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): 20:42072752-43189970

Links

ENSG00000196090NCBI:11122OMIM:608712HGNC:9682Uniprot:O14522AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • not_specified (139 variants)
  • PTPRT-related_disorder (45 variants)
  • not_provided (39 variants)
  • Abnormal_brain_morphology (2 variants)
  • Abnormality_of_neuronal_migration (1 variants)
  • Autism_spectrum_disorder (1 variants)
  • PTPRT-associated_neurodevelopmentaldisorder (1 variants)
  • Intellectual_disability (1 variants)

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. These statistics are base on transcript: NM_000007050.6. 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.

EffectPLPVUSLBBSum
synonymous
18
clinvar
19
clinvar
37
missense
1
clinvar
141
clinvar
6
clinvar
4
clinvar
152
nonsense
4
clinvar
4
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 1 147 24 23

Highest pathogenic variant AF is 0.00000249022

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PTPRTprotein_codingprotein_codingENST00000373187 311117219
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.008.55e-81247910111248020.0000441
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.146128730.7010.00005399387
Missense in Polyphen213381.020.559024044
Synonymous-0.3553533451.020.00002252827
Loss of Function7.48880.30.09960.00000460816

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003000.0000300
Ashkenazi Jewish0.000.00
East Asian0.00005920.0000556
Finnish0.00009310.0000928
European (Non-Finnish)0.00005470.0000530
Middle Eastern0.00005920.0000556
South Asian0.000.00
Other0.0001650.000165

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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