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PKNOX1

gene
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Also known as PREP1

Summary

PKNOX1 (PBX/knotted 1 homeobox 1, HGNC:9022) is a protein-coding gene on chromosome 21q22.3, encoding Homeobox protein PKNOX1 (P55347). Activates transcription in the presence of PBX1A and HOXA1.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in angiogenesis. Predicted to act upstream of or within camera-type eye development; hemopoiesis; and positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleus.

Source: NCBI Gene 5316 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 54 total
  • Transcription factor: yes — 20 downstream targets (CollecTRI)
  • MANE Select transcript: NM_004571

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9022
Approved symbolPKNOX1
NamePBX/knotted 1 homeobox 1
Location21q22.3
Locus typegene with protein product
StatusApproved
AliasesPREP1
Ensembl geneENSG00000160199
Ensembl biotypeprotein_coding
OMIM602100
Entrez5316

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 18 protein_coding, 6 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000291547, ENST00000418336, ENST00000432907, ENST00000456957, ENST00000474336, ENST00000480179, ENST00000557820, ENST00000558955, ENST00000560448, ENST00000607049, ENST00000607150, ENST00000883905, ENST00000883906, ENST00000883907, ENST00000883908, ENST00000883909, ENST00000883910, ENST00000883911, ENST00000883912, ENST00000911563, ENST00000911564, ENST00000911565, ENST00000911566, ENST00000911567, ENST00000911568, ENST00000963001, ENST00000963002

RefSeq mRNA: 3 — MANE Select: NM_004571 NM_001286258, NM_001320694, NM_004571

CCDS: CCDS13692, CCDS68211

Canonical transcript exons

ENST00000291547 — 11 exons

ExonStartEnd
ENSE000034918384300432643004432
ENSE000035138024301005343010224
ENSE000035205814302130343021431
ENSE000035511714301690843017007
ENSE000035720374302989043033931
ENSE000035974934301813343018230
ENSE000036271864300749143007618
ENSE000036992234302487143024947
ENSE000037003494302870243028874
ENSE000037382214301306843013238
ENSE000038896894297456242974664

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 89.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7104 / max 123.5973, expressed in 1796 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
1893487.48001755
1893491.93431112
1893521.1153538
1893510.6547354
1893500.4699277
1893550.03796
1893540.01255
1893530.00573

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.76gold quality
right lobe of thyroid glandUBERON:000111988.79gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.98gold quality
left testisUBERON:000453387.93gold quality
thyroid glandUBERON:000204687.92gold quality
testisUBERON:000047387.80gold quality
right testisUBERON:000453487.34gold quality
left lobe of thyroid glandUBERON:000112087.20gold quality
ganglionic eminenceUBERON:000402386.75gold quality
ventricular zoneUBERON:000305386.12gold quality
sural nerveUBERON:001548886.11gold quality
cortical plateUBERON:000534385.73gold quality
stromal cell of endometriumCL:000225585.54gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451185.24gold quality
embryoUBERON:000092284.97gold quality
endometriumUBERON:000129584.27gold quality
bloodUBERON:000017884.08gold quality
middle temporal gyrusUBERON:000277183.11gold quality
calcaneal tendonUBERON:000370183.00gold quality
cerebellumUBERON:000203782.91gold quality
cerebellar cortexUBERON:000212982.81gold quality
cerebellar hemisphereUBERON:000224582.81gold quality
mucosa of sigmoid colonUBERON:000499382.69gold quality
adrenal tissueUBERON:001830382.67gold quality
spermCL:000001982.54gold quality
islet of LangerhansUBERON:000000682.31gold quality
ovaryUBERON:000099282.09gold quality
right hemisphere of cerebellumUBERON:001489082.08gold quality
left ovaryUBERON:000211982.00gold quality
entorhinal cortexUBERON:000272881.97gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.44
E-MTAB-7303no129.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

20 targets.

