PTPN7

gene
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Also known as HEPTPLC-PTP

Summary

PTPN7 (protein tyrosine phosphatase non-receptor type 7, HGNC:9659) is a protein-coding gene on chromosome 1q32.1, encoding Tyrosine-protein phosphatase non-receptor type 7 (P35236). Protein phosphatase that acts preferentially on tyrosine-phosphorylated MAPK1.

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This gene is preferentially expressed in a variety of hematopoietic cells, and is an early response gene in lymphokine stimulated cells. The non-catalytic N-terminus of this PTP can interact with MAP kinases and suppress the MAP kinase activities. This PTP was shown to be involved in the regulation of T cell antigen receptor (TCR) signaling, which was thought to function through dephosphorylating the molecules related to MAP kinase pathway. Multiple alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 5778 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 81 total
  • Druggable target: yes — 2 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_002832

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9659
Approved symbolPTPN7
Nameprotein tyrosine phosphatase non-receptor type 7
Location1q32.1
Locus typegene with protein product
StatusApproved
AliasesHEPTP, LC-PTP
Ensembl geneENSG00000143851
Ensembl biotypeprotein_coding
OMIM176889
Entrez5778

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 17 protein_coding, 4 nonsense_mediated_decay, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000309017, ENST00000367279, ENST00000435759, ENST00000462815, ENST00000464870, ENST00000467283, ENST00000468385, ENST00000476061, ENST00000477554, ENST00000477625, ENST00000479092, ENST00000480836, ENST00000486116, ENST00000491584, ENST00000492451, ENST00000492977, ENST00000495688, ENST00000496197, ENST00000629151, ENST00000691036, ENST00000854611, ENST00000854612, ENST00000854613, ENST00000854614, ENST00000854615

RefSeq mRNA: 5 — MANE Select: NM_002832 NM_001199797, NM_001364877, NM_001364878, NM_002832, NM_080588

CCDS: CCDS1422, CCDS1423

Canonical transcript exons

ENST00000691036 — 10 exons

ExonStartEnd
ENSE00001927044202160545202160602
ENSE00003519003202157739202157823
ENSE00003552765202154186202154323
ENSE00003581167202155533202155609
ENSE00003676719202153725202153835
ENSE00003685300202152542202152699
ENSE00003693260202150311202150424
ENSE00003790609202158118202158301
ENSE00003928474202147016202148699
ENSE00004282191202159281202159454

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 96.39.

FANTOM5 (CAGE): breadth broad, TPM avg 14.2904 / max 863.6909, expressed in 550 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1670512.3266529
167040.9593187
167080.3261106
167090.3165110
167020.1913109
167030.108927
167070.029210
167100.01656
167110.01044
167060.00561

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009496.39gold quality
lymph nodeUBERON:000002992.07gold quality
bone marrow cellCL:000209290.77gold quality
vermiform appendixUBERON:000115490.06gold quality
thymusUBERON:000237088.84gold quality
bloodUBERON:000017888.26gold quality
spleenUBERON:000210688.11gold quality
adrenal tissueUBERON:001830386.99gold quality
bone marrowUBERON:000237184.84gold quality
right testisUBERON:000453484.71gold quality
caecumUBERON:000115384.37gold quality
left testisUBERON:000453384.10gold quality
putamenUBERON:000187483.67gold quality
right adrenal gland cortexUBERON:003582781.98gold quality
testisUBERON:000047381.85gold quality
leukocyteCL:000073881.68gold quality
caudate nucleusUBERON:000187381.44gold quality
gall bladderUBERON:000211080.79gold quality
small intestine Peyer’s patchUBERON:000345480.72gold quality
mononuclear cellCL:000084280.60gold quality
monocyteCL:000057680.53gold quality
ileal mucosaUBERON:000033180.26gold quality
left adrenal gland cortexUBERON:003582579.83gold quality
left adrenal glandUBERON:000123479.45gold quality
adrenal glandUBERON:000236979.33gold quality
right adrenal glandUBERON:000123378.93gold quality
tonsilUBERON:000237278.90gold quality
adrenal cortexUBERON:000123578.68gold quality
rectumUBERON:000105278.51gold quality
small intestineUBERON:000210878.41gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-9467yes33.09
E-MTAB-10287yes29.19
E-CURD-112yes9.05
E-HCAD-10yes6.68
E-GEOD-70580no922.59
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

81 targeting PTPN7, 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-6851-5P100.0065.631294
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-3689D100.0066.141181
HSA-MIR-450099.9972.722367
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-449299.8768.253611
HSA-MIR-607999.8468.541170
HSA-MIR-132199.8465.301811
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-473999.8465.251832
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-120099.7170.421838
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-29899.6367.561916
HSA-MIR-425-5P99.5967.67900
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-426999.5569.891373
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-4753-5P99.5468.511356
HSA-MIR-444199.4966.563216
HSA-MIR-608199.4866.071446

Literature-anchored findings (GeneRIF, showing 4)

