PTPRT
Basic information
Region (hg38): 20:42072752-43189970
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 18 | 19 | 37 | |||
missense | 141 | 152 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 1 | 147 | 24 | 23 |
Highest pathogenic variant AF is 0.00000249022
GnomAD
Source:
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:
- 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