TargetRegulation
ALDH1A2Unknown
BCL2L1Unknown
CCL2Activation
FABP7
FASNRepression
GATA1Activation
HOXB1Unknown
HOXB2Unknown
IL10Activation
INPPL1Activation
MEIS1Unknown
NR5A1Unknown
PAX3Repression
PF4Unknown
PGK2
PTPN6Activation
RENUnknown
RNF6Activation
SYPActivation
UGT2B17

JASPAR motifs

MotifNameFamily
MA0782.1PKNOX1TALE-type homeo domain factors
MA0782.2PKNOX1TALE-type homeo domain factors
MA0782.3PKNOX1TALE-type homeo domain factors

JASPAR matrix evidence (PMIDs): PMID:25233378, PMID:23602564

Upstream regulators (CollecTRI, top): HOXA9

miRNA regulators (miRDB)

148 targeting PKNOX1, 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-8485100.0077.574731
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3646100.0073.565283
HSA-MIR-3613-3P100.0076.367965
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-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-223-3P99.9970.141140
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-453199.9969.703181
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-480399.9871.993117
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-365899.9673.874379
HSA-MIR-570-3P99.9672.414910
HSA-MIR-6825-5P99.9669.813431

Literature-anchored findings (GeneRIF, showing 15)

  • PREP1 regulates PF4 gene expression. (PMID:12732210)
  • PKNOX1 gene-dosage imbalance is associated with overexpression of FABP7 in Down syndrome fetal brains. (PMID:12771203)
  • PREP-1 has a role in F9 teratocarcinoma cells: it causes an increase of PBX-2 by preventing its degradation (PMID:12871956)
  • Interleukin-10 expression in macrophages during phagocytosis of apoptotic cells is mediated by homeodomain proteins Pbx1 and Prep-1. (PMID:18093541)
  • Immunohistochemistry on tissue micrroarrays (TMA) generated from three distinct human cohorts comprising a total of some 1000 human tumors revealed that 70% of the tumors express no or extremely low levels of Prep1, unlike normal tissues. (PMID:20106730)
  • analysis of the regulatory region of the zebrafish Prep1.1 gene and the promoter of human PREP1 (PMID:21203543)
  • The tumor suppressor role of Prep1 is associated with the maintenance of genomic stability. (PMID:21715654)
  • High levels of MEIS1 and PREP1, and low levels of PBX4 expression were founded in samples of patients with ALL. (PMID:22185299)
  • Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia (PMID:22347417)
  • PREP1 modulates the cellular sensitivity to TGF-beta by inducing the small mothers against decapentaplegic homolog 3 (SMAD3) nuclear translocation. (PMID:25157139)
  • the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor (PMID:29453404)
  • These data implicate the upregulated hepatic expression of Pknox1 in type 2 diabetes mellitus (T2DM) complicated with nonalcoholic fatty liver disease (NAFLD) may be caused by the reduced expression of miR-17 family, indicating that developing miRNA-mediated regulation strategies on Pknox1 may provide new therapeutic options for metabolic disease (PMID:30338914)
  • Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis. (PMID:33033354)
  • Polyunsaturated fatty acids ameliorate renal stone-induced renal tubular damage via miR-93-5p/Pknox1 axis. (PMID:36356379)
  • PKNOX1 acts as a transcription factor of DHH and promotes the progression of stomach adenocarcinoma by regulating the Hedgehog signalling pathway. (PMID:37864517)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriopknox1.1ENSDARG00000018765
danio_reriopknox1.2ENSDARG00000036542
mus_musculusPknox1ENSMUSG00000006705
rattus_norvegicusPknox1ENSRNOG00000001184
drosophila_melanogasterexdFBGN0000611
drosophila_melanogasterhthFBGN0001235
drosophila_melanogastervisFBGN0033748
drosophila_melanogasterachiFBGN0033749
caenorhabditis_elegansWBGENE00000443
caenorhabditis_elegansWBGENE00006796
caenorhabditis_elegansWBGENE00017690

