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TPP2

gene
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Also known as TPPII

Summary

TPP2 (tripeptidyl peptidase 2, HGNC:12016) is a protein-coding gene on chromosome 13q33.1, encoding Tripeptidyl-peptidase 2 (P29144). Cytosolic tripeptidyl-peptidase that releases N-terminal tripeptides from polypeptides and is a component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway.

This gene encodes a mammalian peptidase that, at neutral pH, removes tripeptides from the N terminus of longer peptides. The protein has a specialized function that is essential for some MHC class I antigen presentation. The protein is a high molecular mass serine exopeptidase; the amino acid sequence surrounding the serine residue at the active site is similar to the peptidases of the subtilisin class rather than the trypsin class.

Source: NCBI Gene 7174 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): immunodeficiency 78 with autoimmunity and developmental delay (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 1
  • Clinical variants (ClinVar): 860 total — 17 pathogenic, 4 likely-pathogenic (top 4% of genes corpus-wide)
  • Regional missense constraint (gnomAD): 1 of 7 regions constrained (≈2% of expected missense variation)
  • GTEx eGene: eQTL in 16 tissues, sQTL in 11 (q < 0.05)
  • Phenotypes (HPO): 30
  • ChEMBL bioactivity: 1 clinical-phase molecule tested; no curated mechanism-of-action drug
  • Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.29 (highly constrained)
  • MANE Select transcript: NM_001330588

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12016
Approved symbolTPP2
Nametripeptidyl peptidase 2
Location13q33.1
Locus typegene with protein product
StatusApproved
AliasesTPPII
Ensembl geneENSG00000134900
Ensembl biotypeprotein_coding
OMIM190470
Entrez7174

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 15 retained_intron, 14 nonsense_mediated_decay, 13 protein_coding, 3 protein_coding_CDS_not_defined

MANE Select: ENST00000376052

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 2, TSL 3: 2, TSL 5: 3

ENST00000376052, ENST00000376065, ENST00000466153, ENST00000482393, ENST00000490010, ENST00000490420, ENST00000493770, ENST00000496126, ENST00000650757, ENST00000651448, ENST00000651544, ENST00000651748, ENST00000651823, ENST00000651921, ENST00000652033, ENST00000652308, ENST00000698381, ENST00000698382, ENST00000698383, ENST00000698384, ENST00000698385, ENST00000698386, ENST00000698387, ENST00000698388, ENST00000698389, ENST00000698390, ENST00000698391, ENST00000698392, ENST00000698393, ENST00000854161, ENST00000912746, ENST00000959512, ENST00001008644, ENST00001008645, ENST00001054861, ENST00001054862, ENST00001054863, ENST00001054864, ENST00001089795, ENST00001089796, ENST00001089797, ENST00001089798, ENST00001089799, ENST00001089800, ENST00001114176

RefSeq mRNA: 3 — MANE Select: NM_001330588 NM_001330588, NM_001367947, NM_003291

CCDS: CCDS81777, CCDS9502

Canonical transcript exons

ENST00000376052 — 30 exons

ExonStartEnd
ENSE00000917076102636224102636392
ENSE00001469250102651359102651397
ENSE00003973486102649408102649486
ENSE00003973488102644557102644673
ENSE00003973489102596986102597203
ENSE00003973490102643222102643376
ENSE00003973491102676296102676415
ENSE00003973492102648907102649151
ENSE00003973495102604793102604921
ENSE00003973497102627848102627924
ENSE00003973498102640270102640376
ENSE00003973499102616396102616500
ENSE00003973500102627012102627166
ENSE00003973501102638239102638315
ENSE00003973504102678227102679958
ENSE00003973505102674283102674490
ENSE00003973508102663648102663744
ENSE00003973509102664795102664925
ENSE00003973511102633950102634098
ENSE00003973513102622877102623040
ENSE00003973516102629482102629609
ENSE00003973517102646294102646390
ENSE00003973518102618722102618846
ENSE00003973519102647207102647344
ENSE00003973520102657056102657207
ENSE00003973521102635587102635702
ENSE00003973523102637082102637239
ENSE00003973524102644909102645009
ENSE00003973526102630096102630195
ENSE00003973527102614101102614196

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 97.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 45.2460 / max 531.6882, expressed in 1823 samples.