  • structure of the protein tyrosine phosphatase catalytic domain of HePTP, residues 44-339 (PMID:16226275)
  • determined high-resolution structures of all of the human family members of Mitogen-Activated Protein Kinase-specific protein tyrosine phosphatases (PMID:16441242)
  • Interactions at the active site between KIM (kinase interaction motif)-phosphatases and their substrates are predominantly nonspecific, with the majority of the KIM-phosphatase residues coordinating the peptide backbone rather than residue side chains. (PMID:19053285)
  • PTPN7 regulates platelet functional responses downstream of GPCR agonists, but not GPVI agonists, through inhibition of ERK activation and thromboxane generation. (PMID:31266805)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusPtpn7ENSMUSG00000031506
rattus_norvegicusPtpn7ENSRNOG00000005807

Paralogs (35): PTPRN (ENSG00000054356), PTPRU (ENSG00000060656), PTPN3 (ENSG00000070159), PTPN21 (ENSG00000070778), PTPN18 (ENSG00000072135), PTPN23 (ENSG00000076201), PTPRH (ENSG00000080031), PTPRC (ENSG00000081237), PTPN4 (ENSG00000088179), PTPRS (ENSG00000105426), PTPRZ1 (ENSG00000106278), PTPN5 (ENSG00000110786), PTPN6 (ENSG00000111679), PTPRB (ENSG00000127329), PTPN12 (ENSG00000127947), PTPRE (ENSG00000132334), PTPRA (ENSG00000132670), PTPN22 (ENSG00000134242), PTPRF (ENSG00000142949), PTPRG (ENSG00000144724), PTPRJ (ENSG00000149177), PTPRO (ENSG00000151490), PTPN14 (ENSG00000152104), PTPRK (ENSG00000152894), PTPRR (ENSG00000153233), PTPRD (ENSG00000153707), PTPRN2 (ENSG00000155093), PTPN13 (ENSG00000163629), PTPN9 (ENSG00000169410), PTPRM (ENSG00000173482), PTPN2 (ENSG00000175354), PTPN11 (ENSG00000179295), PTPRT (ENSG00000196090), PTPN1 (ENSG00000196396), PTPN20 (ENSG00000204179)

Protein

Protein identifiers

Tyrosine-protein phosphatase non-receptor type 7P35236 (reviewed: P35236)

Alternative names: Hematopoietic protein-tyrosine phosphatase, Protein-tyrosine phosphatase LC-PTP

All UniProt accessions (12): P35236, C9IYI6, C9JAW7, C9JBA9, E7EUM0, E9PE54, F8WEY3, F8WF08, F8WF66, H7C4T8, H7C5I3, J3KR55

UniProt curated annotations — full annotation on UniProt →

Function. Protein phosphatase that acts preferentially on tyrosine-phosphorylated MAPK1. Plays a role in the regulation of T and B-lymphocyte development and signal transduction.

Subunit / interactions. Monomer. Interacts with MAPK1, MAPK3 and several other MAP kinases.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Expressed exclusively in thymus and spleen.

Post-translational modifications. Phosphorylated on serine residues in resting T-cells. Phosphorylation increases upon exposure to stimuli that increase intracellular cAMP levels. Phosphorylation leads to dissociation of bound MAP kinases. Oxidized at active site cysteine. Treatment with pervanadate (vanadate and H(2)O(2)) or with antigen enhanced oxidation of active site cysteine.

Activity regulation. Inhibited in cells after FCER1A triggering.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
P35236-11yes
P35236-22
P35236-33

RefSeq proteins (5): NP_001186726, NP_001351806, NP_001351807, NP_002823, NP_542155 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000242PTP_catDomain
IPR000387Tyr_Pase_domDomain
IPR003595Tyr_Pase_catDomain
IPR008356Tyr_Pase_KIM-conFamily
IPR016130Tyr_Pase_ASActive_site
IPR029021Prot-tyrosine_phosphatase-likeHomologous_superfamily

Pfam: PF00102

Enzyme classification (BRENDA):

  • EC 3.1.3.48 — protein-tyrosine-phosphatase (BRENDA: 59 organisms, 501 substrates, 1326 inhibitors, 270 Km, 165 kcat entries)

Substrate kinetics (BRENDA)

70 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
4-NITROPHENYL PHOSPHATE0.0008–14884
6,8-DIFLUORO-4-METHYLUMBELLIFERYL PHOSPHATE0.0039–0.86227
P-NITROPHENYL PHOSPHATE0.0024–1020
DADEPYLIPQQG0.0003–0.112
PHOSPHOTYROSINE0.012–3011
LYSOZYME0.0003–0.0125
MYELIN BASIC PROTEIN0.0001–0.0225
ACETYL-DADEPY-NH20.0228–0.2194
ACETYL-DADEPYL-NH21.1–97.54
4,6,8-TRIMETHYL-2-OXO-2H-CHROMEN-7-YL DIHYDROGEN0.02–0.1563
SASASPYSASA0.53–2.33
1-NAPHTHYL PHOSPHATE1.19–1.882
3,6-FLUORESCEIN DIPHOSPHATE15–192
4-METHYLUMBELLIFERYL PHOSPHATE0.953–2.412
BOVINE SERUM ALBUMIN0.0001–0.00032

Catalyzed reactions (Rhea), 1 shown:

  • O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (RHEA:10684)

UniProt features (54 total): helix 14, strand 13, mutagenesis site 8, modified residue 6, sequence conflict 3, binding site 3, splice variant 2, region of interest 2, chain 1, domain 1, active site 1

Structure

Experimental structures (PDB)

14 structures.