Paralogs (13): MEIS3 (ENSG00000105419), PBX4 (ENSG00000105717), TGIF2 (ENSG00000118707), MEIS2 (ENSG00000134138), MEIS1 (ENSG00000143995), TGIF2LX (ENSG00000153779), PKNOX2 (ENSG00000165495), PBX3 (ENSG00000167081), TGIF2LY (ENSG00000176679), TGIF1 (ENSG00000177426), PBX1 (ENSG00000185630), MEIS3P2 (ENSG00000188013), PBX2 (ENSG00000204304)

Protein

Protein identifiers

Homeobox protein PKNOX1 — P55347 (reviewed: P55347)

Alternative names: Homeobox protein PREP-1, PBX/knotted homeobox 1

All UniProt accessions (4): P55347, E7EPN6, H0YM69, Q96I87

UniProt curated annotations — full annotation on UniProt →

Function. Activates transcription in the presence of PBX1A and HOXA1.

Subunit / interactions. Interacts with MN1.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous. Isoform 2 is expressed in all examined tissues except in bone marrow.

Similarity. Belongs to the TALE/MEIS homeobox family.

Isoforms (2)

UniProt IDNamesCanonical?
P55347-11yes
P55347-22, PKNOX1B

RefSeq proteins (3): NP_001273187, NP_001307623, NP_004562* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR008422KN_HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR032453PKNOX/Meis_NDomain
IPR050224TALE_homeoboxFamily

Pfam: PF05920, PF16493

UniProt features (20 total): sequence variant 3, sequence conflict 3, helix 3, region of interest 2, compositionally biased region 2, modified residue 2, chain 1, domain 1, turn 1, DNA-binding region 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1X2NSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P55347-F161.970.25

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 (2): 33, 41

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5617472Activation of anterior HOX genes in hindbrain development during early embryogenesis

MSigDB gene sets: 198 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, MULLIGHAN_NPM1_SIGNATURE_3_UP, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3, DORSAM_HOXA9_TARGETS_UP, GOBP_MYELOID_CELL_HOMEOSTASIS, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_ERYTHROCYTE_HOMEOSTASIS, TATTATA_MIR374, WEI_MYCN_TARGETS_WITH_E_BOX, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, FISCHER_G2_M_CELL_CYCLE, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, GOBP_BLOOD_VESSEL_MORPHOGENESIS, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN

GO Biological Process (9): angiogenesis (GO:0001525), transcription by RNA polymerase II (GO:0006366), T cell differentiation (GO:0030217), erythrocyte differentiation (GO:0030218), camera-type eye development (GO:0043010), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), hemopoiesis (GO:0030097)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), chromatin binding (GO:0003682), DNA-binding transcription factor activity (GO:0003700), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), transcription regulator complex (GO:0005667), cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Activation of HOX genes during differentiation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
DNA-templated transcription2
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
regulation of DNA-templated transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
binding2
blood vessel morphogenesis1
anatomical structure formation involved in morphogenesis1
lymphocyte differentiation1
T cell activation1
myeloid cell differentiation1
erythrocyte homeostasis1
eye development1
positive regulation of DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cell development1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
transcription cis-regulatory region binding1
transcription regulator activity1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
DNA binding1
chromosome1
intracellular membrane-bounded organelle1
protein-containing complex1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

1572 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PKNOX1PBX1P40424988
PKNOX1PBX2P40425808
PKNOX1HOXB1P14653772
PKNOX1HOXB2P10913721
PKNOX1WDR4P57081674
PKNOX1PTTG1IPP53801641
PKNOX1NDUFV3P56181634
PKNOX1PAX6P26367613
PKNOX1JAM2P57087589
PKNOX1H7C2H4H7C2H4570
PKNOX1P0DN79P0DN79569
PKNOX1U2AF1Q01081559
PKNOX1SYNJ1O43426544
PKNOX1DYRK1AQ13627526
PKNOX1UBR1Q8IWV7517

IntAct

121 interactions, top by confidence:

