PTPRCAP

Summary

PTPRCAP (protein tyrosine phosphatase receptor type C associated protein, HGNC:9667) is a protein-coding gene on chromosome 11q13.2, encoding Protein tyrosine phosphatase receptor type C-associated protein (Q14761).

The protein encoded by this gene was identified as a transmembrane phosphoprotein specifically associated with tyrosine phosphatase PTPRC/CD45, a key regulator of T- and B-lymphocyte activation. The interaction with PTPRC may be required for the stable expression of this protein.

Source: NCBI Gene 5790 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 1 total
• Druggable target: yes
• MANE Select transcript: NM_005608

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9667
Approved symbol	PTPRCAP
Name	protein tyrosine phosphatase receptor type C associated protein
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	LPAP, CD45-AP
Ensembl gene	ENSG00000213402
Ensembl biotype	protein_coding
OMIM	601577
Entrez	5790

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000326294

RefSeq mRNA: 1 — MANE Select: NM_005608 NM_005608

CCDS: CCDS8163

Canonical transcript exons

ENST00000326294 — 2 exons

Exon	Start	End
ENSE00001288436	67435510	67436350
ENSE00001422363	67437617	67437682

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 99.43.

FANTOM5 (CAGE): breadth broad, TPM avg 74.5959 / max 3229.1796, expressed in 367 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120925	73.2190	365
120924	1.3004	132
120922	0.0647	48
120923	0.0118	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	99.43	gold quality
spleen	UBERON:0002106	98.64	gold quality
blood	UBERON:0000178	97.34	gold quality
lymph node	UBERON:0000029	97.06	gold quality
vermiform appendix	UBERON:0001154	95.86	gold quality
mucosa of transverse colon	UBERON:0004991	93.09	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.66	gold quality
bone marrow cell	CL:0002092	90.13	gold quality
small intestine	UBERON:0002108	88.35	gold quality
bone marrow	UBERON:0002371	87.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.59	gold quality
right uterine tube	UBERON:0001302	83.73	gold quality
leukocyte	CL:0000738	83.63	gold quality
duodenum	UBERON:0002114	82.88	gold quality
fundus of stomach	UBERON:0001160	82.12	gold quality
monocyte	CL:0000576	82.10	gold quality
upper lobe of left lung	UBERON:0008952	81.81	gold quality
transverse colon	UBERON:0001157	81.30	gold quality
right lobe of liver	UBERON:0001114	80.03	gold quality
body of stomach	UBERON:0001161	80.02	gold quality
right lobe of thyroid gland	UBERON:0001119	79.93	gold quality
left uterine tube	UBERON:0001303	79.15	gold quality
right coronary artery	UBERON:0001625	78.67	gold quality
right lung	UBERON:0002167	78.30	gold quality
intestine	UBERON:0000160	78.29	gold quality
saliva-secreting gland	UBERON:0001044	77.71	gold quality
minor salivary gland	UBERON:0001830	77.51	gold quality
apex of heart	UBERON:0002098	77.51	gold quality
omental fat pad	UBERON:0010414	77.20	gold quality
tonsil	UBERON:0002372	77.10	gold quality

Single-cell (SCXA)

Detected in 29 experiment(s), a significant marker in 22.

Experiment	Marker?	Max mean expression
E-HCAD-15	yes	1113.17
E-MTAB-9801	yes	194.35
E-HCAD-4	yes	139.00
E-HCAD-1	yes	135.41
E-MTAB-6701	yes	112.30
E-MTAB-10553	yes	67.05
E-CURD-122	yes	62.36
E-MTAB-8410	yes	46.10
E-CURD-88	yes	40.82
E-MTAB-6678	yes	38.93
E-HCAD-10	yes	37.61
E-MTAB-10287	yes	35.81
E-GEOD-135922	yes	32.57
E-HCAD-9	yes	28.89
E-MTAB-9067	yes	25.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting PTPRCAP, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-6811-3P	98.62	66.54	944
HSA-MIR-4642	97.52	67.60	916
HSA-MIR-656-5P	96.82	67.67	372

Literature-anchored findings (GeneRIF, showing 4)

• We analysed the C77G polymorphism in multiple sclerosis (MS) patients from the genetically homogeneous population of Sardinia. CD45 did not contribute to development of the disease in Sardinian MS. (PMID:15372250)
• Data show that the minor allele of rs869736 in the PTPRCAP promoter is associated with increased susceptibility to diffuse-type gastric cancer by increasing PTPRCAP expression. (PMID:20019842)
• results support the model: following phorbol 12-myristate 13-acetate (PMA) or TCR/CD3 activation of T cells, LPAP is rapidly dephosphorylated at Ser-99 and Ser-172 and slowly phosphorylated at Ser-163. Ser-153 exhibited a high basal level of phosphorylation in both resting and activated cells (PMID:28827793)
• LPAP is a substrate for protein kinase CK2 that phosphorylates it at Ser153, presumably ensuring LPAP resistance to degradation. (PMID:30482149)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ptprcap	ENSMUSG00000045826
rattus_norvegicus	Ptprcap	ENSRNOG00000021724