Highest expression (Bgee): testis, sperm, calcaneal tendon, male germ cell, colonic epithelium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

TPP2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 16 tissues and its splicing (sQTL) in 11 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 27 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Skin Not Sun Exposed Suprapubicsqtl8.3e-11-0.5113:102677662:C:T
Adipose Subcutaneoussqtl5.4e-10-0.4113:102659348:A:T
Whole Bloodeqtl3.4e-08+0.0913:102684075:A:T
Skin Sun Exposed Lower legsqtl3.4e-08-0.4113:102637059:A:G
Muscle Skeletaleqtl5.5e-08-0.1513:102727286:A:C
Breast Mammary Tissuesqtl5.1e-05-0.4013:102677662:C:T
Nerve Tibialsqtl5.9e-05-0.3213:102637059:A:G
Esophagus Gastroesophageal Junctioneqtl1.2e-04+0.1713:102598836:C:G
Thyroideqtl3.6e-04+0.1013:102614644:G:A
Cells EBV-transformed lymphocytessqtl3.7e-04-0.4713:102637059:A:G
Lungsqtl5.0e-04+0.4213:102602691:A:C
Testissqtl7.2e-04+0.3713:102672957:A:G
Colon Transverseeqtl9.0e-04+0.1413:102599006:G:A
Artery Tibialsqtl1.1e-03-0.2813:102659348:A:T
Testiseqtl1.7e-03+0.0913:102603875:T:TAGG
Ovarysqtl3.1e-03+0.7213:102645983:AGTT:A
Breast Mammary Tissueeqtl4.9e-03-0.1313:101972738:A:G
Artery Tibialeqtl6.8e-03+0.2013:102586116:T:C
Cells EBV-transformed lymphocyteseqtl8.3e-03+1.0713:102290730:G:A
Skin Not Sun Exposed Suprapubiceqtl1.2e-02-0.4313:103426877:A:T

FANTOM5 promoters

6 alternative TSS:

Promoter IDTPM avgSamples expressed
13591938.37671822
1359183.44971338
1359172.60651129
1359200.7449459
1359230.04086
1359240.02743

Top tissues by expression

showing 100 of 295 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453397.52gold quality
right testisUBERON:000453497.19gold quality
testisUBERON:000047396.48gold quality
spermCL:000001996.44gold quality
calcaneal tendonUBERON:000370196.35gold quality
male germ cellCL:000001594.98gold quality
colonic epitheliumUBERON:000039794.52gold quality
monocyteCL:000057694.41gold quality
mononuclear cellCL:000084294.24gold quality
rectumUBERON:000105294.04gold quality
leukocyteCL:000073894.03gold quality
adrenal tissueUBERON:001830393.79gold quality
tendonUBERON:000004393.68gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047393.39gold quality
hindlimb stylopod muscleUBERON:000425293.22gold quality
right uterine tubeUBERON:000130292.99gold quality
right lungUBERON:000216792.99gold quality
gastrocnemiusUBERON:000138892.98gold quality
muscle of legUBERON:000138392.93gold quality
right ovaryUBERON:000211892.80gold quality
ventricular zoneUBERON:000305392.74gold quality
right lobe of thyroid glandUBERON:000111992.68gold quality
left ovaryUBERON:000211992.66gold quality
seminal vesicleUBERON:000099892.65gold quality
left lobe of thyroid glandUBERON:000112092.52gold quality
upper lobe of left lungUBERON:000895292.47gold quality
bone marrow cellCL:000209292.35gold quality
mucosa of stomachUBERON:000119992.35gold quality
tibial nerveUBERON:000132392.32gold quality
thyroid glandUBERON:000204692.22gold quality
spleenUBERON:000210692.21gold quality
upper lobe of lungUBERON:000894892.06gold quality
cortical plateUBERON:000534391.98gold quality
body of uterusUBERON:000985391.92gold quality
right lobe of liverUBERON:000111491.89gold quality
body of pancreasUBERON:000115091.86gold quality
ganglionic eminenceUBERON:000402391.78gold quality
endocervixUBERON:000045891.77gold quality
granulocyteCL:000009491.76gold quality
lymph nodeUBERON:000002991.75gold quality
left uterine tubeUBERON:000130391.68gold quality
subcutaneous adipose tissueUBERON:000219091.66gold quality
ectocervixUBERON:001224991.63gold quality
small intestine Peyer’s patchUBERON:000345491.55gold quality
transverse colonUBERON:000115791.43gold quality
muscle organUBERON:000163091.37gold quality
adipose tissueUBERON:000101391.26gold quality
connective tissueUBERON:000238491.22gold quality
omental fat padUBERON:001041491.08gold quality
peritoneumUBERON:000235891.07gold quality
ovaryUBERON:000099291.06gold quality
adipose tissue of abdominal regionUBERON:000780891.06gold quality
vermiform appendixUBERON:000115491.04gold quality
gall bladderUBERON:000211091.03gold quality
skin of abdomenUBERON:000141691.00gold quality
bone marrowUBERON:000237190.88gold quality
cerebellar hemisphereUBERON:000224590.81gold quality
right hemisphere of cerebellumUBERON:001489090.72gold quality
cerebellar cortexUBERON:000212990.70gold quality
skin of legUBERON:000151190.67gold quality
diaphragmUBERON:000110390.66gold quality
left coronary arteryUBERON:000162690.63gold quality
corpus epididymisUBERON:000435990.61gold quality
tibial arteryUBERON:000761090.58gold quality
oocyteCL:000002390.57gold quality
popliteal arteryUBERON:000225090.56gold quality
descending thoracic aortaUBERON:000234590.50gold quality
muscle layer of sigmoid colonUBERON:003580590.46gold quality
small intestineUBERON:000210890.45gold quality
endometriumUBERON:000129590.44gold quality
right atrium auricular regionUBERON:000663190.42gold quality
colonUBERON:000115590.40gold quality
intestineUBERON:000016090.39gold quality
vaginaUBERON:000099690.36gold quality
pancreasUBERON:000126490.32gold quality
bronchial epithelial cellCL:000232890.29gold quality
corpus callosumUBERON:000233690.28gold quality
large intestineUBERON:000005990.25gold quality
minor salivary glandUBERON:000183090.23gold quality
aortaUBERON:000094790.19gold quality
metanephros cortexUBERON:001053390.14gold quality
coronary arteryUBERON:000162190.13gold quality
body of stomachUBERON:000116190.10gold quality
caecumUBERON:000115390.01gold quality
sigmoid colonUBERON:000115989.92gold quality
right coronary arteryUBERON:000162589.91gold quality
stomachUBERON:000094589.86gold quality
esophagogastric junction muscularis propriaUBERON:003584189.86gold quality
uterusUBERON:000099589.83gold quality
thoracic aortaUBERON:000151589.79gold quality
ascending aortaUBERON:000149689.78gold quality
embryoUBERON:000092289.77gold quality
female reproductive systemUBERON:000047489.75gold quality
cardiac atriumUBERON:000208189.70gold quality
triceps brachiiUBERON:000150989.66gold quality
lower esophagusUBERON:001347389.61gold quality
lower esophagus muscularis layerUBERON:003583389.61gold quality
zone of skinUBERON:000001489.54gold quality
liverUBERON:000210789.39gold quality
skeletal muscle tissueUBERON:000113489.29gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-134144yes27.56
E-ANND-3yes10.13
E-GEOD-93593yes5.07
E-GEOD-110499no378.94