ABTypeScore
PBX1PKNOX1psi-mi:“MI:0915”(physical association)0.810
PKNOX1PBX1psi-mi:“MI:0915”(physical association)0.810
PKNOX1PBX2psi-mi:“MI:0915”(physical association)0.740
PBX2PKNOX1psi-mi:“MI:0915”(physical association)0.740
PKNOX1NUP58psi-mi:“MI:0915”(physical association)0.720
NUP58PKNOX1psi-mi:“MI:0915”(physical association)0.720
VPS37CPKNOX1psi-mi:“MI:0915”(physical association)0.670
HMGB2PKNOX1psi-mi:“MI:0915”(physical association)0.670
PKNOX1PBX4psi-mi:“MI:0915”(physical association)0.670
PKNOX1FHL2psi-mi:“MI:0915”(physical association)0.670
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
PKNOX1BORCS6psi-mi:“MI:0915”(physical association)0.600
PKNOX1EGD1psi-mi:“MI:0915”(physical association)0.560
EGD1PKNOX1psi-mi:“MI:0915”(physical association)0.560

BioGRID (97): PKNOX1 (Two-hybrid), VPS37C (Two-hybrid), PKNOX1 (Affinity Capture-RNA), VPS33A (Affinity Capture-MS), PBX1 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PBX4 (Affinity Capture-MS), VPS16 (Affinity Capture-MS), SAR1B (Affinity Capture-MS), PKNOX1 (Affinity Capture-Western), PBX1 (Affinity Capture-Western), PBX4 (Affinity Capture-MS), PBX1 (Affinity Capture-MS), PBX2 (Affinity Capture-MS), PKNOX1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8H0H2, A0JN51, A4QNP0, F8VPJ6, O13186, O46567, O57415, O70477, O94842, P09775, P15257, P22361, P28324, P32519, P36197, P37275, P50534, P55347, P59759, P79686, Q05041, Q07243, Q0P5K4, Q14872, Q15723, Q2HJ84, Q2KHR2, Q3UH06, Q5R6A9, Q5W1J6, Q60542, Q60775, Q61321, Q62947, Q64318, Q6DJL0, Q6IRR0, Q6XLJ0, Q86T24, Q8AYC1

Diamond homologs: A1YGI6, A6NDR6, A8K0S8, A8WL06, B7ZRT8, O00470, O04136, O14770, O22300, O42261, O46339, O65685, O70477, P41779, P41817, P46606, P48000, P48001, P48002, P48731, P53147, P54269, P55347, P56659, P56660, P56664, P56665, P56669, P70284, P78412, P78413, P78414, P78415, P79937, P81067, P81068, P97367, P97368, Q0E3C3, Q0J6N4

SIGNOR signaling

5 interactions.

AEffectBMechanism
PKNOX1“up-regulates activity”HOXA1binding
PKNOX1“up-regulates quantity by expression”SYP“transcriptional regulation”
PKNOX1“up-regulates quantity by expression”PTPN6“transcriptional regulation”
PKNOX1“up-regulates activity”PBX1binding
PKNOX1“up-regulates activity”HOXB1binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 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.

GO biological processes:

GO termPartnersFoldFDR
eye development635.7×5e-06
animal organ morphogenesis722.7×5e-06
brain development79.4×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1759 predictions. Top by Δscore:

VariantEffectΔscore
21:42974664:GGTA:Gdonor_loss1.0000
21:42974666:T:Adonor_loss1.0000
21:43004321:TCCA:Tacceptor_loss1.0000
21:43004322:CCA:Cacceptor_loss1.0000
21:43004323:CA:Cacceptor_loss1.0000
21:43004324:A:ACacceptor_loss1.0000
21:43004324:A:AGacceptor_gain1.0000
21:43004325:G:GGacceptor_gain1.0000
21:43004325:GA:Gacceptor_gain1.0000
21:43004325:GAC:Gacceptor_gain1.0000
21:43004325:GACA:Gacceptor_gain1.0000
21:43004325:GACAC:Gacceptor_gain1.0000
21:43004428:AACAG:Adonor_loss1.0000
21:43004429:ACAGG:Adonor_loss1.0000
21:43004433:G:GAdonor_loss1.0000
21:43004434:T:Adonor_loss1.0000
21:43007487:ACAG:Aacceptor_loss1.0000
21:43007488:CA:Cacceptor_loss1.0000
21:43007489:A:ACacceptor_loss1.0000
21:43007489:A:AGacceptor_gain1.0000
21:43007489:AGAT:Aacceptor_gain1.0000
21:43007490:G:GAacceptor_gain1.0000
21:43007490:GATG:Gacceptor_gain1.0000
21:43007490:GATGC:Gacceptor_gain1.0000
21:43010048:CTCA:Cacceptor_loss1.0000
21:43010050:CA:Cacceptor_loss1.0000
21:43010051:A:ACacceptor_loss1.0000
21:43010051:A:AGacceptor_gain1.0000
21:43010052:G:GCacceptor_loss1.0000
21:43010052:G:GGacceptor_gain1.0000