PDBMethodResolution (Å)
1ZC0X-RAY DIFFRACTION1.85
2GPHX-RAY DIFFRACTION1.9
3D44X-RAY DIFFRACTION1.9
3O4SX-RAY DIFFRACTION1.9
2QDCX-RAY DIFFRACTION2
2GP0X-RAY DIFFRACTION2.05
2QDMX-RAY DIFFRACTION2.05
8YP8X-RAY DIFFRACTION2.14
3O4UX-RAY DIFFRACTION2.25
2HVLX-RAY DIFFRACTION2.4
3D42X-RAY DIFFRACTION2.46
2A3KX-RAY DIFFRACTION2.55
3O4TX-RAY DIFFRACTION2.6
2QDPX-RAY DIFFRACTION2.72

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P35236-F186.390.70

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 291 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (3): 257; 291–297; 335

Post-translational modifications (6): 93, 110, 143, 291, 44, 66

Mutagenesis-validated functional residues (8):

PositionPhenotype
44prevents dissociation of bound map kinase and enhances their dephosphorylation.
44reduces binding of map kinase.
66prevents dissociation of bound map kinase and enhances their dephosphorylation; when associated with a-93.
93prevents dissociation of bound map kinase and enhances their dephosphorylation; when associated with a-66.
125strongly reduced catalytic activity.
257loss of catalytic activity.
291loss of catalytic activity.
335reduced catalytic activity.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-5675221Negative regulation of MAPK pathway
R-HSA-9008059Interleukin-37 signaling

MSigDB gene sets: 169 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, KEGG_MAPK_SIGNALING_PATHWAY, MODULE_45, AP4_Q6, MODULE_16, ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN, MODULE_118, WEI_MYCN_TARGETS_WITH_E_BOX, AML_Q6, PID_TCR_RAS_PATHWAY, MODULE_213, ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN, MARZEC_IL2_SIGNALING_UP, MAF_Q6

GO Biological Process (4): MAPK cascade (GO:0000165), protein dephosphorylation (GO:0006470), signal transduction (GO:0007165), dephosphorylation (GO:0016311)

GO Molecular Function (5): protein tyrosine phosphatase activity (GO:0004725), non-membrane spanning protein tyrosine phosphatase activity (GO:0004726), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (7): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), cytoplasmic side of plasma membrane (GO:0009898), microtubule cytoskeleton (GO:0015630), mitotic spindle (GO:0072686), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
RAF/MAP kinase cascade1
Interleukin-1 family signaling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
intracellular signaling cassette1
dephosphorylation1
protein modification process1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
phosphate-containing compound metabolic process1
phosphoprotein phosphatase activity1
protein tyrosine phosphatase activity1
phosphatase activity1
catalytic activity, acting on a protein1
binding1
catalytic activity1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
plasma membrane1
cytoplasmic side of membrane1
cytoskeleton1
spindle1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1266 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PTPN7PTSQ03393923
PTPN7MAPK1P28482919
PTPN7MAPK14Q16539700
PTPN7DUSP3P51452640
PTPN7MAPK3P27361575
PTPN7DUSP6Q16828558
PTPN7MAP2K1Q02750537
PTPN7RPS6KA1Q15418530
PTPN7OSBPP22059520
PTPN7RPS6KA3P51812516
PTPN7PTPN11Q06124516
PTPN7DUSP23Q9BVJ7488
PTPN7PLPP1O14494472
PTPN7ACP1P24666463
PTPN7DUSP10Q9Y6W6461

IntAct

27 interactions, top by confidence:

ABTypeScore
PTPN7MAPK1psi-mi:“MI:0915”(physical association)0.770
PTPN7MAPK1psi-mi:“MI:2364”(proximity)0.770
PTPN7MAPK1psi-mi:“MI:0203”(dephosphorylation reaction)0.770
PTPN7Mapk14psi-mi:“MI:0915”(physical association)0.590
Mapk14PTPN7psi-mi:“MI:0915”(physical association)0.590
PTPN7CCDC57psi-mi:“MI:0915”(physical association)0.560
PTPN7FLJ13057psi-mi:“MI:0915”(physical association)0.560
CCDC57PTPN7psi-mi:“MI:0915”(physical association)0.560
FLJ13057PTPN7psi-mi:“MI:0915”(physical association)0.560
Mapk1PTPN7psi-mi:“MI:0407”(direct interaction)0.440
PTPN7AATKpsi-mi:“MI:0915”(physical association)0.370
PTPN7EGFRpsi-mi:“MI:0915”(physical association)0.370
PTPN7ERBB3psi-mi:“MI:0915”(physical association)0.370
PTPN7ROR2psi-mi:“MI:0915”(physical association)0.370
PTPN7PTK7psi-mi:“MI:0915”(physical association)0.370
PTPN7EPHA2psi-mi:“MI:0915”(physical association)0.370
PTPN7ERBB4psi-mi:“MI:0915”(physical association)0.370
PTPN7IGF1Rpsi-mi:“MI:0915”(physical association)0.370
PTPN7MAPK14psi-mi:“MI:2364”(proximity)0.270
PTPN7CDH2psi-mi:“MI:0203”(dephosphorylation reaction)0.000