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Testistissue45.8high
Bone marrowtissue29.0low
Caudate putamentissue27.4
Cerebral cortextissue26.6high
Somatosensory cortextissue26.6
Occipital cortextissue26.4
Cerebellumtissue25.9high
Frontal cortextissue25.1
Motor cortextissue24.7
Hippocampal formationtissue24.4
Retrosplenial and cingulate cortextissue23.6
Olfactory bulbtissue23.4
Prefrontal cortextissue22.7
Putamentissue22.7
Retrosplenial cortextissue22.3
Superior colliculitissue22.1
Temporal cortextissue22.0
Ponstissue21.8
Thalamustissue21.4
Entorhinal cortextissue21.4
Skeletal muscletissue21.3medium
Insular cortextissue21.2
Midbraintissue20.5
Medulla oblongatatissue20.2
Ventral forebraintissue20.2
Amygdalatissue19.6
Tonguetissue19.5
Septumtissue19.3
Basal gangliatissue18.9high
Hypothalamustissue18.9
Periaqueductal graytissue18.6
Substantia nigratissue18.3
Livertissue17.2high
Spinal cordtissue17.2
Corpus callosumtissue17.1
Thyroid glandtissue16.3medium
Choroid plexustissue15.9
Rectumtissue15.3high
Lymph nodetissue14.8high
Seminal vesicletissue14.8medium
Placentatissue14.7high
Spleentissue14.6low
Retinatissue14.4
Nucleus accumbenstissue14.0
Tonsiltissue13.9medium
Thymustissue13.6
Breasttissue13.5medium
Epididymistissue13.5high
Endometrium 1tissue12.3medium
Lungtissue12.0medium
Colontissue11.8high
Postcentral gyrustissue11.8
Heart muscletissue11.6medium
Locus coeruleustissue11.4
Hippocampustissue11.2high
Urinary bladdertissue11.1high
Appendixtissue11.1high
Cervixtissue11.0medium
Smooth muscletissue10.6low
Esophagustissue10.3medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Dorsal hippocampus (24.4), Ventral hippocampus (22.6), Subiculum (21.0), Cerebellar cortex (20.4), Parieto-temporal junction (white matter) (20.4).

