PTPRF

Summary

PTPRF (protein tyrosine phosphatase receptor type F, HGNC:9670) is a protein-coding gene on chromosome 1p34.2, encoding Receptor-type tyrosine-protein phosphatase F (P10586). Possible cell adhesion receptor.

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 PTP possesses an extracellular region, a single transmembrane region, and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains three Ig-like domains, and nine non-Ig like domains similar to that of neural-cell adhesion molecule. This PTP was shown to function in the regulation of epithelial cell-cell contacts at adherents junctions, as well as in the control of beta-catenin signaling. An increased expression level of this protein was found in the insulin-responsive tissue of obese, insulin-resistant individuals, and may contribute to the pathogenesis of insulin resistance. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported.

Source: NCBI Gene 5792 — RefSeq curated summary.

At a glance

• Gene–disease (curated): breasts and/or nipples, aplasia or hypoplasia of, 2 (Strong, GenCC)
• GWAS associations: 40
• Clinical variants (ClinVar): 366 total — 1 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 13
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_002840

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9670
Approved symbol	PTPRF
Name	protein tyrosine phosphatase receptor type F
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000142949
Ensembl biotype	protein_coding
OMIM	179590
Entrez	5792

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 32 protein_coding, 8 protein_coding_CDS_not_defined

ENST00000359947, ENST00000372405, ENST00000372407, ENST00000412568, ENST00000414879, ENST00000429895, ENST00000436724, ENST00000437607, ENST00000438120, ENST00000463041, ENST00000467464, ENST00000477970, ENST00000481019, ENST00000496043, ENST00000496447, ENST00000617451, ENST00000850943, ENST00000850944, ENST00000882999, ENST00000883000, ENST00000883001, ENST00000883002, ENST00000883003, ENST00000883004, ENST00000883005, ENST00000883006, ENST00000883007, ENST00000915777, ENST00000915778, ENST00000915779, ENST00000915780, ENST00000915781, ENST00000915782, ENST00000915783, ENST00000915784, ENST00000915785, ENST00000915786, ENST00000954134, ENST00000954135, ENST00000954136

RefSeq mRNA: 6 — MANE Select: NM_002840 NM_001329137, NM_001329138, NM_001329139, NM_001329140, NM_002840, NM_130440

CCDS: CCDS489, CCDS490

Canonical transcript exons

ENST00000359947 — 34 exons

Exon	Start	End
ENSE00000957339	43592457	43592601
ENSE00000957341	43597748	43598053
ENSE00000957342	43598720	43598913
ENSE00000957343	43602071	43602097
ENSE00001369939	43538198	43538277
ENSE00001705341	43578810	43578920
ENSE00001714914	43590972	43591553
ENSE00003463090	43619680	43619858
ENSE00003465004	43618630	43618749
ENSE00003467902	43605190	43605443
ENSE00003499665	43603416	43603533
ENSE00003503035	43619288	43619573
ENSE00003503771	43621097	43621232
ENSE00003516850	43609383	43609498
ENSE00003522250	43603611	43604189
ENSE00003524756	43617445	43617568
ENSE00003529514	43620838	43620992
ENSE00003530969	43620095	43620221
ENSE00003547371	43619048	43619202
ENSE00003552417	43606240	43606458
ENSE00003556825	43604903	43605000
ENSE00003567951	43591812	43591948
ENSE00003580809	43553492	43553637
ENSE00003582514	43606814	43606968
ENSE00003595829	43588731	43589000
ENSE00003605803	43613618	43613715
ENSE00003605838	43605529	43605622
ENSE00003606990	43621935	43623666
ENSE00003618083	43569590	43569778
ENSE00003626070	43617736	43617911
ENSE00003640065	43553800	43553941
ENSE00003663889	43545031	43545166
ENSE00003684029	43620454	43620579
ENSE00003843228	43530883	43531090

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 98.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.7950 / max 439.8101, expressed in 1502 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2528	25.0349	1492
2524	1.2099	73
2529	0.2793	140
2526	0.0918	37
2527	0.0845	42
2522	0.0373	6
2525	0.0311	12
2521	0.0262	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gingival epithelium	UBERON:0001949	98.93	gold quality
bronchial epithelial cell	CL:0002328	98.90	gold quality
nipple	UBERON:0002030	98.86	gold quality
esophagus squamous epithelium	UBERON:0006920	98.86	gold quality
parotid gland	UBERON:0001831	98.84	gold quality
epithelium of bronchus	UBERON:0002031	98.84	gold quality
hair follicle	UBERON:0002073	98.82	gold quality
germinal epithelium of ovary	UBERON:0001304	98.81	gold quality
bronchus	UBERON:0002185	98.79	gold quality
gingiva	UBERON:0001828	98.77	gold quality
jejunal mucosa	UBERON:0000399	98.67	gold quality
upper arm skin	UBERON:0004263	98.64	gold quality
squamous epithelium	UBERON:0006914	98.61	gold quality
epithelium of esophagus	UBERON:0001976	98.55	gold quality
upper leg skin	UBERON:0004262	98.54	gold quality
epithelium of nasopharynx	UBERON:0001951	98.44	gold quality
nasal cavity epithelium	UBERON:0005384	98.31	gold quality
mammalian vulva	UBERON:0000997	98.17	gold quality
penis	UBERON:0000989	98.15	gold quality
corpus epididymis	UBERON:0004359	98.14	gold quality
epithelium of mammary gland	UBERON:0003244	98.07	gold quality
mucosa of paranasal sinus	UBERON:0005030	98.07	gold quality
ventricular zone	UBERON:0003053	98.04	gold quality
mammary duct	UBERON:0001765	97.96	gold quality
pharyngeal mucosa	UBERON:0000355	97.89	gold quality
seminal vesicle	UBERON:0000998	97.88	gold quality
colonic mucosa	UBERON:0000317	97.85	gold quality
duodenum	UBERON:0002114	97.78	gold quality
trachea	UBERON:0003126	97.70	gold quality
oviduct epithelium	UBERON:0004804	97.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	1191.05
E-GEOD-75688	yes	893.56
E-MTAB-10287	yes	45.77
E-MTAB-6678	yes	17.98
E-GEOD-137537	yes	5.90
E-GEOD-75367	no	545.47
E-CURD-10	no	364.93
E-GEOD-99795	no	359.49
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PPARA