BioGRID (84): GMCL1 (Two-hybrid), CCDC57 (Two-hybrid), MAPK1 (Co-localization), MAPK14 (Co-localization), PTPN7 (Biochemical Activity), PTPN7 (Biochemical Activity), PTPN7 (Two-hybrid), PTPN7 (Two-hybrid), PTPN7 (Two-hybrid), DHPS (Affinity Capture-MS), MAPK1 (Affinity Capture-MS), MAPK14 (Affinity Capture-MS), MAPK3 (Affinity Capture-MS), ME1 (Affinity Capture-MS), OPA1 (Affinity Capture-MS)

ESM2 similar proteins: A2ALK8, A5D6R3, B2GV87, O08617, O35239, O55082, P0C599, P0C5A1, P18052, P18433, P23469, P25044, P26045, P28202, P28204, P28205, P28206, P28209, P28219, P29350, P29351, P35234, P35235, P35236, P41499, P43378, P49445, P49446, P54755, P54830, P81718, Q03348, Q06124, Q15256, Q4JDL3, Q4RQD3, Q5I127, Q5I139, Q5I141, Q5I142

Diamond homologs: A0A6I8TCE0, A1L1L3, A2ALK8, A4IFW2, B0V2N1, B0X4T2, B1AUH1, B2GV87, B2RU80, B3DK56, B9EKR1, E9Q0N2, E9Q612, F1NWE3, G5EC24, G5EGJ9, H2KZM6, O02695, O08617, O13016, O35239, O55082, P06800, P16620, P17706, P18031, P18052, P18433, P20417, P23467, P23468, P23469, P23470, P23471, P26045, P28191, P29074, P29350, P29351, P29352

SIGNOR signaling

22 interactions.

AEffectBMechanism
CD40LGdown-regulatesPTPN7
PRKACAdown-regulatesPTPN7phosphorylation
PTPN7down-regulatesMAPK14binding
PTPN7“down-regulates activity”MAPK1dephosphorylation
PTPN7“down-regulates activity”MAPK14dephosphorylation
PRKCQ“up-regulates activity”PTPN7phosphorylation
PTPN7down-regulatesMAPK1dephosphorylation
MAPK1“up-regulates activity”PTPN7phosphorylation
MAPK3“up-regulates activity”PTPN7phosphorylation
MAPK14“down-regulates activity”PTPN7phosphorylation
Gbeta“up-regulates activity”PTPN7phosphorylation
ERK1/2“up-regulates activity”PTPN7phosphorylation
PRKD1“up-regulates activity”PTPN7phosphorylation
PRKCZ“up-regulates activity”PTPN7phosphorylation
PRKCD“up-regulates activity”PTPN7phosphorylation
PRKCH“up-regulates activity”PTPN7phosphorylation
PRKCE“up-regulates activity”PTPN7phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 15 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
positive regulation of MAPK cascade533.6×2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance62
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2071 predictions. Top by Δscore:

VariantEffectΔscore
1:202148696:CCCT:Cacceptor_gain1.0000
1:202148697:CCT:Cacceptor_gain1.0000
1:202148697:CCTC:Cacceptor_gain1.0000
1:202148698:CT:Cacceptor_gain1.0000
1:202148698:CTC:Cacceptor_gain1.0000
1:202148699:TCTGC:Tacceptor_gain1.0000
1:202152537:CGCA:Cdonor_loss1.0000
1:202152538:GCA:Gdonor_loss1.0000
1:202152539:CA:Cdonor_loss1.0000
1:202152540:ACCT:Adonor_loss1.0000
1:202152696:GGTA:Gacceptor_gain1.0000
1:202152697:GTA:Gacceptor_gain1.0000
1:202152698:TA:Tacceptor_gain1.0000
1:202152698:TAC:Tacceptor_loss1.0000
1:202152700:C:CCacceptor_gain1.0000
1:202152701:T:Aacceptor_loss1.0000
1:202152705:T:TCacceptor_gain1.0000
1:202153721:GTA:Gdonor_loss1.0000
1:202153722:TA:Tdonor_loss1.0000
1:202153723:ACCT:Adonor_loss1.0000
1:202153831:CATTT:Cacceptor_gain1.0000
1:202153832:ATTT:Aacceptor_gain1.0000
1:202153833:TTT:Tacceptor_gain1.0000
1:202153834:TT:Tacceptor_gain1.0000
1:202153834:TTCTA:Tacceptor_loss1.0000
1:202153835:TCTA:Tacceptor_loss1.0000
1:202153836:C:Aacceptor_loss1.0000
1:202153837:T:Gacceptor_loss1.0000
1:202154184:ACCT:Adonor_gain1.0000
1:202154185:CCTC:Cdonor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000434821 (1:202162125 T>C), RS1000493902 (1:202158468 C>T), RS1000543952 (1:202153788 G>A), RS1000602285 (1:202152834 A>C), RS1001040410 (1:202163276 G>A), RS1001085084 (1:202147957 G>A,T), RS1001105306 (1:202147545 G>A), RS1001229189 (1:202150258 G>A), RS1001264429 (1:202148944 C>T), RS1001317357 (1:202160303 A>G,T), RS1001324290 (1:202156116 A>C), RS1001868389 (1:202159121 G>C), RS1002284043 (1:202157338 C>T), RS1002388356 (1:202151970 G>A), RS1002562499 (1:202163398 A>G)