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.29, missense Z 4.58 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000376052 splits into 7 regions with different missense tolerance; 1 is missense-constrained (≈2% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
13:102,597,039–102,627,872300 / 398.30.75no
13:102,627,873–102,634,07563 / 165.70.38no
13:102,634,076–102,647,231325 / 463.70.70no
13:102,647,232–102,647,3004 / 24.40.16yes (p 3.5e-05)
13:102,647,301–102,664,848179 / 274.70.65no
13:102,664,849–102,676,303116 / 117.30.99no
13:102,676,304–102,678,31341 / 78.30.52no

Literature-anchored findings (GeneRIF, showing 20)

  • the promoter could be localized to a 215 bp fragment upstream of the initiation codon. (PMID:15716107)
  • TPPII appears to promote malignant cell growth by allowing exit from mitosis and the survival of cells with severe mitotic spindle damage. (PMID:16762321)
  • TPP2 plays a specialized role in antigen processing and one that is not essential for the generation of most presented peptides. (PMID:16849449)
  • This investigation reveals that TPP II expression could be regulated through both positive and negative regulatory elements. (PMID:17343995)
  • Expression of mRNA for MuRF-1 increased approximately 3-fold at 10 days without changes in MAFbx or tripeptidyl peptidase II mRNA, but all decreased between 10 and 21 days of muscle disuse. (PMID:17901116)
  • Results indicate that TPPII is dispensable for the generation of proteasome-dependent HLA class I ligands and, the enzyme is not involved significantly in generating the proteasome-independent HLA-B27-bound peptide repertoire. (PMID:18286573)
  • Cross-presentation of NY-ESO-1/ISCOMATRIX cancer vaccine was proteasome independent and requires the cytosolic protease tripeptidyl peptidase II. (PMID:19155470)
  • MHC class I-restricted LMP1 epitopes studied in this work are two of very few epitopes known to date to be processed proteasome independently by tripeptidyl peptidase II. (PMID:19587004)
  • Results suggest an important function of TPPII in the maintenance of viral growth and may have implications for anti-viral therapy. (PMID:21134372)
  • Current knowledge about TPPII with a focus on structural aspects. (PMID:21771670)
  • Previously unknown differences between TPP II orthologues and subtilisin as well as features that might be conserved within the entire family of subtilisin-like serine peptidases. (PMID:22266401)
  • obtained a 3D structure of the human TPPII (PMID:22483107)
  • Study showed that overexpression of Tripeptidyl peptidase II (TPP2) occurs frequently during oral carcinogenesis and might be associated with the progression of Oral Squamous Cell Carcinoma (OSCC) via Spindle Assembly Checkpoint(SAC) activation. (PMID:22986808)
  • TPPII, MYBBP1A and CDK2 form a protein-protein interaction network. (PMID:25303791)
  • Early-onset Evans syndrome, immunodeficiency, and premature immunosenescence associated with TPP2 deficiency have been described in two consanguineous siblings. (PMID:25414442)
  • Study found that autosomal recessive TPP2 mutations cause recurrent infections, autoimmunity, and neurodevelopmental delay in humans. (PMID:25525876)
  • TPP2 mediates many important cellular functions by controlling ERK1 and ERK2 phosphorylation. (PMID:26041847)
  • Novel interactions of TPPII, p53, and SIRT7 presented in this study might contribute to the knowledge of the regulatory effects of these proteins on apoptotic pathways and to the understanding mechanisms of aging and lifespan regulation. (PMID:26169984)
  • Immune deficiency, autoimmune disease and intellectual disability: A pleiotropic disorder caused by biallelic variants in the TPP2 gene. (PMID:33586135)
  • Unveiling a novel serpinB2-tripeptidyl peptidase II signaling axis during senescence. (PMID:35466366)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotpp2ENSDARG00000078751
mus_musculusTpp2ENSMUSG00000041763
rattus_norvegicusTpp2ENSRNOG00000011194
drosophila_melanogasterTppIIFBGN0020370
caenorhabditis_elegansWBGENE00017686

Paralogs (9): PCSK5 (ENSG00000099139), PCSK4 (ENSG00000115257), PCSK2 (ENSG00000125851), PCSK6 (ENSG00000140479), FURIN (ENSG00000140564), MBTPS1 (ENSG00000140943), PCSK7 (ENSG00000160613), PCSK9 (ENSG00000169174), PCSK1 (ENSG00000175426)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:102724) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 34 distinct phenotype terms.