Literature-anchored findings (GeneRIF, showing 21)

• regulation of expression by cell density through functional E-cadherin complexes (PMID:12095414)
• interactions between RPTP-domain1s and RPTP-domain 2s are a common but specific mechanism that is likely to be regulated- domain2s and the wedge structures are crucial determinants of binding specificity, thus regulating cross-talk between RPTPs (PMID:12376545)
• LAR PTPase domains play distinct functional roles in phosphorylation and dephosphorylation (PMID:12496362)
• LAR as a crucial regulator of the sensitivity of two key insulin signalling pathways to insulin (PMID:15896785)
• Results identify a protein tyrosine phosphatase as a potential substrate of TACE and describe proteolytic processing of PTP-LAR as a means of regulating phosphatase activity downstream and thus under the control of EGFR-mediated signaling pathways. (PMID:16478662)
• PS/gamma-secretase-mediated cleavage of LAR controls LAR-beta-catenin interaction, suggesting an essential role for PS/gamma-secretase in the regulation of LAR signaling (PMID:17259169)
• Regulated degradation of liprinalpha1 is important for proper LAR receptor distribution, and could provide a mechanism for localized control of dendrite and synapse morphogenesis by activity and CaMKII. (PMID:17419996)
• LAR and Src are identified as Death-associated protein kinase (DAPK) regulators through their reciprocal modification of DAPK Y491/492 residues and establishes a functional link of this DAPK-regulatory circuit to tumor progression. (PMID:17803936)
• the PTPase activity in patients with insulin receptor gene mutation and severe insulin resistance may differ from that in ordinary type 2 diabetes (PMID:18925540)
• LAR functions as a negative regulator of adipogenesis. (PMID:19910497)
• Trans-synaptic adhesions between netrin-G ligand-3 (NGL-3) and receptor tyrosine phosphatases LAR, protein-tyrosine phosphatase delta (PTPdelta), and PTPsigma via specific domains regulate excitatory synapse formation. (PMID:20139422)
• Interaction between the tripartite NGL-1, netrin-G1 and LAR adhesion complex promotes development of excitatory synapses. (PMID:23986473)
• PTPRF is down-regulated in hepatocellular carcinoma-facilitated tumor development. (PMID:24470239)
• Homozygous truncating PTPRF mutation causes athelia. (PMID:24781087)
• PTPRF may have value as a predictive marker to identify which patients can obtain the greatest benefit from erlotinib in the post-first-line setting. (PMID:26291013)
• transferred nuclear Overhauser effects (trNOEs) have been employed in the docking program HADDOCK to generate models for the LAR-fondaparinux complex. These models are further analyzed by postprocessing energetic analysis to identify key binding interactions. (PMID:29570275)
• Data show that protein tyrosine phosphatase receptor type F (PTPRF) activity suppressed CD133/transmembrane 4L six family member 5 (TM4SF5)-mediated sphere growth. (PMID:30217560)
• PPARgamma inhibits breast cancer progression by upregulating PTPRF expression. (PMID:31799666)
• Crystal and solution structures of fragments of the human leucocyte common antigen-related protein. (PMID:32355037)
• Inhibition of protein tyrosine phosphatase receptor type F suppresses Wnt signaling in colorectal cancer. (PMID:32973331)
• Cytoneme-like protrusion formation induced by LAR is promoted by receptor dimerization. (PMID:35735010)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ptprfb	ENSDARG00000005754
danio_rerio	ptprfa	ENSDARG00000103479
mus_musculus	Ptprf	ENSMUSG00000033295
rattus_norvegicus	Ptprf	ENSRNOG00000019977

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), PTPN7 (ENSG00000143851), 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

Receptor-type tyrosine-protein phosphatase F — P10586 (reviewed: P10586)

Alternative names: Leukocyte common antigen related

All UniProt accessions (6): P10586, A2A437, H0Y380, H0Y4H1, H0Y6Z7, H0Y7Z9

UniProt curated annotations — full annotation on UniProt →

Function. Possible cell adhesion receptor. It possesses an intrinsic protein tyrosine phosphatase activity (PTPase) and dephosphorylates EPHA2 regulating its activity. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one.

Subunit / interactions. Interacts with GRIP1. Interacts with PPFIA1, PPFIA2 and PPFIA3. Interacts with INSR.

Subcellular location. Membrane.

Disease relevance. Aplasia or hypoplasia of the breasts and/or nipples 2 (BNAH2) [MIM:616001] A group of congenital deformities encompassing total absence of breasts and nipple (amastia), absence of the nipple (athelia), and absence of the mammary gland (amazia). The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the protein-tyrosine phosphatase family. Receptor class 2A subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
P10586-1	1	yes
P10586-2	2

RefSeq proteins (6): NP_001316066, NP_001316067, NP_001316068, NP_001316069, NP_002831, NP_569707 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000242	PTP_cat	Domain
IPR000387	Tyr_Pase_dom	Domain
IPR003595	Tyr_Pase_cat	Domain
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR016130	Tyr_Pase_AS	Active_site
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050713	RTP_Phos/Ushers	Family

Pfam: PF00041, PF00102, PF07679

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.

