSG00000135903), ALX3 (ENSG00000156150), HESX1 (ENSG00000163666), PITX2 (ENSG00000164093), UNCX (ENSG00000164853), PHOX2A (ENSG00000165462), OTX2 (ENSG00000165588), DRGX (ENSG00000165606), PRRX2 (ENSG00000167157), SHOX2 (ENSG00000168779), OTP (ENSG00000171540), RAX2 (ENSG00000173976), EVX2 (ENSG00000174279), PROP1 (ENSG00000175325), ISX (ENSG00000175329), ALX1 (ENSG00000180318), SHOX (ENSG00000185960)

Protein

Protein identifiers

Homeobox protein MIXL1Q9H2W2 (reviewed: Q9H2W2)

Alternative names: Homeodomain protein MIX, MIX1 homeobox-like protein 1, Mix.1 homeobox-like protein

All UniProt accessions (1): Q9H2W2

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that play a central role in proper axial mesendoderm morphogenesis and endoderm formation. Required for efficient differentiation of cells from the primitive streak stage to blood, by acting early in the recruitment and/or expansion of mesodermal progenitors to the hemangioblastic and hematopoietic lineages. Also involved in the morphogenesis of the heart and the gut during embryogenesis. Acts as a negative regulator of brachyury expression.

Subcellular location. Nucleus.

Tissue specificity. Restricted to progenitors and secondary lymph tissues. In normal hematopoiesis, it is restricted to immature B- and T-lymphoid cells. Present in differentiating embryonic stem cells (at protein level).

Post-translational modifications. Phosphorylated at multiple sites.

Similarity. Belongs to the paired homeobox family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H2W2-11yes
Q9H2W2-22

RefSeq proteins (2): NP_001269331, NP_114150* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR042917MIXL1Family

Pfam: PF00046

UniProt features (8 total): compositionally biased region 3, chain 1, DNA-binding region 1, region of interest 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H2W2-F167.020.25

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 (1): 20

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-9754189Germ layer formation at gastrulation
R-HSA-9823730Formation of definitive endoderm
R-HSA-1266738Developmental Biology
R-HSA-9758941Gastrulation

MSigDB gene sets: 97 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_FORMATION_OF_PRIMARY_GERM_LAYER, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_MESODERM_DEVELOPMENT, GOBP_CELL_MIGRATION_INVOLVED_IN_GASTRULATION, GOBP_GASTRULATION, GOBP_ENDODERM_DEVELOPMENT, GOBP_REGULATION_OF_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_ENDODERM_FORMATION, GOBP_EMBRYO_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_MESODERM_DEVELOPMENT

GO Biological Process (15): endoderm formation (GO:0001706), hematopoietic progenitor cell differentiation (GO:0002244), regulation of transcription by RNA polymerase II (GO:0006357), gastrulation (GO:0007369), endoderm development (GO:0007492), heart development (GO:0007507), endodermal cell differentiation (GO:0035987), cell migration involved in gastrulation (GO:0042074), positive regulation of transcription by RNA polymerase II (GO:0045944), digestive tract development (GO:0048565), negative regulation of hematopoietic progenitor cell differentiation (GO:1901533), positive regulation of mesoderm development (GO:2000382), regulation of DNA-templated transcription (GO:0006355), hemopoiesis (GO:0030097), cell differentiation (GO:0030154)

GO Molecular Function (9): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), cis-regulatory region sequence-specific DNA binding (GO:0000987), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), protein homodimerization activity (GO:0042803), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), identical protein binding (GO:0042802)

GO Cellular Component (3): chromatin (GO:0000785), nucleoplasm (GO:0005654), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Gastrulation2
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
cell differentiation2
transcription by RNA polymerase II2
endoderm formation2
regulation of transcription by RNA polymerase II2
cellular anatomical structure2
formation of primary germ layer1
endoderm development1
hemopoiesis1
regulation of DNA-templated transcription1
ectoderm formation1
mesoderm formation1
embryonic morphogenesis1
tissue development1
animal organ development1
circulatory system development1
ameboidal-type cell migration1
gastrulation1
positive regulation of DNA-templated transcription1
tube development1
digestive system development1
hematopoietic progenitor cell differentiation1
negative regulation of cell differentiation1
regulation of hematopoietic progenitor cell differentiation1
mesoderm development1
positive regulation of developmental process1
regulation of mesoderm development1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cell development1
cellular developmental process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
transcription cis-regulatory region binding1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
identical protein binding1

Protein interactions and networks

STRING

1042 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MIXL1FOXH1O75593856
MIXL1SOX17Q9H6I2839
MIXL1FOXA2Q9Y261793
MIXL1EOMESO95936775
MIXL1NANOGQ9H9S0742
MIXL1FOXA1P55317689
MIXL1POU5F1P31359650
MIXL1GATA4P43694645
MIXL1SOX1O00570632
MIXL1TBX6O95947628
MIXL1GATA6P78327618
MIXL1MESP1Q9BRJ9614
MIXL1NODALQ96S42597
MIXL1BMP4P12644591
MIXL1GATA1P15976591

IntAct

2 interactions, top by confidence:

ABTypeScore
MIXL1TBXTpsi-mi:“MI:0915”(physical association)0.400

BioGRID (1): MIXL1 (Proximity Label-MS)

ESM2 similar proteins: A1YEV8, A1YF08, A1YG25, A1YG85, A2RU54, A2T711, A2T756, A8MTQ0, O14813, O15522, O35160, O35602, O43763, O70218, P28360, P42580, P43687, P50223, P52945, P52946, P52947, P70118, P70354, P81062, Q06348, Q2VL79, Q2VL84, Q2VL85, Q2VL87, Q2VL88, Q61663, Q62066, Q62782, Q6XYB7, Q7YRX0, Q96IS3, Q99811, Q9DED6, Q9ER42, Q9GK08