Mouse phenotype (MP)Records
enlarged spleen2
decreased leukocyte cell number1
extramedullary hematopoiesis1
focal hair loss1
abnormal spleen morphology1
enlarged lymph nodes1
abnormal immune system cell morphology1
weight loss1
disheveled coat1
abnormal antigen presentation1
abnormal level of surface class I molecules1
premature death1
abnormal immune system organ morphology1
abnormal cell cycle1
thymus atrophy1
increased autoantibody level1
premature aging1
abnormal lymphocyte physiology1
increased anti-nuclear antigen antibody level1
increased B cell number1
increased T cell number1
decreased T cell number1
abnormal cytotoxic T cell physiology1
increased double-negative T cell number1
decreased double-positive T cell number1

+9 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Bos taurusA5PK3996.6%Diamond
Arabidopsis thalianaF4JVN665.5%Diamond
Oryza sativa Japonica GroupQ6ESI765.4%Diamond
Schizosaccharomyces pombe 972h-Q9UT0535.0%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
FGF14-AS1ncRNA100874081
METTL21Cprotein-coding196541
FGF14protein-coding2259
FGF14-IT1ncRNA283480
FGF14-AS2ncRNA283481
LRTM3protein-coding643677
TEX30protein-coding93081
MIR2681ncRNA100616110
MIR4705ncRNA100616239
LINC00411ncRNA100874161
NALCN-AS1ncRNA100885778
NALCNprotein-coding259232
ITGBL1protein-coding9358

Protein

Protein identifiers

Tripeptidyl-peptidase 2 — P29144 (reviewed: P29144)

Alternative names: Tripeptidyl aminopeptidase, Tripeptidyl-peptidase II

All UniProt accessions (10): A0A494C0A3, A0A494C0U1, A0A494C0X4, A0A494C159, A0A494C1B8, A0A494C1L2, A0A494C1S4, A0A494C1S6, P29144, Q5VZU9

UniProt curated annotations — full annotation on UniProt →

Function. Cytosolic tripeptidyl-peptidase that releases N-terminal tripeptides from polypeptides and is a component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It plays an important role in intracellular amino acid homeostasis. Stimulates adipogenesis.

Subcellular location. Cytoplasm. Nucleus.

Disease relevance. Immunodeficiency 78 with autoimmunity and developmental delay (IMD78) [MIM:619220] An autosomal recessive disorder characterized by immune dysregulation, increased susceptibility to bacterial, viral and fungal infections, recurrent sinopulmonary or skin infections, and autoimmune abnormalities including hemolytic anemia and autoimmune cytopenias. Patients also have global developmental delay with speech delay and variable intellectual disability. Disease onset is in infancy or early childhood. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. The limitation of proteolytic products to tripeptides is achieved by tailoring the size of the substrate-binding cleft: the two negatively charged residues Glu-305 and Glu-331 that are blocking position P4 limit the number of residues that can be accommodated in the binding cleft and thus create a molecular ruler. At the same time, they orient substrates so that the tripeptides are removed exclusively from the N-terminus.

Similarity. Belongs to the peptidase S8 family.

RefSeq proteins (3): NP_001317517, NP_001354876, NP_003282 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000209Peptidase_S8/S53_domDomain
IPR015500Peptidase_S8_subtilisin-relFamily
IPR022229TPPII_Ig-like-2Domain
IPR022232TPPII_C_artDomain
IPR022398Peptidase_S8_His-ASActive_site
IPR023828Peptidase_S8_Ser-ASActive_site
IPR034051TPP_II_domainDomain
IPR036852Peptidase_S8/S53_dom_sfHomologous_superfamily
IPR046939TPPII_C_sfHomologous_superfamily
IPR046940TPPII_Ig-like_sfHomologous_superfamily
IPR048383TPPII_Ig-like-1Domain
IPR048384TPPII_GBDDomain
IPR050131Peptidase_S8_subtilisin-likeFamily

Pfam: PF00082, PF12580, PF12583, PF21223, PF21316

Enzyme classification (BRENDA)

  • EC 3.4.14.10 — tripeptidyl-peptidase II (BRENDA: 16 organisms, 80 substrates, 143 inhibitors, 120 Km, 111 kcat entries)

Substrate kinetics (BRENDA)

9 substrates with measured Km, best-characterized 9. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
L-ALA-L-ALA-L-ALA 4-NITROANILIDE0.008–2030
L-ALA-L-ALA-L-PHE 4-NITROANILIDE0.017–3030
ALA-ALA-PHE-4-NITROANILIDE0.012–0.8825
ALA-ALA-ALA-4-NITROANILIDE0.0036–0.1324
ALA-ALA-PHE-7-AMIDO-4-METHYLCOUMARIN0.11–0.473
ARG-ARG-ALA-(PHOSPHO)SER-VAL-ALA0.008–0.0153
L-ALA-L-ALA-L-PHE-P-NITROANILIDE0.013–13
ALA-ALA-PHE 4-METHYLCOUMARIN 7-AMIDE0.0161
ALA-ALA-PHE-P-NITROANILIDE0.021