Disease associations

OMIM: gene MIM:176889 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001930_15Breast cancer1.000000e-08
GCST90002380_117Basophil percentage of white cells5.000000e-10
GCST90002380_118Basophil percentage of white cells6.000000e-10
GCST90002397_789Mean spheric corpuscular volume3.000000e-12
GCST90002400_534Plateletcrit9.000000e-19

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007992basophil percentage of leukocytes
EFO:0007985platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2219 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

2 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 327,449 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1440TETRACYCLINE4324,384
CHEMBL1632CEPHALOTHIN SODIUM43,065

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

Binding affinities (BindingDB)

316 measured of 520 human assays (581 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
MLS000116276EC500.00207 nM
2-[[7-(2-furanylmethyl)-5,6-diphenyl-4-pyrrolo[2,3-d]pyrimidinyl]amino]ethanolEC500.00424 nM
SMR000071260EC5015.5 nM
3-[2-(hydroximinomethyl)pyrrol-1-yl]benzoic acidIC5023 nM
4-chloranyl-N-(3,4-dihydro-2H-thiochromen-4-yl)-3-sulfamoyl-benzamideIC50121 nM
7-hexacosenoic acidIC50220 nM
4-amino-3-(4-methylphenyl)-5-[(4-methyl-1-piperazinyl)carbonyl]-1,3-thiazole-2(3H)-thioneIC50250 nM
1-(2,6-dichlorophenyl)-3-(2-phenylethyl)thioureaIC50342 nM
4-[[2-bromanyl-4-[(E)-2-cyano-2-(3-fluorophenyl)ethenyl]phenoxy]methyl]benzoic acidIC50400 nM
2-[2-chloranyl-6-ethoxy-4-[(E)-[2-(naphthalen-2-ylamino)-4-oxidanylidene-1,3-thiazol-5-ylidene]methyl]phenoxy]ethanoic acidIC50440 nM
MLS-0054638.0001IC50478 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-(2-methoxyethyl)ureaIC50492 nM
MLS000050448IC50716 nM
MLS-0109562.0001IC50727 nM
cid_6161440IC50730 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-(2-phenylethyl)ureaIC50814 nM
CephalothinIC50920 nM
2-[4-[(E)-[[4-[2-(4-chloroanilino)-1,3-thiazol-4-yl]benzoyl]hydrazinylidene]methyl]phenoxy]acetic acidIC50924 nM
3-[(5E)-5-[[4-[(4-chlorophenyl)methoxy]-3-methoxyphenyl]methylidene]-4-oxo-2-sulfanylidene-3-thiazolidinyl]benzoic acidIC50953 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-butylureaIC50966 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-phenylureaIC50968 nM
2-[4-[(Z)-[2-(4-fluoroanilino)-4-keto-2-thiazolin-5-ylidene]methyl]phenoxy]acetic acid methyl esterIC501050 nM
2-[3-[2-hydroxyethyl(dimethyl)azaniumyl]propanoylamino]-2-methyl-propane-1-sulfonateEC501160 nM
2-[2-chloranyl-6-methoxy-4-[(Z)-[3-[2-[(4-methylphenyl)amino]-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)-1,3-thiazolidin-5-ylidene]methyl]phenoxy]ethanoic acidIC501180 nM
2-[2,6-bis(chloranyl)-4-[(Z)-[3-[2-[(4-methylphenyl)amino]-2-oxidanylidene-ethyl]-2,4-bis(oxidanylidene)-1,3-thiazolidin-5-ylidene]methyl]phenoxy]ethanoic acidIC501200 nM
(7Z)-3-bromanyl-7-(furan-2-ylmethylidene)-[1,3]thiazolo[4,5]imidazo[1,2-b]pyridin-8-oneIC501230 nM
3-(2-{(E)-[1-(4-chlorophenyl)-2,5-dioxoimidazolidin-4-ylidene]methyl}-1H-pyrrol-1-yl)benzoic acidIC501230 nM
3-[(5E)-5-[1-(2-chlorobenzyl)-2-keto-indolin-3-ylidene]-4-keto-2-thioxo-thiazolidin-3-yl]propionic acidIC501230 nM
2-[5-[(Z)-(3-bromanyl-8-oxidanylidene-[1,3]thiazolo[4,5]imidazo[1,2-b]pyridin-7-ylidene)methyl]furan-2-yl]benzoic acidIC501250 nM
3-(3-chloranyl-4-methoxy-phenyl)-1-(3-methylbutyl)-1-(1-propan-2-ylpiperidin-4-yl)thioureaIC501260 nM
4-[3-[(5Z)-4-keto-2-thioxo-5-veratrylidene-thiazolidin-3-yl]propanoylamino]benzoic acidIC501270 nM
2-[4-[[[4-[2-(4-chloroanilino)-1,3-thiazol-4-yl]benzoyl]hydrazinylidene]methyl]phenoxy]acetic acidIC501300 nM
3-[[2,3-bis(2-furyl)quinoxalin-6-yl]carbamoylamino]propionic acid ethyl esterIC501420 nM
1-ethyl-6-methyl-3-[(E)-2-phenylethenyl]pyrimido[5,4-e][1,2,4]triazine-5,7-dioneEC501440 nM
cid_9595040IC501490 nM
2-hydroxy-4-({4-[5-(2-methyl-3-phenyl-2-propen-1-ylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]butanoyl}amino)benzoic acidIC501560 nM
MLS-0202048.0001IC501600 nM
1,3,6-Trimethyl-1H-pyrimido[5,4-e][1,2,4]triazine-5,7-dioneEC501610 nM
4-keto-5-methyl-2-[(E)-2-(4-methyl-3-nitro-phenyl)vinyl]-3H-thieno[2,3-d]pyrimidine-6-carboxylic acidIC501620 nM
9-octacosynoic acidIC501760 nM
1,6-dimethyl-3-propyl-pyrimido[5,4-e][1,2,4]triazine-5,7-dioneEC501770 nM
MLS-0336006.0001IC501830 nM
4-[[5-(4-bromophenyl)-2-furoyl]thiocarbamoylamino]benzoic acidIC501880 nM
5,6-dihydro-4H-cyclopenta[b]thiophene-2-carboxylic acid [2-[(1,1-diketothiolan-3-yl)-isobutyl-amino]-2-keto-ethyl] esterIC501910 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-(1-naphthalenyl)ureaIC502040 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-(4-chlorophenyl)ureaIC502140 nM
2-(5,6-dihydro-4H-cyclopent[d]isoxazole-3-carbonylamino)benzoic acid methyl esterIC502180 nM
N-[5-(1,3-benzothiazol-2-yl)-2-methylphenyl]-2-chloro-5-(4H-1,2,4-triazol-4-yl)benzamideIC502210 nM
1-[2,3-bis(2-furanyl)-6-quinoxalinyl]-3-methylureaIC502300 nM
MLS000527911IC502310 nM

