PTP4A2
Basic information
Region (hg38): 1:31906421-31944856
Previous symbols: [ "PTP4A" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTP4A2 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in PTP4A2
This is a list of pathogenic ClinVar variants found in the PTP4A2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-31908874-T-C | not specified | Uncertain significance (Jul 12, 2023) | ||
| 1-31910077-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-31915941-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 1-31918995-T-C | not specified | Uncertain significance (Mar 23, 2022) | ||
| 1-31919061-T-C | not specified | Uncertain significance (Sep 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTP4A2 | protein_coding | protein_coding | ENST00000344035 | 5 | 38436 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.966 | 0.0337 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.07 | 37 | 93.2 | 0.397 | 0.00000518 | 1084 |
| Missense in Polyphen | 9 | 32.236 | 0.27919 | 403 | ||
| Synonymous | -0.472 | 35 | 31.6 | 1.11 | 0.00000171 | 319 |
| Loss of Function | 3.01 | 0 | 10.5 | 0.00 | 6.76e-7 | 117 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein tyrosine phosphatase which stimulates progression from G1 into S phase during mitosis. Promotes tumors. Inhibits geranylgeranyl transferase type II activity by blocking the association between RABGGTA and RABGGTB. {ECO:0000269|PubMed:14643450}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation;Signaling events mediated by PRL
(Consensus)
Recessive Scores
- pRec
- 0.0861
Intolerance Scores
- loftool
- 0.151
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.0899
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ptp4a2
- Phenotype
- embryo phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- peptidyl-tyrosine dephosphorylation;post-translational protein modification
- Cellular component
- nucleus;cytoplasm;early endosome;cytosol;plasma membrane
- Molecular function
- protein tyrosine phosphatase activity;prenylated protein tyrosine phosphatase activity