Substrate	Km (mM)	Measurements
4-NITROPHENYL PHOSPHATE	0.0008–148	84
6,8-DIFLUORO-4-METHYLUMBELLIFERYL PHOSPHATE	0.0039–0.862	27
P-NITROPHENYL PHOSPHATE	0.0024–10	20
DADEPYLIPQQG	0.0003–0.1	12
PHOSPHOTYROSINE	0.012–30	11
LYSOZYME	0.0003–0.012	5
MYELIN BASIC PROTEIN	0.0001–0.022	5
ACETYL-DADEPY-NH2	0.0228–0.219	4
ACETYL-DADEPYL-NH2	1.1–97.5	4
4,6,8-TRIMETHYL-2-OXO-2H-CHROMEN-7-YL DIHYDROGEN	0.02–0.156	3
SASASPYSASA	0.53–2.3	3
1-NAPHTHYL PHOSPHATE	1.19–1.88	2
3,6-FLUORESCEIN DIPHOSPHATE	15–19	2
4-METHYLUMBELLIFERYL PHOSPHATE	0.953–2.41	2
BOVINE SERUM ALBUMIN	0.0001–0.0003	2

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (168 total): strand 87, helix 27, domain 13, turn 12, glycosylation site 5, binding site 4, disulfide bond 3, sequence variant 3, region of interest 2, topological domain 2, active site 2, sequence conflict 2, signal peptide 1, chain 1, modified residue 1, transmembrane region 1, splice variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

13 structures.

PDB	Method	Resolution (Å)
4N5U	X-RAY DIFFRACTION	1.46
6TPU	X-RAY DIFFRACTION	1.55
6TPV	X-RAY DIFFRACTION	1.8
1LAR	X-RAY DIFFRACTION	2
2YD8	X-RAY DIFFRACTION	2.05
2YD5	X-RAY DIFFRACTION	2.2
6KR4	X-RAY DIFFRACTION	2.85
6TPW	X-RAY DIFFRACTION	2.9
6TPT	X-RAY DIFFRACTION	3.2
2DJU	SOLUTION NMR
2DN7	SOLUTION NMR
2EDX	SOLUTION NMR
2EDY	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P10586-F1	82.43	0.34

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 (2): 1548 (phosphocysteine intermediate); 1839 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (4): 68–77; 1516; 1548–1554; 1592

Post-translational modifications (1): 1305

Disulfide bonds (3): 54–107, 156–207, 253–298

Glycosylation sites (5): 117, 250, 295, 721, 966

Mutagenesis-validated functional residues (1):

Position	Phenotype
1548	loss of activity.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-388844	Receptor-type tyrosine-protein phosphatases
R-HSA-77387	Insulin receptor recycling
R-HSA-8849932	Synaptic adhesion-like molecules

MSigDB gene sets: 337 (showing top): REACTOME_SIGNALING_BY_INSULIN_RECEPTOR, WANG_CLIM2_TARGETS_UP, GOBP_REGULATION_OF_PROTEIN_BINDING, TSENG_IRS1_TARGETS_UP, MODULE_255, MAZ_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_317, GOBP_REGENERATION, GOBP_NEUROGENESIS, GOBP_RESPONSE_TO_AXON_INJURY, GGGTGGRR_PAX4_03, GOBP_REGULATION_OF_RECEPTOR_BINDING, HUMMERICH_SKIN_CANCER_PROGRESSION_DN

GO Biological Process (14): cell adhesion (GO:0007155), signal transduction (GO:0007165), cell surface receptor protein tyrosine phosphatase signaling pathway (GO:0007185), nervous system development (GO:0007399), cell migration (GO:0016477), neuron projection regeneration (GO:0031102), peptidyl-tyrosine dephosphorylation (GO:0035335), regulation of axon regeneration (GO:0048679), synaptic membrane adhesion (GO:0099560), negative regulation of receptor binding (GO:1900121), protein dephosphorylation (GO:0006470), regulation of neuron projection development (GO:0010975), dephosphorylation (GO:0016311), synapse organization (GO:0050808)

GO Molecular Function (9): phosphoprotein phosphatase activity (GO:0004721), protein tyrosine phosphatase activity (GO:0004725), transmembrane receptor protein tyrosine phosphatase activity (GO:0005001), heparin binding (GO:0008201), chondroitin sulfate proteoglycan binding (GO:0035373), protein-containing complex binding (GO:0044877), cell adhesion molecule binding (GO:0050839), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (5): plasma membrane (GO:0005886), neuron projection (GO:0043005), neuronal cell body (GO:0043025), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Protein-protein interactions at synapses	2
Signaling by Insulin receptor	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	2
neuron projection development	2
binding	2
cell communication	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
enzyme-linked receptor protein signaling pathway	1
system development	1
cell motility	1
regeneration	1
cellular response to stress	1
protein dephosphorylation	1
axon regeneration	1
regulation of response to external stimulus	1
regulation of neuron projection regeneration	1
regulation of response to wounding	1
synapse organization	1
cell-cell adhesion	1
signaling receptor binding	1
negative regulation of protein binding	1
regulation of receptor binding	1
dephosphorylation	1
protein modification process	1
regulation of plasma membrane bounded cell projection organization	1
phosphate-containing compound metabolic process	1
cell junction organization	1
phosphatase activity	1
catalytic activity, acting on a protein	1
phosphoprotein phosphatase activity	1
protein tyrosine phosphatase activity	1
transmembrane receptor protein phosphatase activity	1
glycosaminoglycan binding	1
sulfur compound binding	1
proteoglycan binding	1
protein binding	1
catalytic activity	1
membrane	1
cell periphery	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

1982 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTPRF	PPFIA1	Q13136	986
PTPRF	PPFIBP1	Q86W92	917
PTPRF	PPFIA3	O75145	910
PTPRF	LRRC4B	Q9NT99	817
PTPRF	PTS	Q03393	725
PTPRF	CTNNB1	P35222	645
PTPRF	IL1RAPL1	Q9NZN1	636
PTPRF	RTN4RL1	Q86UN2	622
PTPRF	SLITRK1	Q96PX8	621
PTPRF	LRFN3	Q9BTN0	590
PTPRF	GPC1	P35052	544
PTPRF	NTRK2	Q16620	517
PTPRF	CDH17	Q12864	489
PTPRF	IL1RAPL2	Q9NP60	489
PTPRF	LRFN2	Q9ULH4	485

IntAct

164 interactions, top by confidence:

A	B	Type	Score
CD9	ADAM10	psi-mi:“MI:0914”(association)	0.750
EGFR	CTNND1	psi-mi:“MI:0914”(association)	0.750
IL1RAP	PTPRF	psi-mi:“MI:0915”(physical association)	0.730
IL1RAP	PTPRF	psi-mi:“MI:0407”(direct interaction)	0.730
PTPRF	IL1RAP	psi-mi:“MI:0407”(direct interaction)	0.730
IL1RAP	PTPRF	psi-mi:“MI:0403”(colocalization)	0.730
SCN2B	EXOC5	psi-mi:“MI:0914”(association)	0.640
PDGFRB	PIK3R2	psi-mi:“MI:0914”(association)	0.610
EGFR	PTPRF	psi-mi:“MI:0915”(physical association)	0.550
PTPRF	LRFN5	psi-mi:“MI:0915”(physical association)	0.540
PTPRF	LRFN1	psi-mi:“MI:0915”(physical association)	0.540
LRFN4	PTPRF	psi-mi:“MI:0915”(physical association)	0.540
LRFN1	PTPRF	psi-mi:“MI:0407”(direct interaction)	0.540
LRFN4	PTPRF	psi-mi:“MI:0407”(direct interaction)	0.540
LRFN5	PTPRF	psi-mi:“MI:0407”(direct interaction)	0.540
ARRDC4	WWP2	psi-mi:“MI:0914”(association)	0.530
CLEC4A	SEMA7A	psi-mi:“MI:0914”(association)	0.530
TMEM30B	KLRG2	psi-mi:“MI:0914”(association)	0.530
MANSC1	KLRG2	psi-mi:“MI:0914”(association)	0.530
IL13RA2	METTL15	psi-mi:“MI:0914”(association)	0.530
PCDHGB1	FAM171A2	psi-mi:“MI:0914”(association)	0.530
PCDHB16	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
MRAP2	GOLIM4	psi-mi:“MI:0914”(association)	0.530
FCGRT	GOLIM4	psi-mi:“MI:0914”(association)	0.530
NPDC1	TCAF2	psi-mi:“MI:0914”(association)	0.530
MRAP2	PODXL	psi-mi:“MI:0914”(association)	0.530
DLK1	SCAMP3	psi-mi:“MI:0914”(association)	0.530
CTLA4	B4GALT5	psi-mi:“MI:0914”(association)	0.530

BioGRID (327): PTPRF (Affinity Capture-MS), PTPRF (Affinity Capture-MS), PTPRF (Affinity Capture-MS), PTPRF (Affinity Capture-MS), PTPRF (Affinity Capture-MS), PTPRF (Affinity Capture-MS), PTPRF (Affinity Capture-RNA), PTPRF (Affinity Capture-MS), ADRBK1 (Co-fractionation), DNAAF5 (Co-fractionation), NAA50 (Co-fractionation), NPLOC4 (Co-fractionation), PFKM (Co-fractionation), PICALM (Co-fractionation), PPWD1 (Co-fractionation)

ESM2 similar proteins: A2A8L5, A4IFW2, A7MBJ4, B0V2N1, F1NWE3, O00533, O42414, O55005, O89026, O94856, O97394, P10586, P11627, P16621, P22063, P23468, P28685, P32004, P70232, P97685, P97686, Q02246, Q05695, Q13332, Q28902, Q2EY14, Q2EY15, Q2VWP7, Q2VWP9, Q3UH53, Q589G5, Q58EX2, Q61330, Q64487, Q64604, Q64605, Q6V4S5, Q7Z5N4, Q810U3, Q810U4

Diamond homologs: A0A6I8TCE0, A1L1L3, A2A8L5, A2ALK8, A4IFW2, A7MBJ4, B0V2N1, B0X4T2, B1AUH1, B2RU80, B3DK56, B9EKR1, E9Q0N2, E9Q612, F1NWE3, O13016, O14522, O35239, O55082, O82656, O88488, P04157, P06800, P08575, P0C5E4, P10586, P16621, P17706, P18031, P20417, P23467, P23468, P23470, P23471, P26045, P28191, P28192, P28827, P28828, P29074

SIGNOR signaling

26 interactions.

A	Effect	B	Mechanism
PTPRF	down-regulates	AKT1	dephosphorylation
PTPRF	up-regulates	DAPK1	dephosphorylation
PTPRF	down-regulates	INSR	dephosphorylation
PTPRF	“up-regulates activity”	LRRC4B	binding
LRFN5	“up-regulates activity”	PTPRF	binding
PTPRF	up-regulates	Synaptic_plasticity
PPFIA1	“up-regulates activity”	PTPRF	relocalization
MARCHF9	“down-regulates quantity by destabilization”	PTPRF	ubiquitination
PTPRF	“up-regulates activity”	DAPK1	dephosphorylation
PTPRF	“down-regulates quantity by destabilization”	BCAR1	dephosphorylation
PTPRF	“down-regulates activity”	EGFR	dephosphorylation
PTPRF	down-regulates	PLCG1	dephosphorylation
PTPRF	down-regulates	RET	dephosphorylation
PTPRF	up-regulates	FYN	dephosphorylation
PTPRF	down-regulates	FYN	dephosphorylation
PTPRF	up-regulates	LCK	dephosphorylation
FYN	“up-regulates activity”	PTPRF	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 203 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:

Pathway	Partners	Fold	FDR
Synaptic adhesion-like molecules	5	20.6×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
regulation of postsynaptic density assembly	5	25.2×	8e-04
synaptic membrane adhesion	6	19.8×	6e-04
regulation of heart rate by cardiac conduction	6	12.8×	3e-03

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	256
Likely benign	49
Benign	21

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
155912	NM_002840.5(PTPRF):c.1847_1848del (p.Val616fs)	Pathogenic
4845793	NM_002840.5(PTPRF):c.959del (p.Lys320fs)	Likely pathogenic

SpliceAI

6940 predictions. Top by Δscore:

Variant	Effect	Δscore
1:43531087:GGCG:G	donor_gain	1.0000
1:43531088:GCG:G	donor_gain	1.0000
1:43531088:GCGG:G	donor_gain	1.0000
1:43531091:G:GG	donor_gain	1.0000
1:43545167:G:GG	donor_gain	1.0000
1:43553488:CCAG:C	acceptor_loss	1.0000
1:43553489:CAGGC:C	acceptor_loss	1.0000
1:43553490:A:AG	acceptor_gain	1.0000
1:43553490:AGG:A	acceptor_loss	1.0000
1:43553491:G:GG	acceptor_gain	1.0000
1:43553491:GGC:G	acceptor_gain	1.0000
1:43569586:GCA:G	acceptor_loss	1.0000
1:43569587:CA:C	acceptor_loss	1.0000
1:43569587:CAG:C	acceptor_gain	1.0000
1:43569588:A:AG	acceptor_gain	1.0000
1:43569588:A:C	acceptor_loss	1.0000
1:43569588:AGA:A	acceptor_gain	1.0000
1:43569588:AGAG:A	acceptor_gain	1.0000
1:43569589:G:C	acceptor_gain	1.0000
1:43569589:G:GA	acceptor_gain	1.0000
1:43569589:GA:G	acceptor_gain	1.0000
1:43569589:GAGG:G	acceptor_gain	1.0000
1:43569589:GAGGA:G	acceptor_gain	1.0000
1:43569777:AGGTG:A	donor_loss	1.0000
1:43569778:GGTGA:G	donor_loss	1.0000
1:43569779:GTG:G	donor_loss	1.0000
1:43569780:T:G	donor_loss	1.0000
1:43572493:G:GG	donor_gain	1.0000
1:43589001:G:A	donor_loss	1.0000
1:43589002:T:G	donor_loss	1.0000

AlphaMissense

12445 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:43553555:T:C	F52S	1.000
1:43553560:T:C	C54R	1.000
1:43553596:T:A	W66R	1.000
1:43553596:T:C	W66R	1.000
1:43553597:G:C	W66S	1.000
1:43553598:G:C	W66C	1.000
1:43553598:G:T	W66C	1.000
1:43553834:T:A	L91H	1.000
1:43553834:T:C	L91P	1.000
1:43553875:T:G	Y105D	1.000
1:43553881:T:C	C107R	1.000
1:43553883:T:G	C107W	1.000
1:43553888:C:A	A109D	1.000
1:43553927:T:C	L122P	1.000
1:43569676:T:C	C156R	1.000
1:43569677:G:A	C156Y	1.000
1:43569678:T:G	C156W	1.000
1:43569712:T:A	W168R	1.000
1:43569712:T:C	W168R	1.000
1:43569714:G:C	W168C	1.000
1:43569714:G:T	W168C	1.000
1:43578816:T:C	L192S	1.000
1:43578854:T:G	Y205D	1.000
1:43578860:T:A	C207S	1.000
1:43578860:T:C	C207R	1.000
1:43578861:G:C	C207S	1.000
1:43578862:T:G	C207W	1.000
1:43578909:T:C	L223P	1.000
1:43588752:T:C	F234S	1.000
1:43588803:T:C	L251P	1.000

dbSNP variants (sampled 300 via entrez): RS1000014440 (1:43623410 G>C,T), RS1000017414 (1:43525744 G>T), RS1000049349 (1:43593847 G>A,T), RS1000070143 (1:43613344 C>T), RS1000096127 (1:43560611 C>T), RS1000147368 (1:43557247 C>A,T), RS1000162258 (1:43557456 A>C), RS1000275991 (1:43530525 T>C), RS1000279453 (1:43531696 C>T), RS1000296404 (1:43579775 A>G,T), RS1000317659 (1:43568466 C>T), RS1000352481 (1:43586458 C>T), RS1000385927 (1:43552257 A>G), RS1000406372 (1:43536827 G>A), RS1000407641 (1:43609736 C>T)

Disease associations

OMIM: gene MIM:179590 | disease phenotypes: MIM:616001

GenCC curated gene-disease

Disease	Classification	Inheritance
breasts and/or nipples, aplasia or hypoplasia of, 2	Strong	Autosomal recessive

Mondo (1): breasts and/or nipples, aplasia or hypoplasia of, 2 (MONDO:0014450)

Orphanet (0):

HPO phenotypes

13 total (13 of 13 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000319	Smooth philtrum
HP:0000385	Small earlobe
HP:0000455	Broad nasal tip
HP:0000463	Anteverted nares
HP:0000687	Widely spaced teeth
HP:0002553	Highly arched eyebrow
HP:0002557	Hypoplastic nipples
HP:0002561	Absent nipple
HP:0007598	Bilateral single transverse palmar creases
HP:0032077	Male urethral meatus stenosis
HP:0100853	Hypoplastic areola

GWAS associations

40 associations (top):

Study	Trait	p-value
GCST001663_2	Amyotrophic lateral sclerosis (age of onset)	5.000000e-06
GCST002539_29	Schizophrenia	3.000000e-10
GCST003496_4	Educational attainment	1.000000e-08
GCST004521_235	Autism spectrum disorder or schizophrenia	4.000000e-10
GCST004946_9	Schizophrenia	1.000000e-12
GCST005141_39	Cognitive ability (MTAG)	5.000000e-11
GCST005316_447	Intelligence (MTAG)	4.000000e-10
GCST005316_472	Intelligence (MTAG)	9.000000e-09
GCST005316_473	Intelligence (MTAG)	6.000000e-09
GCST005316_476	Intelligence (MTAG)	3.000000e-11
GCST006269_1201	General cognitive ability	4.000000e-08
GCST006269_617	General cognitive ability	1.000000e-12
GCST006269_754	General cognitive ability	4.000000e-09
GCST006803_94	Schizophrenia	1.000000e-11
GCST006983_5	Attention deficit hyperactivity disorder or cannabis use	3.000000e-11
GCST006983_7	Attention deficit hyperactivity disorder or cannabis use	2.000000e-08
GCST007201_221	Schizophrenia	4.000000e-09
GCST007201_47	Schizophrenia	1.000000e-10
GCST007324_138	Adventurousness	1.000000e-10
GCST007325_78	General risk tolerance (MTAG)	7.000000e-10
GCST007543_14	Attention deficit hyperactivity disorder	1.000000e-08
GCST007603_23	Smoking initiation	7.000000e-11
GCST008526_68	Coffee consumption	4.000000e-06
GCST008759_29	Intake of total sugars	2.000000e-07
GCST008810_22	Smoking initiation (ever regular vs never regular)	3.000000e-12
GCST008971_115	Urate levels	8.000000e-06
GCST008972_21	Urate levels	5.000000e-08
GCST009524_159	Household income (MTAG)	5.000000e-12
GCST009524_169	Household income (MTAG)	1.000000e-08
GCST009524_260	Household income (MTAG)	3.000000e-11

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0004847	age at onset
EFO:0004784	self reported educational attainment
EFO:0004337	intelligence
EFO:0007585	Cannabis use
EFO:0008579	risk-taking behaviour
EFO:0005670	smoking initiation
EFO:0006781	coffee consumption measurement
EFO:0010158	sugar consumption measurement
EFO:0004531	urate measurement
EFO:0009695	household income
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3521 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 20,825 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL169	URSOLIC ACID	2	20,825

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

GtoPdb / IUPHAR curated pharmacology

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

Target class: catalytic receptor — Receptor tyrosine phosphatase (RTP) family

Most potent curated ligand interactions (1 total), top 1:

Ligand	Action	Affinity	Parameter
illudalic acid	Inhibition	5.89	pIC50

Binding affinities (BindingDB)

2 measured of 22 human assays (22 total across all organisms); most potent 2 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
Sodium orthovanadate (SOV)	IC50	25.4 nM
US8987474, NSC-87877	IC50	84500 nM	US-8987474: Inhibition of Shp2/PTPN11 protein tyrosine phosphatase by NSC-87877, NSC-117199 and their analogs