Protein

Protein identifiers

Protein tyrosine phosphatase receptor type C-associated protein — Q14761 (reviewed: Q14761)

Alternative names: CD45-associated protein, Lymphocyte phosphatase-associated phosphoprotein

All UniProt accessions (1): Q14761

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with CD45/PTPRC.

Subcellular location. Membrane.

Post-translational modifications. Phosphorylated on tyrosine residues.

RefSeq proteins (1): NP_005599* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016553	PTPRCAP	Family

Pfam: PF15713

UniProt features (7 total): modified residue 2, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14761-F1	58.14	0.08

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): 99, 153

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 220 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, VERHAAK_AML_WITH_NPM1_MUTATED_DN, MODULE_45, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, MODULE_16, chr11q13, GGAANCGGAANY_UNKNOWN, BRN2_01, MODULE_171, ZHAN_MULTIPLE_MYELOMA_LB_DN, MODULE_88, WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN

GO Biological Process (1): defense response (GO:0006952)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to stress	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

786 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTPRCAP	PTPRC	P08575	971
PTPRCAP	LCK	P06239	683
PTPRCAP	CCND1	P24385	490
PTPRCAP	CD4	P01730	472
PTPRCAP	H1-4	P10412	460
PTPRCAP	CTSW	P56202	450
PTPRCAP	H1-6	P22492	442
PTPRCAP	USP47	Q96K76	438
PTPRCAP	KRT9	P35527	437
PTPRCAP	H1-2	P16403	415
PTPRCAP	TFRC	P02786	410
PTPRCAP	KRT1	P04264	409
PTPRCAP	DCD	P58461	409
PTPRCAP	RPS2	P15880	399
PTPRCAP	RPS6	P08227	394

IntAct

9 interactions, top by confidence:

A	B	Type	Score
PTPRCAP	DCDC2	psi-mi:“MI:0915”(physical association)	0.560
TSC22D1	KRT1	psi-mi:“MI:0914”(association)	0.460
PTPRCAP	MYO1C	psi-mi:“MI:0914”(association)	0.350
PTPRCAP	PGRMC1	psi-mi:“MI:0914”(association)	0.350
PTPRCAP	DCDC2	psi-mi:“MI:0915”(physical association)	0.000
PTPRCAP		psi-mi:“MI:0915”(physical association)	0.000
PTPRCAP	EEF1A1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): MYO1C (Affinity Capture-MS), TPM4 (Affinity Capture-MS), PTPRCAP (Affinity Capture-Western), LCK (Affinity Capture-Western), EEF1A1 (Two-hybrid), PTPRCAP (Two-hybrid), PTPRCAP (Reconstituted Complex), C1orf27 (Affinity Capture-MS), STX5 (Affinity Capture-MS), UFSP2 (Affinity Capture-MS), CMTM6 (Affinity Capture-MS), PGRMC1 (Affinity Capture-MS), STX10 (Affinity Capture-MS), OSBPL8 (Affinity Capture-MS), GOSR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7

Diamond homologs: Q14761, Q64697

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CSNK2A1	“up-regulates quantity by stabilization”	PTPRCAP	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

199 predictions. Top by Δscore:

Variant	Effect	Δscore
11:67436349:GCC:G	acceptor_loss	0.9700
11:67436350:CCTG:C	acceptor_loss	0.9700
11:67436351:C:CG	acceptor_loss	0.9700
11:67436352:T:A	acceptor_loss	0.9700
11:67437611:GCTT:G	donor_loss	0.9700
11:67437613:TTAC:T	donor_loss	0.9700
11:67437614:TACC:T	donor_loss	0.9700
11:67436351:C:CC	acceptor_gain	0.9500
11:67437615:A:AC	donor_gain	0.9300
11:67437616:C:CC	donor_gain	0.9300
11:67436347:GAGC:G	acceptor_gain	0.9200
11:67436346:AGAGC:A	acceptor_gain	0.9100
11:67436349:GC:G	acceptor_gain	0.9000
11:67436350:CC:C	acceptor_gain	0.9000
11:67437008:C:CA	donor_gain	0.8800
11:67436356:GGAGA:G	acceptor_loss	0.8500
11:67437615:AC:A	donor_gain	0.8400
11:67437616:CC:C	donor_gain	0.8400
11:67436354:TGGGA:T	acceptor_loss	0.8300
11:67436355:GGGAG:G	acceptor_loss	0.8300
11:67436361:C:CT	acceptor_loss	0.8100
11:67437164:C:CA	donor_gain	0.8000
11:67437313:C:CT	donor_gain	0.8000
11:67437616:CCA:C	donor_gain	0.8000
11:67437384:C:A	donor_gain	0.7900
11:67437066:T:C	donor_gain	0.7700
11:67436348:AGC:A	acceptor_gain	0.7500
11:67437383:T:TA	donor_gain	0.7400
11:67436356:G:T	acceptor_gain	0.7100
11:67436987:G:C	donor_gain	0.7100

AlphaMissense

1293 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:67435805:A:C	F183L	0.991
11:67435805:A:T	F183L	0.991
11:67435807:A:G	F183L	0.991
11:67435787:C:A	W189C	0.990
11:67435787:C:G	W189C	0.990
11:67436194:A:G	W54R	0.980
11:67436194:A:T	W54R	0.980
11:67435789:A:G	W189R	0.979
11:67435789:A:T	W189R	0.979
11:67435796:G:C	S186R	0.978
11:67435796:G:T	S186R	0.978
11:67435798:T:G	S186R	0.978
11:67435806:A:C	F183C	0.978
11:67435806:A:G	F183S	0.976
11:67436180:G:C	S58R	0.953
11:67436180:G:T	S58R	0.953
11:67436182:T:G	S58R	0.953
11:67436099:G:C	S85R	0.952
11:67436099:G:T	S85R	0.952
11:67436101:T:G	S85R	0.952
11:67435807:A:T	F183I	0.946
11:67435801:C:G	G185R	0.943
11:67436209:C:G	G49R	0.943
11:67436154:G:T	P67Q	0.934
11:67435800:C:T	G185D	0.932
11:67435737:A:G	L206P	0.931
11:67435743:G:A	T204I	0.929
11:67436161:A:C	Y65D	0.929
11:67435788:C:A	W189L	0.927
11:67435797:C:A	S186I	0.925

dbSNP variants (sampled 300 via entrez): RS1000306398 (11:67435820 ACTCAGCAGGGC>A), RS1001235173 (11:67438919 C>A,G,T), RS1001436161 (11:67437788 C>G,T), RS1001510902 (11:67437490 C>T), RS1001846227 (11:67436570 ACAGCTG>A), RS1002413848 (11:67439405 C>T), RS1003132261 (11:67437156 G>A,T), RS1003260668 (11:67436866 T>G), RS1005761369 (11:67436960 G>A), RS1005792555 (11:67436761 C>G,T), RS1006984046 (11:67436515 C>T), RS1007583552 (11:67436070 G>C), RS1008216582 (11:67438297 T>C), RS1008292987 (11:67438155 C>CA), RS1008755861 (11:67437374 T>C)

Disease associations

OMIM: gene MIM:601577 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009194_1	Ventral diencephalon volume	6.000000e-06
GCST010002_241	Refractive error	3.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4806 (SINGLE PROTEIN)

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

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
5-[3’-(1-adamantyl)-2-chloro-4’-hydroxy-4-biphenyl]-1H-tetrazole	IC50	1200 nM

ChEMBL bioactivities

3 potent at pChembl≥5 of 5 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.92	IC50	1200	nM	CHEMBL227622
5.64	IC50	2300	nM	CHEMBL376571
5.28	IC50	5300	nM	NORNUCIFERINE

PubChem BioAssay actives

2 with measured affinity, of 26 total; 2 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
2-(1-adamantyl)-4-[2-chloro-4-(2H-tetrazol-5-yl)phenyl]phenol	288593: Inhibition of CD45 PTP by fluorescence spectrometry	ic50	1.2000	uM
(5Z)-5-[[4-[3-(1-adamantyl)-4-hydroxyphenyl]-3-chlorophenyl]methylidene]-1,3-thiazolidine-2,4-dione	288593: Inhibition of CD45 PTP by fluorescence spectrometry	ic50	2.3000	uM

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Nickel	increases expression	2
GSK-J4	decreases expression	1
propionaldehyde	decreases expression	1
pentanal	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Aspirin	decreases expression	1
Vehicle Emissions	decreases expression	1
Calcitriol	decreases expression	1
Choline	affects expression	1
Cisplatin	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	increases expression	1
Estradiol	decreases expression	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Pantothenic Acid	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Gold Compounds	increases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	decreases expression	1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL655665	Binding	Compound was tested for inhibition of CD45 tyrosine phosphatase at a concentration of 10 uM in fluorometric assay using DiFMUP	Design and synthesis of phosphotyrosine mimetics. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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