ChEMBL bioactivities

315 potent at pChembl≥5 of 441 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.84IC5014.4nMCHEMBL1605172
7.60IC5025nMCHEMBL1322542
7.46IC5034.5nMCHEMBL1408579
7.23IC5058.6nMCHEMBL1304193
7.18IC5066nMCHEMBL1460470
7.07IC5084.6nMCHEMBL1608642
7.00IC50100nMCEFAMANDOLE SODIUM
6.98IC50105nMCHEMBL1445488
6.97IC50108nMCHEMBL1505246
6.90IC50125nMCHEMBL454668
6.90IC50127nMCHEMBL1603381
6.89IC50130nMCHEMBL4750435
6.89IC50129nMCHEMBL1407203
6.80IC50159nMCHEMBL1371869
6.75IC50180nMCHEMBL1448629
6.71IC50196nMCHEMBL1447397
6.71IC50193nMCHEMBL1701224
6.70IC50200nMCHEMBL492894
6.70IC50200nMCHEMBL1527520
6.70IC50198nMCHEMBL1501132
6.68IC50209nMCHEMBL1536896
6.64IC50227nMCHEMBL1393151
6.60IC50250nMCHEMBL454668
6.59IC50256nMCHEMBL1407368
6.55IC50280nMCHEMBL1334633
6.55IC50284nMCHEMBL1449836
6.55IC50280nMCHEMBL1526088
6.52IC50304nMCHEMBL1414679
6.51IC50312nMCHEMBL1438889
6.50IC50314nMCHEMBL1393151
6.48IC50329nMCHEMBL1371777
6.48IC50331nMCHEMBL1327648
6.46IC50343nMCHEMBL1390354
6.43IC50373nMCHEMBL1732016
6.41IC50391nMCHEMBL1414679
6.41IC50394nMCHEMBL1704862
6.40IC50400nMCHEMBL1539325
6.39IC50410nMCHEMBL1324051
6.39IC50410nMCHEMBL1376870
6.38IC50420nMCHEMBL1978364
6.38IC50420nMCHEMBL259355
6.38IC50419nMCHEMBL1424189
6.35IC50447nMCHEMBL1408579
6.35IC50450nMCHEMBL1715328
6.34IC50455nMCHEMBL1605172
6.34IC50452nMCHEMBL1702580
6.33IC50472nMCHEMBL1725599
6.33IC50466nMCHEMBL1732016
6.33IC50465nMCHEMBL1488869
6.32IC50483nMCHEMBL501993