Diamond homologs: A0A1W2PPF3, A1YEV8, A1YG25, A1YGA2, A2T711, A2T777, A6NLW8, F1NEA7, L8E946, O35602, O42201, O42250, O42356, O42357, O42358, O42567, O43186, O43812, O54751, O73592, O75360, O97039, O97670, P06601, P09082, P09083, P0CJ85, P0CJ86, P0CJ87, P0CJ88, P0CJ89, P0CJ90, P21711, P22810, P23759, P23760, P24610, P32242, P32243, P47239

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

111 predictions. Top by Δscore:

VariantEffectΔscore
1:226224071:CCAGG:Cdonor_loss1.0000
1:226224072:CAGGT:Cdonor_loss1.0000
1:226224073:AGGTG:Adonor_loss1.0000
1:226224074:GGTGA:Gdonor_loss1.0000
1:226224075:GTG:Gdonor_loss1.0000
1:226225502:TCCA:Tacceptor_loss1.0000
1:226225504:CA:Cacceptor_loss1.0000
1:226225505:A:Tacceptor_loss1.0000
1:226225506:GGT:Gacceptor_gain1.0000
1:226225506:GGTAT:Gacceptor_gain1.0000
1:226224075:G:GGdonor_gain0.9900
1:226225506:GGTA:Gacceptor_gain0.9900
1:226225503:CCAGG:Cacceptor_gain0.9800
1:226225504:CAGG:Cacceptor_gain0.9800
1:226225505:A:AGacceptor_gain0.9800
1:226225505:AG:Aacceptor_gain0.9800
1:226225506:G:GAacceptor_gain0.9800
1:226225506:GG:Gacceptor_gain0.9800
1:226225502:TCCAG:Tacceptor_gain0.9700
1:226225505:AGGTA:Aacceptor_gain0.9600
1:226225506:G:Tacceptor_gain0.9400
1:226224176:C:Tdonor_gain0.9200
1:226225501:TTCCA:Tacceptor_gain0.8900
1:226224068:G:GTdonor_gain0.8200
1:226224134:C:Adonor_gain0.8200
1:226224194:GCTC:Gdonor_gain0.8200
1:226225748:A:Cacceptor_gain0.8200
1:226224224:A:AGdonor_gain0.8000
1:226224522:C:Tdonor_gain0.7800
1:226224165:G:Tdonor_gain0.7200

AlphaMissense

1474 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:226223994:T:CF105L1.000
1:226223996:C:AF105L1.000
1:226223996:C:GF105L1.000
1:226225513:T:CF134L1.000
1:226225515:C:AF134L1.000
1:226225515:C:GF134L1.000
1:226223958:T:CF93L0.999
1:226223960:C:AF93L0.999
1:226223960:C:GF93L0.999
1:226225510:T:AW133R0.999
1:226225510:T:CW133R0.999
1:226225512:G:CW133C0.999
1:226225512:G:TW133C0.999
1:226225513:T:GF134V0.999
1:226225514:T:CF134S0.999
1:226225514:T:GF134C0.999
1:226225519:A:GN136D0.999
1:226225520:A:GN136S0.999
1:226225521:C:AN136K0.999
1:226225521:C:GN136K0.999
1:226223959:T:CF93S0.998
1:226223959:T:GF93C0.998
1:226223994:T:AF105I0.998
1:226223994:T:GF105V0.998
1:226223995:T:CF105S0.998
1:226224010:A:GY110C0.998
1:226224012:C:TP111S0.998
1:226224013:C:AP111H0.998
1:226224070:T:CI130T0.998
1:226225513:T:AF134I0.998

dbSNP variants (sampled 300 via entrez): RS1000995714 (1:226221872 T>C), RS1001495271 (1:226221925 T>G), RS1001642615 (1:226222575 T>C), RS1001716258 (1:226222173 G>A), RS1003169200 (1:226223395 G>A), RS1003391854 (1:226223747 C>A,G,T), RS1004083090 (1:226226488 G>A), RS1005484128 (1:226224932 G>A,T), RS1005622947 (1:226223757 G>A,T), RS1006095294 (1:226223043 G>T), RS1006211732 (1:226222218 G>C), RS1006636683 (1:226222633 TAAG>T), RS1006729625 (1:226223377 T>A,C), RS1007603776 (1:226222656 A>G), RS1007802946 (1:226222962 G>A,C)

Disease associations

OMIM: gene MIM:609852 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases methylation, affects methylation, decreases expression3
Cyclosporinedecreases expression3
Tetrachlorodibenzodioxindecreases expression2
Aflatoxin B1affects expression, decreases expression2
aristolochic acid Iincreases expression1
dicrotophosincreases expression1
bisphenol Aaffects expression1
terbufosincreases methylation1
tris(2-butoxyethyl) phosphateaffects expression1
Sunitinibdecreases expression1
Leflunomideincreases expression1
Dolutegravirincreases expression1
Azathioprinedecreases expression1
Cadmiumdecreases expression1
Carbamazepineaffects expression1
Fonofosincreases methylation1
Hydrogen Peroxideaffects expression1
Leaddecreases expression1
Parathionincreases methylation1
Quercetindecreases expression1
Tretinoinaffects expression1
Triclosandecreases expression1
Valproic Acidaffects expression1
Oxyquinolinedecreases expression1
Sodium Seleniteincreases expression1
Cadmium Chloridedecreases expression1
tert-Butylhydroperoxideaffects expression1
Vitamin K 3affects 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.