UniProt features (16 total): sequence variant 4, modified residue 3, active site 3, initiator methionine 1, chain 1, sequence conflict 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P29144-F191.980.80

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Hydrolases, Peptidases, Serine-type peptidases, Predicted intracellular proteins, Plasma proteins, Disease related genes, Potential drug targets, Human disease related genes, Primary immunodeficiency

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nuclear bodies

Antibody reliability (HPA): IH approved · IF supported

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 (3)

PositionRole
44charge relay system
264charge relay system
449charge relay system

Post-translational modifications (3)

TypePositions
Phosphoserine915
N-acetylalanine2
N6-acetyllysine401

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradationcurated
R-HSA-1280218Adaptive Immune System—
R-HSA-983169Class I MHC mediated antigen processing & presentation—
R-HSA-168256Immune System—

MSigDB gene sets: 249 (showing top): FREAC2_01, HNF3ALPHA_Q6, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, MORF_BRCA1, MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP, PUJANA_CHEK2_PCC_NETWORK, MARTINEZ_RB1_TARGETS_UP, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, ONKEN_UVEAL_MELANOMA_UP, KONDO_COLON_CANCER_HCP_WITH_H3K27ME1, GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION

GO Biological Process (3): protein polyubiquitination (GO:0000209), proteolysis (GO:0006508), intracellular amino acid homeostasis (GO:0080144)

GO Molecular Function (10): endopeptidase activity (GO:0004175), aminopeptidase activity (GO:0004177), serine-type endopeptidase activity (GO:0004252), tripeptidyl-peptidase activity (GO:0008240), identical protein binding (GO:0042802), protein binding (GO:0005515), peptidase activity (GO:0008233), serine-type peptidase activity (GO:0008236), exopeptidase activity (GO:0008238), hydrolase activity (GO:0016787)

GO Cellular Component (4): cytoplasm (GO:0005737), cytosol (GO:0005829), nuclear body (GO:0016604), nucleus (GO:0005634)

Reactome top-level categories

3 top-level categories:

CategoryPathways
Class I MHC mediated antigen processing & presentation1
Immune System1
Adaptive Immune System1

GO top-level categories

20 GO namespaces:

CategoryTerms
peptidase activity3
cellular anatomical structure2
protein ubiquitination1
protein metabolic process1
intracellular chemical homeostasis1
exopeptidase activity1
endopeptidase activity1
serine-type peptidase activity1
serine-type exopeptidase activity1
protein binding1
binding1
hydrolase activity1
catalytic activity, acting on a protein1
serine hydrolase activity1
catalytic activity1
intracellular anatomical structure1
cytoplasm1
nucleoplasm1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 17 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO termNSEvidence
intracellular amino acid homeostasisBPmutant phenotype
cytosolCCdirect assay
nuclear bodyCCdirect assay
aminopeptidase activityMFmutant phenotype
identical protein bindingMFphysical interaction

Protein interactions and networks

STRING

showing 15 of 1,036 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
TPP2ERAP2Q6P179879
TPP2ERAP1Q9NZ08852
TPP2THOP1P52888624
TPP2BLMHQ13867558
TPP2NRDCO43847554
TPP2LNPEPQ9UIQ6552
TPP2COL3A1P02461550
TPP2NPEPPSP55786508
TPP2TAPBPO15533468
TPP2CASTP20810427
TPP2LRBAP50851420
TPP2DPP3Q9NY33417
TPP2TPP1O14773416
TPP2CCKP06307416
TPP2IDEP14735407

IntAct

Human interaction partners of TPP2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

14 partners by confidence:

PartnerInteraction typeMIscoreRecords
POLBphysical association0.7808
EHHADHphysical association0.6705
PPP1R16Aphysical association0.6704
NCALDassociation0.5302
DOK3association0.5301
CHIAassociation0.3502
PTPRDassociation0.3501
SNX2association0.3501
TAS2R31association0.3501
VDRassociation0.3501
ZNF75Aassociation0.3501
HLA-Bphysical association0.0001
MCCphysical association0.0001
MTNR1Aphysical association0.0001

BioGRID (156 interactions; top human partners by supporting records): C9orf41 (Affinity Capture-MS; 3 records), CHIA (Affinity Capture-MS; 3 records), CYP1A1 (Affinity Capture-MS; 3 records), DENND2D (Affinity Capture-MS; 3 records), DOK3 (Affinity Capture-MS; 3 records), ALOX5 (Affinity Capture-MS; 2 records), CDH19 (Affinity Capture-MS; 2 records), CSE1L (Co-fractionation; 2 records), GTF2E2 (Affinity Capture-MS; 2 records), KBTBD7 (Affinity Capture-MS; 2 records), KLHL36 (Affinity Capture-MS; 2 records), NAA40 (Affinity Capture-MS; 2 records), PARK2 (Affinity Capture-MS; 2 records), PCDHGB4 (Affinity Capture-MS; 2 records), POLB (Two-hybrid; 2 records)