ChEMBL bioactivities

60 potent at pChembl≥5 of 108 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.18	IC50	66	nM	ILLUDALIC ACID
6.42	IC50	380	nM	CHEMBL564699
6.42	IC50	382.3	nM	CHEMBL556636
6.39	IC50	410	nM	OXALYLAMINOBENZOIC ACID
6.38	IC50	420	nM	CHEMBL324232
6.34	IC50	458.3	nM	CHEMBL549372
6.31	IC50	493	nM	CHEMBL556076
6.20	IC50	624.7	nM	CHEMBL550662
6.16	IC50	690	nM	CHEMBL200117
6.12	IC50	765.3	nM	CHEMBL570779
5.89	Ki	1300	nM	CHEMBL324968
5.89	IC50	1300	nM	ILLUDALIC ACID
5.88	IC50	1323	nM	CHEMBL1242458
5.85	IC50	1400	nM	SODIUM ORTHOVANAD
5.82	IC50	1530	nM	CHEMBL518277
5.82	IC50	1500	nM	CHEMBL108721
5.80	Ki	1600	nM	CHEMBL4077342
5.71	IC50	1941	nM	CHEMBL564124
5.70	IC50	1981	nM	CHEMBL1242827
5.68	IC50	2100	nM	ILLUDALIC ACID
5.68	IC50	2067	nM	CHEMBL1242553
5.68	IC50	2102	nM	CHEMBL1242826
5.68	IC50	2065	nM	CHEMBL1241469
5.67	IC50	2144	nM	CHEMBL1242643
5.62	IC50	2375	nM	CHEMBL556914
5.62	IC50	2386	nM	CHEMBL562469
5.60	IC50	2490	nM	CHEMBL51447
5.58	IC50	2647	nM	CHEMBL1242736
5.57	IC50	2686	nM	CHEMBL1242457
5.55	IC50	2846	nM	CHEMBL557393
5.54	IC50	2872	nM	CHEMBL1242552
5.53	IC50	2942	nM	CHEMBL1242642
5.52	IC50	2989	nM	CHEMBL1242362
5.49	IC50	3250	nM	CHEMBL365490
5.49	IC50	3248	nM	CHEMBL1242735
5.48	IC50	3285	nM	CHEMBL564439
5.45	IC50	3574	nM	CHEMBL1241314
5.43	IC50	3752	nM	CHEMBL1242363
5.42	IC50	3800	nM	URSOLIC ACID
5.39	IC50	4072	nM	CHEMBL554726
5.36	IC50	4368	nM	CHEMBL551671
5.33	IC50	4658	nM	CHEMBL562135
5.30	IC50	4982	nM	CHEMBL562468
5.30	IC50	5061	nM	CHEMBL556913
5.27	IC50	5360	nM	CHEMBL4164960
5.23	IC50	5912	nM	CHEMBL550462
5.23	IC50	5858	nM	CHEMBL557655
5.23	IC50	5859	nM	CHEMBL557861
5.22	IC50	5982	nM	CHEMBL562392
5.19	IC50	6469	nM	CHEMBL549505