AlphaMissense

2877 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:43010061:T:CL63P1.000
21:43010093:T:CC74R1.000
21:43010095:T:GC74W1.000
21:43013077:G:CA121P1.000
21:43013090:T:CL125S1.000
21:43013093:G:CR126P1.000
21:43013096:T:CI127T1.000
21:43013096:T:GI127S1.000
21:43013098:C:GH128D1.000
21:43013099:A:GH128R1.000
21:43013100:T:AH128Q1.000
21:43013100:T:GH128Q1.000
21:43013102:T:CL129P1.000
21:43013105:T:CL130P1.000
21:43013107:G:AE131K1.000
21:43013108:A:TE131V1.000
21:43013109:G:CE131D1.000
21:43013109:G:TE131D1.000
21:43013111:T:CL132P1.000
21:43013129:T:AL138H1.000
21:43013129:T:CL138P1.000
21:43013132:G:AC139Y1.000
21:43013133:C:GC139W1.000
21:43013140:T:AF142I1.000
21:43013140:T:CF142L1.000
21:43013141:T:CF142S1.000
21:43013141:T:GF142C1.000
21:43013142:C:AF142L1.000
21:43013142:C:GF142L1.000
21:43013145:C:GC143W1.000

dbSNP variants (sampled 300 via entrez): RS1000082680 (21:43005178 C>A,T), RS1000170550 (21:42982547 T>C,G), RS1000191057 (21:42980829 T>A,C), RS1000311611 (21:42988752 T>C), RS1000331560 (21:43017064 G>A,T), RS1000344515 (21:42977803 T>C), RS1000349769 (21:43011128 T>C), RS1000464208 (21:43021668 C>T), RS1000474673 (21:43005298 T>A), RS1000556048 (21:43015590 A>G), RS1000574293 (21:42992469 A>G), RS1000581486 (21:42998456 A>G), RS1000604011 (21:42981482 G>T), RS1000630780 (21:42987163 C>T), RS1000673911 (21:42973130 C>T)

Disease associations

OMIM: gene MIM:602100 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST000328_10Biochemical measures8.000000e-06
GCST000328_8Biochemical measures8.000000e-06
GCST000579_6Cognitive performance2.000000e-07
GCST000905_11Information processing speed6.000000e-06
GCST002670_11Blood and toenail selenium levels3.000000e-08
GCST002670_12Blood and toenail selenium levels5.000000e-09
GCST002670_4Blood and toenail selenium levels4.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004574total cholesterol measurement
EFO:0003926neuropsychological test
EFO:0004363information processing speed

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2839629PKNOX10.000

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
FR900359increases phosphorylation1
bisphenol Adecreases methylation1
sodium arseniteincreases expression1
cobaltous chloridedecreases expression1
di-n-butylphosphoric acidaffects expression1
PCI 5002affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenic Trioxidedecreases expression1
Acetaminophenincreases expression1
Ethyl Methanesulfonatedecreases expression1
Phthalic Acidsincreases methylation1
Plant Extractsaffects cotreatment, increases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Valproic Acidaffects expression1
Zincaffects cotreatment, increases expression1
Aflatoxin B1increases methylation1
beta-Naphthoflavoneincreases expression1
Acrylamideincreases expression1
Particulate Matterincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E2GUHAP1 PKNOX1 (-)Cancer cell lineMale

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot