PTPRT

protein tyrosine phosphatase receptor type T, the group of Fibronectin type III domain containing|Immunoglobulin like domain containing|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 20:42072751-43189970

Links

ENSG00000196090 ∙ NCBI:11122 ∙ OMIM:608712 ∙ HGNC:9682 ∙ Uniprot:O14522 ∙ 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 PTPRT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRT 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				18	19	37
missense		1	70	6	6	83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region		1		1	1	3
non coding					5	5
Total	0	1	71	24	30

Variants in PTPRT

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

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

Position	Type	Phenotype	Significance	ClinVar
20-42079239-C-T			Benign (Feb 18, 2020)
20-42080915-T-C		PTPRT-related disorder	Likely benign (Dec 11, 2019)
20-42081914-G-A		Abnormality of neuronal migration	Benign (Oct 31, 2014)
20-42081942-A-C		not specified	Uncertain significance (Dec 28, 2023)
20-42081986-C-T		not specified	Uncertain significance (Jun 16, 2023)
20-42082003-C-T		PTPRT-related disorder	Benign/Likely benign (Nov 01, 2022)
20-42084674-G-A		PTPRT-related disorder	Benign (May 23, 2019)
20-42084700-C-T		not specified	Uncertain significance (Sep 22, 2022)
20-42084713-C-T		not specified	Uncertain significance (Jan 23, 2023)
20-42084745-C-G		PTPRT-associated neurodevelopmentaldisorder	Uncertain significance (Sep 03, 2021)
20-42084780-C-T		PTPRT-related disorder	Likely benign (Sep 05, 2019)
20-42084781-G-A		Intellectual disability	Uncertain significance (Dec 01, 2013)
20-42084793-G-A		not specified	Uncertain significance (Apr 13, 2022)
20-42085729-C-T		not specified	Uncertain significance (May 05, 2023)
20-42085747-C-T		not specified	Uncertain significance (Feb 12, 2024)
20-42085817-A-T		PTPRT-related disorder	Likely benign (Apr 11, 2019)
20-42085820-C-T		not specified	Uncertain significance (Sep 27, 2022)
20-42085839-G-A		PTPRT-related disorder	Benign (Oct 17, 2019)
20-42098498-C-T		not specified	Uncertain significance (Mar 24, 2023)
20-42098522-T-C		PTPRT-related disorder	Likely benign (Aug 22, 2019)
20-42098528-C-G		not specified	Uncertain significance (Aug 12, 2021)
20-42098534-C-T		not specified	Uncertain significance (Mar 28, 2024)
20-42102135-C-T			Likely benign (Jul 26, 2018)
20-42102191-C-T		not specified	Uncertain significance (May 10, 2022)
20-42102208-G-A		PTPRT-related disorder	Likely benign (Dec 23, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRT	protein_coding	protein_coding	ENST00000373187	31	1117219

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.55e-8	124791	0	11	124802	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.14	612	873	0.701	0.0000539	9387
Missense in Polyphen		213	381.02	0.55902		4044
Synonymous	-0.355	353	345	1.02	0.0000225	2827
Loss of Function	7.48	8	80.3	0.0996	0.00000460	816

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000300	0.0000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000592	0.0000556
Finnish	0.0000931	0.0000928
European (Non-Finnish)	0.0000547	0.0000530
Middle Eastern	0.0000592	0.0000556
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in both signal transduction and cellular adhesion in the CNS.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0898
• rvis_EVS: -1.03
• rvis_percentile_EVS: 7.87

Haploinsufficiency Scores

• pHI: 0.397
• hipred: Y
• hipred_score: 0.639
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.268

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ptprt
• Phenotype: homeostasis/metabolism phenotype; neoplasm

Gene ontology

• Biological process: protein dephosphorylation;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;negative regulation of cell migration;peptidyl-tyrosine dephosphorylation;cellular response to interleukin-6;negative regulation of STAT cascade;peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface;integral component of membrane
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding;beta-catenin binding;protein phosphatase binding;protein homodimerization activity;alpha-catenin binding;gamma-catenin binding;cadherin binding;delta-catenin binding;STAT family protein binding