PTPRE
Basic information
Region (hg38): 10:127907103-128085855
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 79 | 83 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 79 | 5 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PTPRE | protein_coding | protein_coding | ENST00000254667 | 19 | 178795 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000816 | 0.999 | 125707 | 0 | 41 | 125748 | 0.000163 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.08 | 310 | 431 | 0.718 | 0.0000258 | 4635 |
Missense in Polyphen | 112 | 179.41 | 0.62426 | 1880 | ||
Synonymous | 0.703 | 167 | 179 | 0.933 | 0.0000128 | 1297 |
Loss of Function | 4.47 | 15 | 48.7 | 0.308 | 0.00000296 | 479 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000268 | 0.000268 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000124 | 0.000123 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000397 | 0.000392 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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