PubChem BioAssay actives

59 with measured affinity, of 714 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
3,6-dihydroxy-8,8-dimethyl-1-oxo-3,4,7,9-tetrahydrocyclopenta[h]isochromene-5-carbaldehyde	2139793: Covalent inhibition of wildtype LAR catalytic domain D1 (unknown origin)	ic50	0.0660	uM
(3S)-6-[5-(2,2-dimethyl-1,3-dithiolan-4-yl)pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	0.3800	uM
(3S)-7-[5-(2,2-dimethyl-1,3-dithiolan-4-yl)pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	0.3823	uM
2-[2-ethyl-4-[[(2R)-4-[4-(3-hydroxy-2-methoxycarbonylphenoxy)butyl]-3,6-dioxopiperazin-2-yl]methyl]-N-oxaloanilino]benzoic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	0.4100	uM
(2R)-2-[2,6-dibromo-4-(6-bromonaphtho[3,2-b][1]benzofuran-11-yl)phenoxy]-3-phenylpropanoic acid	165327: The compound was tested in vitro for the inhibitory activity against LAR (human Protein-tyrosine phosphatase F)	ic50	0.4200	uM
(3S)-7-[3-(2,2-dimethyl-1,3-dithiolan-4-yl)propanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	0.4583	uM
(3S)-6-[3-(2,2-dimethyl-1,3-dithiolan-4-yl)propanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	0.4930	uM
(3S)-7-(4-thiophen-2-ylbutanoylamino)-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	0.6247	uM
2-[4-[7-(4-tetradecylbenzoyl)cyclopenta[d]oxazin-4-yl]phenoxy]acetic acid	259930: Inhibitory activity against LAR protein tyrosine phosphatase	ic50	0.6900	uM
(3S)-6-(4-thiophen-2-ylbutanoylamino)-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	0.7653	uM
3-[5-[[2-acetamido-3-[4-(2-carboxy-N-oxaloanilino)naphthalen-1-yl]propanoyl]amino]pentoxy]naphthalene-2-carboxylic acid	342509: Inhibition of LAR	ki	1.3000	uM
8-[2-(4-methylphenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	1.3230	uM
2-[2,6-dibromo-4-(6-bromonaphtho[3,2-b][1]benzothiol-11-yl)phenoxy]acetic acid	165327: The compound was tested in vitro for the inhibitory activity against LAR (human Protein-tyrosine phosphatase F)	ic50	1.5000	uM
3-hydroxy-6-methoxy-8,8-dimethyl-1-oxo-3,4,7,9-tetrahydrocyclopenta[h]isochromene-5-carbaldehyde	342510: Inhibition of human recombinant LAR	ic50	1.5300	uM
[fluoro-[4-[2-fluoro-3-[(2,4,5-trichlorophenyl)methyl]phenyl]phenyl]-morpholin-4-ylsulfonylmethyl]phosphonic acid	1477075: Inhibition of LAR (unknown origin) using pNPP as substrate preincubated for 5 mins followed by substrate addition measured for 20 mins by spectrophotometric analysis	ki	1.6000	uM
(3S)-7-[5-[(3R)-dithiolan-3-yl]pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	1.9410	uM
8-[2-[4-[(E)-2-carboxyethenyl]phenyl]-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	1.9810	uM
8-[2-[3-[(E)-2-carboxyethenyl]phenyl]-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.0650	uM
8-[2-(4-piperidin-1-ylphenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.0670	uM
8-[2-(3-iodophenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.1020	uM
8-[2-[4-(2,6-dimethylmorpholin-4-yl)phenyl]-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.1440	uM
(3S)-7-[5-(dithiolan-3-yl)pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	2.3750	uM
(3S)-6-[5-[(3R)-dithiolan-3-yl]pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	2.3860	uM
4-phenylnaphthalene-1,2-dione	99955: In vitro inhibitory activity against recombinant human LAR using fluorescein diphosphate (FDP) as a substrate	ic50	2.4900	uM
8-[2-(4-iodophenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.6470	uM
8-[2-(4-aminophenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.6860	uM
(3S)-6-[5-(dithiolan-3-yl)pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	2.8460	uM
8-[2-(4-nitrophenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.8720	uM
8-[2-(4-morpholin-4-ylphenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.9420	uM
8-[2-(4-pyrrolidin-1-ylphenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	2.9890	uM
8-[2-(4-carboxyphenyl)-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	3.2480	uM
(2S)-2-[4-[4-(2-benzyl-1-benzofuran-3-yl)phenyl]phenoxy]-3-phenylpropanoic acid	1942817: Inhibition of LAR (unknown origin)	ic50	3.2500	uM
(2S)-3-[4-[5-[(3R)-dithiolan-3-yl]pentanoylamino]phenyl]-2-ethoxypropanoic acid	429210: Inhibition of LAR	ic50	3.2850	uM
8-[2-[3,5-dibromo-4-[(2S)-2-carboxy-3-phenylpropanoyl]phenyl]-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	3.5740	uM
8-[2-[4-(dimethylamino)phenyl]-1,3-thiazol-4-yl]dibenzofuran-4-carboxylic acid	510870: Inhibition of human recombinant LAR after 30 mins by spectrophotometry	ic50	3.7520	uM
(1S,2R,4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-hydroxy-1,2,6a,6b,9,9,12a-heptamethyl-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydro-1H-picene-4a-carboxylic acid	687543: Inhibition of human recombinant LAR expressed in Escherichia coli TB1 using p-nitrophenyl phosphate as substrate after 1 hr	ic50	3.8000	uM
(3S)-6-[5-[(4R)-1,3-dithian-4-yl]pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	4.0720	uM
(3S)-7-[5-[(4R)-1,3-dithian-4-yl]pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	4.3680	uM
(2S)-3-[4-[5-[(3R)-dithiolan-3-yl]pentanoylamino]phenyl]-2-methoxypropanoic acid	429210: Inhibition of LAR	ic50	4.6580	uM
(3S)-6-[3-(2,2-diphenyl-1,3-dithiolan-4-yl)propanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	4.9820	uM
(3S)-7-[3-(2,2-diphenyl-1,3-dithiolan-4-yl)propanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	5.0610	uM
methyl 5-[[2,5-diethoxy-4-(methanesulfonamido)phenyl]methylcarbamoylamino]-2-ethoxybenzoate	1351468: Inhibition of human GST-tagged LAR D1 (1275 to 1613 residues) expressed in Escherichia coli BL21-CondenPlus (DE3) using pNNP as substrate	ic50	5.3600	uM
(3S)-7-[5-[(3R)-dithiolan-3-yl]pentanoylamino]-1-oxo-3,4-dihydroisochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	5.8580	uM
(2S)-2-butoxy-3-[4-[5-[(3R)-dithiolan-3-yl]pentanoylamino]phenyl]propanoic acid	429210: Inhibition of LAR	ic50	5.8590	uM
(3S)-7-(5-thiophen-2-ylpentanoylamino)-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	5.9120	uM
(2S)-3-[4-[5-[(3R)-dithiolan-3-yl]pentanoylamino]phenyl]-2-propoxypropanoic acid	429210: Inhibition of LAR	ic50	5.9820	uM
(3S)-7-[5-[(4S)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	6.4690	uM
5-[[2,5-diethoxy-4-(methanesulfonamido)phenyl]methylcarbamoylamino]-2-ethoxy-N-(4-methylphenyl)benzamide	1351468: Inhibition of human GST-tagged LAR D1 (1275 to 1613 residues) expressed in Escherichia coli BL21-CondenPlus (DE3) using pNNP as substrate	ic50	6.9500	uM
(3S)-7-[5-[(4R)-2,2-diphenyl-1,3-dithian-4-yl]pentanoylamino]-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	7.0260	uM
(3S)-6-(5-thiophen-2-ylpentanoylamino)-3,4-dihydro-1H-isochromene-3-carboxylic acid	429210: Inhibition of LAR	ic50	7.0340	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Cisplatin	decreases expression, affects cotreatment, affects expression	3
Tretinoin	decreases expression	3
bisphenol A	decreases methylation, decreases expression, affects cotreatment	2
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
cobaltous chloride	decreases expression	2
chloropicrin	decreases expression	2
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	2
Cyclosporine	decreases expression	2
Aflatoxin B1	affects methylation, increases methylation	2
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
terbufos	increases methylation	1
trichostatin A	increases expression	1
arsenite	affects binding, decreases reaction	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
sulindac sulfide	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
coumarin	increases phosphorylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
tamibarotene	decreases expression	1
azoxystrobin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
deguelin	decreases expression	1
2-(oxalylamino)benzoic acid	decreases activity	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
thifluzamide	decreases expression	1

ChEMBL screening assays

136 unique, capped per target: 135 binding, 1 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1038655	Binding	Inhibition of membrane proximal catalytic domain of LAR	Thiazolidinedione derivatives as PTP1B inhibitors with antihyperglycemic and antiobesity effects. — Bioorg Med Chem Lett
CHEMBL812685	Functional	Inhibitory activity against phosphatase (SPH-2) at a concentration of 100 uM	Modification of the N-terminus of peptidomimetic protein tyrosine phosphatase 1B (PTP1B) inhibitors: identification of analogues with cellular activity. — Bioorg Med Chem Lett

Cellosaurus cell lines

2 cell lines: 1 transformed cell line, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3FC	Abcam HEK293T PTPRF KO	Transformed cell line	Female
CVCL_E1E4	Ubigene U-251 MG PTPRF KO	Cancer cell line	Male

Clinical trials (associated diseases)

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