PTPN12
protein tyrosine phosphatase non-receptor type 12, the group of Protein tyrosine phosphatases non-receptor type
Basic information
Region (hg38): 7:77537295-77640069
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (70 variants)
- PTPN12-related_disorder (7 variants)
- not_provided (4 variants)
- Carcinoma_of_colon (1 variants)
- Colorectal_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002835.4. 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 | 7 | |||||
| missense | 69 | 72 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 69 | 8 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTPN12 | protein_coding | protein_coding | ENST00000248594 | 18 | 102797 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000419 | 125715 | 0 | 33 | 125748 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.16 | 330 | 395 | 0.836 | 0.0000184 | 5123 |
| Missense in Polyphen | 60 | 93.927 | 0.6388 | 1229 | ||
| Synonymous | -0.927 | 146 | 132 | 1.10 | 0.00000643 | 1438 |
| Loss of Function | 5.56 | 3 | 41.7 | 0.0719 | 0.00000210 | 537 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000700 | 0.000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000143 | 0.000141 |
| Middle Eastern | 0.000700 | 0.000544 |
| South Asian | 0.000165 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Dephosphorylates a range of proteins, and thereby regulates cellular signaling cascades (PubMed:18559503). Dephosphorylates cellular tyrosine kinases, such as ERBB2 and PTK2B/PYK2, and thereby regulates signaling via ERBB2 and PTK2B/PYK2 (PubMed:17329398, PubMed:27134172). Selectively dephosphorylates ERBB2 phosphorylated at 'Tyr-1112', 'Tyr-1196', and/or 'Tyr-1248' (PubMed:27134172). {ECO:0000269|PubMed:17329398, ECO:0000269|PubMed:18559503, ECO:0000269|PubMed:27134172}.;
- Pathway
- EGF-EGFR Signaling Pathway;SHC1 events in ERBB2 signaling;Signal Transduction;Signaling by PDGF;TCR;EGFR downregulation;Signaling by EGFR;Downregulation of ERBB2 signaling;EGFR1;Signaling by ERBB2;Signaling by Receptor Tyrosine Kinases
(Consensus)
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- loftool
- 0.350
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.65
Haploinsufficiency Scores
- pHI
- 0.376
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.603
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.234
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptpn12
- 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); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); immune system phenotype; liver/biliary system phenotype; embryo phenotype;
Zebrafish Information Network
- Gene name
- ptpn12
- Affected structure
- pharyngeal arch 3-7
- Phenotype tag
- abnormal
- Phenotype quality
- hypoplastic
Gene ontology
- Biological process
- protein dephosphorylation;peptidyl-tyrosine dephosphorylation;ERBB2 signaling pathway;regulation of epidermal growth factor receptor signaling pathway;tissue regeneration;cellular response to cytokine stimulus;cellular response to epidermal growth factor stimulus;negative regulation of ERBB signaling pathway;negative regulation of platelet-derived growth factor receptor-beta signaling pathway
- Cellular component
- podosome;nucleoplasm;cytoplasm;cytosol;focal adhesion;cell projection
- Molecular function
- phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;non-membrane spanning protein tyrosine phosphatase activity;protein binding;SH3 domain binding