PubChem BioAssay actives

32 with measured affinity, of 171 total; 30 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
2-[4,5-bis(1,3,2-dithiarsolan-2-yl)-3-hydroxy-6-oxoxanthen-9-yl]benzoic acid1495216: Inhibition of allosterically sensitized mutant form of His6-tagged human HePTP catalytic domain using pNPP as substrate incubated for 90 mins by quenched phosphatase activity assayic500.1250uM
4-[1-(4-methoxyphenyl)-3-(2-oxochromen-7-yl)pyrrolo[2,3-b]pyridin-5-yl]benzoic acid1706923: Inhibition of PTPN7 (unknown origin) pre-incubated for 20 mins followed by fluorescence substrate addition and measured after 120 mins by DiFMUP assayic500.1300uM
3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4-carboxylic acid2037695: Inhibition of HEPTP (unknown origin) using pNPP as substrate by high-throughput screening assayic500.2000uM
2-[(5Z)-5-[[3-[4-[(4-chlorophenyl)methoxy]phenyl]-1-phenylpyrazol-4-yl]methylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid443925: Inhibition of recombinant HePTPic500.6200uM
2-[4-[(Z)-[5-(4-chlorophenyl)-7-methyl-3-oxo-6-propan-2-yloxycarbonyl-5H-[1,3]thiazolo[3,2-a]pyrimidin-2-ylidene]methyl]phenoxy]acetic acid569652: Competitive inhibition of recombinant HePTP expressed in Escherichia coli by Michaelis-Menten kinetic analysiski0.6900uM
2-[(5Z)-5-[[3-[4-[(2-fluorophenyl)methoxy]phenyl]-1-phenylpyrazol-4-yl]methylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid443925: Inhibition of recombinant HePTPic500.8700uM
6-hydroxy-3-iodo-1-methyl-2-[3-[[2-oxo-2-(4-thiophen-3-ylanilino)acetyl]amino]phenyl]indole-5-carboxylic acid1182542: Inhibition of HePTP (unknown origin)ic501.0300uM
2-[(5Z)-5-[[3-[4-[(2-chlorophenyl)methoxy]phenyl]-1-phenylpyrazol-4-yl]methylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid443925: Inhibition of recombinant HePTPic501.2000uM
2-[4-[(Z)-[5-(4-chlorophenyl)-6-ethoxycarbonyl-7-methyl-3-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidin-2-ylidene]methyl]phenoxy]acetic acid569641: Inhibition of recombinant HePTP expressed in Escherichia coliic501.3000uM
2-[(5Z)-4-oxo-5-[[1-phenyl-3-(4-phenylmethoxyphenyl)pyrazol-4-yl]methylidene]-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid443925: Inhibition of recombinant HePTPic501.5000uM
2-[4-[(Z)-[6-ethoxycarbonyl-7-methyl-5-(4-methylsulfanylphenyl)-3-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidin-2-ylidene]methyl]phenoxy]acetic acid569641: Inhibition of recombinant HePTP expressed in Escherichia coliic501.8000uM
6-hydroxy-2-phenyl-3-[2-[4-(trifluoromethoxy)phenyl]ethynyl]-1-benzofuran-5-carboxylic acid725030: Inhibition of HEPTP (unknown origin) expressed in Escherichia coli using pNPP substrate after 5 mins by spectrophotometric analysisic501.9000uM
6-hydroxy-2-phenyl-3-[2-[3-(trifluoromethyl)phenyl]ethynyl]-1-benzofuran-5-carboxylic acid725030: Inhibition of HEPTP (unknown origin) expressed in Escherichia coli using pNPP substrate after 5 mins by spectrophotometric analysisic502.1000uM
2-[(5Z)-4-oxo-5-[[1-phenyl-3-(4-piperidin-1-ylsulfonylphenyl)pyrazol-4-yl]methylidene]-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid443925: Inhibition of recombinant HePTPic502.4000uM
3-[2-(3-chlorophenyl)ethynyl]-6-hydroxy-2-[4-[2-oxo-2-(propylamino)ethoxy]phenyl]-1-benzofuran-5-carboxylic acid755776: Inhibition of recombinant HEPTP (unknown origin) using pNPP as substrate by spectrophotometric analysisic503.0000uM
3-[2-(3,5-difluorophenyl)ethynyl]-6-hydroxy-2-phenyl-1-benzofuran-5-carboxylic acid725030: Inhibition of HEPTP (unknown origin) expressed in Escherichia coli using pNPP substrate after 5 mins by spectrophotometric analysisic503.3000uM
3-[1-[4-[(4-chloronaphthalen-1-yl)amino]-4-oxobutyl]triazol-4-yl]-6-hydroxy-2-(4-methylphenyl)-1-benzofuran-5-carboxylic acid566825: Inhibition of HePTPic503.6900uM
6-hydroxy-2-(4-methoxyphenyl)-3-[1-[4-(naphthalen-1-ylamino)-4-oxobutyl]triazol-4-yl]-1-benzofuran-5-carboxylic acid566825: Inhibition of HePTPic503.7000uM
2-[4-[(Z)-[5-(2-chlorophenyl)-6-ethoxycarbonyl-7-methyl-3-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidin-2-ylidene]methyl]-2-methoxy-6-methylphenoxy]acetic acid569641: Inhibition of recombinant HePTP expressed in Escherichia coliic503.7000uM
6-hydroxy-2-(4-methylphenyl)-3-[1-[4-(naphthalen-1-ylamino)-4-oxobutyl]triazol-4-yl]-1-benzofuran-5-carboxylic acid566825: Inhibition of HePTPic504.0700uM
2-[4-[(Z)-[6-ethoxycarbonyl-5-(3-methoxyphenyl)-7-methyl-3-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidin-2-ylidene]methyl]phenoxy]acetic acid569641: Inhibition of recombinant HePTP expressed in Escherichia coliic504.6000uM
6-hydroxy-3-[1-[4-[(6-methoxy-1,3-benzothiazol-2-yl)amino]-4-oxobutyl]triazol-4-yl]-2-(3-methylphenyl)-1-benzofuran-5-carboxylic acid566825: Inhibition of HePTPic506.3600uM
(2S)-2-[4-[4-(2-benzyl-1-benzofuran-3-yl)phenyl]phenoxy]-3-phenylpropanoic acid1942820: Inhibition of HEPTP (unknown origin)ic507.1000uM
16221757286242: Inhibition of HePTPic507.5000uM
3-chloro-N-(5-methyl-1,3-benzothiazol-2-yl)-1-benzothiophene-2-carboxamide695227: Inhibition of HePTP expressed in Escherichia coli BL21 using pNPP substrateic508.0000uM
2-(3-cyano-7,8-dimethylquinolin-2-yl)sulfanyl-N-cyclohexylacetamide695227: Inhibition of HePTP expressed in Escherichia coli BL21 using pNPP substrateic508.0000uM
4-[1-(cyclohexylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-[2-[2-(trifluoromethoxy)phenyl]ethynyl]benzoic acid1206789: Inhibition of HePTP (unknown origin) using pNPP as substrate at pH 7 at 25 degC by spectrophotometric analysisic508.7000uM
2-[(5,6-dimethyl-4-oxo-3H-thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-(6-ethoxy-1,3-benzothiazol-2-yl)acetamide695227: Inhibition of HePTP expressed in Escherichia coli BL21 using pNPP substrateic509.0000uM
(5Z)-3-(3-chlorophenyl)-5-[(4-hydroxy-3-methoxy-5-nitrophenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one1799621: PTP Assay from Article 10.1002/cbic.200600287: “Cellular inhibition of protein tyrosine phosphatase 1B by uncharged thioxothiazolidinone derivatives.”ic509.3000uM
2-(3-cyano-5,8-dimethylquinolin-2-yl)sulfanyl-N-(2-ethyl-6-methylphenyl)acetamide695227: Inhibition of HePTP expressed in Escherichia coli BL21 using pNPP substrateic5010.0000uM

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression2
alpha phellandrenedecreases expression1
triphenyl phosphateaffects expression1
sodium arseniteincreases expression1
benzo(e)pyrenedecreases methylation1
triphenyltindecreases expression1
di-n-butylphosphoric acidaffects expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
Acetaminophenincreases expression1
Benzeneincreases expression1
Catechinaffects cotreatment, decreases expression1
Curcuminincreases expression1
Diurondecreases expression1
Leadincreases expression1
Methapyrilenedecreases methylation1
Nickelincreases expression1
Oxygendecreases expression1
Rotenoneincreases expression1
Tretinoinincreases expression1
Valproic Acidincreases methylation1
Paclitaxelincreases expression1
Antirheumatic Agentsdecreases expression1

ChEMBL screening assays

72 unique, capped per target: 63 binding, 8 functional, 1 admet

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1047963BindingInhibition of recombinant HePTPMultidentate small-molecule inhibitors of vaccinia H1-related (VHR) phosphatase decrease proliferation of cervix cancer cells. — J Med Chem
CHEMBL1613806FunctionalPUBCHEM_BIOASSAY: In Vitro HePTP Dose Response Colorimetric Assay for SAR Study. (Class of assay: confirmatory) [Related pubchem assays: 521 ]PubChem BioAssay data set
CHEMBL4626299ADMETInhibition of HePTP (unknown origin) expressed in Escherichia coli BL21 using p-nitrophenyl phosphate as substrate measured after 30 mins by UV-vis spectrophotometric methodHighly Potent and Selective N-Aryl Oxamic Acid-Based Inhibitors for Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. — J Med Chem

Clinical trials (associated diseases)

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

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