Disease & clinical

Genetic variants

Variant evidence for TPP2: 860 ClinVar records (21 pathogenic / likely pathogenic); 1 GWAS association. Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic17
Likely pathogenic4
Uncertain significance350
Likely benign407
Benign35

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 21 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
650988NM_001330588.2(TPP2):c.2433_2434insA (p.Val812fs)Pathogeniccriteria provided, single submitter1
663284NM_001330588.2(TPP2):c.2843del (p.Pro948fs)Pathogeniccriteria provided, single submitter1
1076853NM_001330588.2(TPP2):c.2420T>G (p.Leu807Ter)Pathogeniccriteria provided, single submitter1
2100401NM_001330588.2(TPP2):c.2619T>G (p.Tyr873Ter)Pathogeniccriteria provided, single submitter1
2413358NM_001330588.2(TPP2):c.3466_3467del (p.Gly1156fs)Pathogeniccriteria provided, single submitter1
2817462NM_001330588.2(TPP2):c.1844dup (p.Tyr616fs)Pathogeniccriteria provided, single submitter1
2856662NM_001330588.2(TPP2):c.3071C>G (p.Ser1024Ter)Pathogeniccriteria provided, single submitter1
2878736NM_001330588.2(TPP2):c.1320_1321del (p.Gly441fs)Pathogeniccriteria provided, single submitter1
2880480NM_001330588.2(TPP2):c.3244C>T (p.Arg1082Ter)Pathogeniccriteria provided, single submitter1
3726063NM_001330588.2(TPP2):c.2563C>T (p.Gln855Ter)Pathogeniccriteria provided, single submitter1
4736460NM_001330588.2(TPP2):c.1066del (p.Tyr356fs)Pathogeniccriteria provided, single submitter1
583012NM_001330588.2(TPP2):c.2952+1G>CLikely pathogeniccriteria provided, single submitter1
1476641NM_001330588.2(TPP2):c.2873+1G>ALikely pathogeniccriteria provided, single submitter1
1804520NM_001330588.2(TPP2):c.2665C>T (p.Arg889Ter)Likely pathogeniccriteria provided, single submitter1
4292206NM_001330588.2(TPP2):c.3012del (p.Tyr1005fs)Likely pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore TPP2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 3,729):

Position(s)EffectΔscoreSites
13:102604785–102604786acceptor_gain1.00002
13:102604792acceptor_loss1.0000
13:102604922–102604923donor_loss1.00005
13:102614099–102614100acceptor_loss1.00004
13:102614186donor_gain1.0000
13:102614197–102614198donor_loss1.00004
13:102616394–102616395acceptor_loss1.00003
13:102622875–102622876acceptor_loss1.00006
13:102622972donor_gain1.0000
13:102627148donor_gain1.0000

AlphaMissense

3,636 missense substitutions predicted likely pathogenic (of 8,283 scored), across 933 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M45090.9971.000
M39190.9840.999
M39290.9760.997
M44590.9701.000
M30490.9530.996
M58990.8730.994
D4480.9991.000
H26480.9991.000
H26780.9991.000
N36280.9991.000
D4880.9960.999
S32880.9961.000
N44680.9951.000
D6980.9940.999
D29880.9940.999
D87180.9920.998
H69180.9880.999
S35980.9841.000
D7580.9730.993
D81180.9710.995

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

3 prognostic cancer types:

CancerPrognosticp-value
Kidney Chromophobe (TCGA)unfavorable8.24e-07
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA)unfavorable0.000129
Glioblastoma Multiforme (validation)favorable0.000398

Disease associations

OMIM: gene MIM:190470 | disease phenotypes: MIM:619220

GenCC curated gene-disease

2 curated gene-disease records:

DiseaseClassificationInheritanceRecords
immunodeficiency 78 with autoimmunity and developmental delayDefinitiveAutosomal recessive4
autoimmune hemolytic anemia-autoimmune thrombocytopenia-primary immunodeficiency syndromeSupportiveAutosomal recessive

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

1 validity classifications:

DiseaseClassificationInheritance
immunodeficiency 78 with autoimmunity and developmental delayDefinitiveAR

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (8 panels, 7 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

8 panels:

PanelRating
COVID-19 researchgreen
DDG2Pgreen
Hypotonic infantgreen
Intellectual disabilitygreen
Leukodystrophy, childhood onsetgreen
Paediatric disordersgreen
Primary immunodeficiency or monogenic inflammatory bowel diseasegreen
Leukodystrophy, adult onsetamber

Mondo (3): immunodeficiency 78 with autoimmunity and developmental delay (MONDO:0030971), thrombocytopenia (MONDO:0002049), autoimmune hemolytic anemia-autoimmune thrombocytopenia-primary immunodeficiency syndrome (MONDO:0018636)

HPO phenotypes

30 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000265Mastoiditis
HP:0000403Recurrent otitis media
HP:0001263Global developmental delay
HP:0001269Hemiparesis
HP:0001297Stroke
HP:0001744Splenomegaly
HP:0001878Hemolytic anemia
HP:0001888Decreased total lymphocyte count
HP:0001890Autoimmune hemolytic anemia
HP:0001904Autoimmune neutropenia
HP:0001973Autoimmune thrombocytopenia
HP:0002110Bronchiectasis
HP:0002716Lymphadenopathy
HP:0002725Systemic lupus erythematosus
HP:0002783Recurrent lower respiratory tract infections
HP:0002960Autoimmunity
HP:0003237Increased circulating IgG concentration
HP:0003496Increased circulating IgM concentration
HP:0003593Infantile onset
HP:0003819Death in childhood
HP:0006268Fluctuating splenomegaly
HP:0011342Mild global developmental delay
HP:0011343Moderate global developmental delay
HP:0011463Childhood onset
HP:0011947Respiratory tract infection
HP:0012115Hepatitis
HP:0032247Persistent CMV viremia
HP:0040167Facial papilloma
HP:0410028Recurrent oral herpes

GWAS associations

1 associations:

StudyTraitp-value
GCST90002404_128Red cell distribution width3e-11

EFO canonical traits (from GWAS)

1 canonical traits:

EFO IDTrait name
EFO:0009188Red cell distribution width

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
D013921ThrombocytopeniaC15.378.140.855; C15.378.243.937

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6156 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,601 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

1 molecules by phase:

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,601

PharmGKB: 1 entry (CPIC guideline: no)

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — S8: Subtilisin

Most potent curated ligand interactions (2 total), top 2:

LigandActionAffinityParameter
example 8 [WO1999033801A1]Inhibition9.44pKi
peptide 4 [PMID: 18294843]Inhibition7.7pKi

Binding affinities (BindingDB)

2 measured of 2 human assays (4 total across all organisms); most potent 2 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValue
CHEMBL263633KI20 nM
CHEMBL5653589KD1440 nM

ChEMBL bioactivities

4 potent at pChembl≥5 of 6 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.70Ki20nMCHEMBL263633
6.31Kd486.9nMCHEMBL5653589
6.31ED50486.9nMCHEMBL5653589
5.52IC502990nMMOLIBRESIB

PubChem BioAssay actives

3 with measured affinity, of 12 total; 3 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
(2S)-2-[[(2S)-2-[2-[[(2S)-2-[[(2S)-2-amino-5-(diaminomethylideneamino)pentanoyl]amino]propanoyl]amino]prop-2-enoylamino]-3-methylbutanoyl]amino]propanoic acid329747: Inhibition of human tripeptidyl peptidase2 from erythrocyteski0.0200uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149646: Binding affinity to human TPP2 incubated for 45 mins by Kinobead based pull down assaykd0.4869uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2178788: Inhibition of TPP2 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysisic502.9900uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
bisphenol Aaffects cotreatment, decreases methylation, decreases expression2
aristolochic acid Idecreases expression1
geldanamycinincreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression, affects localization, increases expression1
arseniteaffects binding, decreases reaction1
2-bromopalmitateincreases abundance, increases palmitoylation, decreases reaction1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
vanadyl sulfatedecreases expression1
di-n-butylphosphoric acidaffects expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
4-(4-fluorophenyl)-2-(4-hydroxyphenyl)-5-(4-pyridyl)imidazoleaffects localization, decreases reaction1
SB 203580affects localization, decreases reaction1
U 0126affects localization, decreases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
torcetrapibincreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, decreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-olincreases expression1
bisphenol AFincreases expression1
Fulvestrantdecreases methylation, affects cotreatment1
Acetaminophendecreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases expression1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1
Dinitrochlorobenzeneaffects binding1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652688BindingBinding affinity to human TPP2 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — *ChemMedChem*

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D1R3Abcam K-562 TPP2 KOCancer cell lineFemale
CVCL_D2MQAbcam Raji TPP2 KOCancer cell lineMale
CVCL_WQ73Abcam Jurkat TPP2 KOCancer cell lineMale

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for TPP2 across ~30M SureChEMBL compounds — explore on Sugi Predict.