PTPRS
protein tyrosine phosphatase receptor type S, the group of Fibronectin type III domain containing|I-set domain containing|Protein tyrosine phosphatases receptor type
Basic information
Region (hg38): 19:5158495-5340812
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (269 variants)
- PTPRS-related_disorder (91 variants)
- not_provided (37 variants)
- Hearing_impairment (2 variants)
- NK-cell_enteropathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002850.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 59 | 18 | 78 | |||
| missense | 273 | 283 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 274 | 65 | 21 |
Highest pathogenic variant AF is 0.0000130234
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTPRS | protein_coding | protein_coding | ENST00000357368 | 37 | 182309 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000169 | 125681 | 0 | 66 | 125747 | 0.000262 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.78 | 911 | 1.29e+3 | 0.704 | 0.0000943 | 12534 |
| Missense in Polyphen | 361 | 591.56 | 0.61026 | 5261 | ||
| Synonymous | -4.58 | 707 | 568 | 1.24 | 0.0000468 | 3986 |
| Loss of Function | 7.38 | 15 | 90.9 | 0.165 | 0.00000473 | 1012 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000309 | 0.000274 |
| Ashkenazi Jewish | 0.000106 | 0.0000992 |
| East Asian | 0.00206 | 0.00201 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000130 | 0.000123 |
| Middle Eastern | 0.00206 | 0.00201 |
| South Asian | 0.0000991 | 0.0000980 |
| Other | 0.000730 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Cell surface receptor that binds to glycosaminoglycans, including chondroitin sulfate proteoglycans and heparan sulfate proteoglycan (PubMed:21454754). Binding to chondroitin sulfate and heparan sulfate proteoglycans has opposite effects on PTPRS oligomerization and regulation of neurite outgrowth. Contributes to the inhibition of neurite and axonal outgrowth by chondroitin sulfate proteoglycans, also after nerve transection. Plays a role in stimulating neurite outgrowth in response to the heparan sulfate proteoglycan GPC2. Required for normal brain development, especially for normal development of the pituitary gland and the olfactory bulb. Functions as tyrosine phosphatase (PubMed:8524829). Mediates dephosphorylation of NTRK1, NTRK2 and NTRK3 (By similarity). Plays a role in down-regulation of signaling cascades that lead to the activation of Akt and MAP kinases (By similarity). Down-regulates TLR9-mediated activation of NF-kappa-B, as well as production of TNF, interferon alpha and interferon beta (PubMed:26231120). {ECO:0000250|UniProtKB:B0V2N1, ECO:0000250|UniProtKB:F1NWE3, ECO:0000269|PubMed:21454754, ECO:0000269|PubMed:26231120, ECO:0000269|PubMed:8524829}.;
- Pathway
- Extracellular matrix organization;Neuronal System;Synaptic adhesion-like molecules;Receptor-type tyrosine-protein phosphatases;ECM proteoglycans;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.159
Intolerance Scores
- loftool
- 0.317
- rvis_EVS
- -4.37
- rvis_percentile_EVS
- 0.1
Haploinsufficiency Scores
- pHI
- 0.308
- hipred
- Y
- hipred_score
- 0.744
- ghis
- 0.624
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.726
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptprs
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; taste/olfaction phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;negative regulation of neuron projection development;spinal cord development;cerebellum development;hippocampus development;cerebral cortex development;corpus callosum development;negative regulation of axon extension;negative regulation of interferon-alpha production;negative regulation of interferon-beta production;negative regulation of toll-like receptor 9 signaling pathway;peptidyl-tyrosine dephosphorylation;negative regulation of collateral sprouting;negative regulation of axon regeneration;modulation of chemical synaptic transmission;negative regulation of dendritic spine development;establishment of endothelial intestinal barrier;regulation of postsynaptic density assembly;synaptic membrane adhesion
- Cellular component
- plasma membrane;integral component of plasma membrane;cell junction;integral component of synaptic vesicle membrane;axon;perikaryon;extracellular exosome;Schaffer collateral - CA1 synapse;glutamatergic synapse;integral component of presynaptic membrane;integral component of postsynaptic density membrane
- Molecular function
- phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein binding;heparin binding;chondroitin sulfate binding;heparan sulfate proteoglycan binding