PTPRU
protein-codingprotein tyrosine phosphatase receptor type U, the group of Fibronectin type III domain containing|Protein tyrosine phosphatases receptor type
Gene summary
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. This PTP was thought to play roles in cell-cell recognition and adhesion. Studies of the similar gene in mice suggested the role of this PTP in early neural development. The expression of this gene was reported to be regulated by phorbol myristate acetate (PMA) or calcium ionophore in Jurkat T lymphoma cells. Alternatively spliced transcript variants have been reported. [provided by RefSeq, Aug 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~90.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PTPRU variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_133178.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 21 | 3 | 27 | ||
| missense | 2 | 226 | 3 | 2 | 233 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 10 | 10 | ||||
| Total | 0 | 2 | 239 | 24 | 5 | 270 |
Highest pathogenic variant AF is 0.00002292768
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_573439.2 | 30 | MANE Select | |
| Ensembl | ENSP00000362884.3 | 30 | MANE Select | |
| RefSeq | NP_001181930.1 | 30 | Standard | |
| RefSeq | NP_005695.3 | 31 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- EPO Receptor Signaling
- Signal Transduction
- KitReceptor
- Signaling by SCF-KIT
- Signaling by Receptor Tyrosine Kinases
Biological Process
- protein dephosphorylation
- cell adhesion
- transmembrane receptor protein tyrosine phosphatase signaling pathway
- negative regulation of cell population proliferation
- cell differentiation
Molecular Function
- protein tyrosine phosphatase activity
- transmembrane receptor protein tyrosine phosphatase activity
- protein binding
- beta-catenin binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- cell-cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000345512
- Coding exons
- 31
- Length
- 90298
- Individuals with no LoFs
- 125704
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 44
- Defined
- 125748
- p
- 0.000175
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 725 | 936 | 0.775 | 0.0000624 | 9373 |
| Missense (PolyPhen) | 282 | 395.68 | 0.7127 | 3798 | ||
| Synonymous | 0.793 | 364 | 384 | 0.949 | 0.0000258 | 2916 |
| Loss of Function | 6.23 | 17 | 75.3 | 0.226 | 0.00000414 | 789 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00024 | 0.00024 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tyrosine-protein phosphatase which dephosphorylates CTNNB1. Regulates CTNNB1 function both in cell adhesion and signaling. May function in cell proliferation and migration and play a role in the maintenance of epithelial integrity. May play a role in megakaryocytopoiesis. {ECO:0000269|PubMed:10397721, ECO:0000269|PubMed:12501215, ECO:0000269|PubMed:16574648}.;
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- LoFtool
- 0.366
- RVIS EVS
- -1.78
- RVIS percentile EVS
- 2.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.938
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |