PTPRE

protein tyrosine phosphatase receptor type E, the group of Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 10:127907103-128085855

Links

ENSG00000132334NCBI:5791OMIM:600926HGNC:9669Uniprot:P23469AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • not_specified (83 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006504.6. 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
1
clinvar
1
missense
79
clinvar
4
clinvar
83
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 79 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PTPREprotein_codingprotein_codingENST00000254667 19178795
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0008160.9991257070411257480.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.083104310.7180.00002584635
Missense in Polyphen112179.410.624261880
Synonymous0.7031671790.9330.00001281297
Loss of Function4.471548.70.3080.00000296479

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002680.000268
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001630.000163
Finnish0.0001390.000139
European (Non-Finnish)0.0001240.000123
Middle Eastern0.0001630.000163
South Asian0.0003970.000392
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Isoform 1 plays a critical role in signaling transduction pathways and phosphoprotein network topology in red blood cells. May play a role in osteoclast formation and function (By similarity). {ECO:0000250}.; FUNCTION: Isoform 1 and isoform 2 act as a negative regulator of FceRI-mediated signal transduction leading to cytokine production and degranulation, most likely by acting at the level of SYK to affect downstream events such as phosphorylation of SLP76 and LAT and mobilization of Ca(2+). {ECO:0000250}.;
Pathway
EGFR1;IL6-mediated signaling events (Consensus)

Recessive Scores

pRec
0.126

Intolerance Scores

loftool
0.304
rvis_EVS
-1.28
rvis_percentile_EVS
5.11

Haploinsufficiency Scores

pHI
0.142
hipred
Y
hipred_score
0.744
ghis
0.552

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.864

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ptpre
Phenotype
cellular phenotype; skeleton phenotype; hematopoietic system 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); limbs/digits/tail phenotype; immune system phenotype;

Gene ontology

Biological process
protein dephosphorylation;peptidyl-tyrosine dephosphorylation;negative regulation of insulin receptor signaling pathway
Cellular component
nucleus;cytoplasm;plasma membrane;integral component of membrane
Molecular function
transmembrane receptor protein tyrosine phosphatase activity;protein binding