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): 19:5158494-5340812

Links

ENSG00000105426 ∙ NCBI:5802 ∙ OMIM:601576 ∙ HGNC:9681 ∙ Uniprot:Q13332 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTPRS gene.

• Inborn genetic diseases (91 variants)
• not provided (36 variants)
• PTPRS-related condition (3 variants)
• Hearing impairment (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				12	13	25
missense			96	4		100
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			1		1	2
Total	0	0	97	16	14

Variants in PTPRS

This is a list of pathogenic ClinVar variants found in the PTPRS region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-5206842-C-G		not specified	Uncertain significance (Jun 06, 2023)
19-5206852-C-A		PTPRS-related disorder	Likely benign (Dec 26, 2023)
19-5207915-T-G		PTPRS-related disorder	Likely benign (Jun 17, 2019)
19-5207928-C-T		PTPRS-related disorder	Likely benign (Jun 13, 2019)
19-5207949-G-C		PTPRS-related disorder	Likely benign (Jun 13, 2019)
19-5207959-A-G		not specified	Uncertain significance (Jun 13, 2023)
19-5207988-G-A		PTPRS-related disorder	Uncertain significance (Nov 08, 2023)
19-5208025-G-T		PTPRS-related disorder	Uncertain significance (Jan 05, 2023)
19-5208050-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-5208305-G-T		not specified	Uncertain significance (Oct 04, 2022)
19-5208308-G-A		PTPRS-related disorder	Benign (Apr 18, 2019)
19-5208324-G-A		PTPRS-related disorder	Likely benign (Jul 25, 2022)
19-5208337-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-5208344-C-T		PTPRS-related disorder	Likely benign (Mar 27, 2019)
19-5210587-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-5210762-T-C			Uncertain significance (Nov 03, 2022)
19-5210766-C-T		PTPRS-related disorder	Likely benign (Feb 21, 2019)
19-5210784-C-T		PTPRS-related disorder	Likely benign (Dec 06, 2019)
19-5210790-G-A		PTPRS-related disorder	Likely benign (Sep 27, 2023)
19-5211601-A-G		PTPRS-related disorder	Benign (Dec 01, 2022)
19-5211608-C-G		not specified	Uncertain significance (Jan 18, 2022)
19-5211613-G-A		PTPRS-related disorder	Benign (Dec 31, 2019)
19-5211674-T-C		not specified	Uncertain significance (May 01, 2023)
19-5211695-C-T		not specified	Uncertain significance (May 23, 2023)
19-5211696-G-A		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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
• 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