PTN
pleiotrophin, the group of Receptor ligands
Basic information
Region (hg38): 7:137227341-137343774
Previous symbols: [ "NEGF1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 PTN 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 | 6 | |||||
| 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 | 1 | 0 |
Variants in PTN
This is a list of pathogenic ClinVar variants found in the PTN region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-137251230-C-A | Likely benign (Dec 01, 2022) | |||
| 7-137251241-G-A | not specified | Uncertain significance (Oct 06, 2024) | ||
| 7-137251323-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| 7-137254945-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 7-137254946-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 7-137254947-C-G | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTN | protein_coding | protein_coding | ENST00000348225 | 4 | 116524 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00751 | 0.931 | 125706 | 0 | 9 | 125715 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 58 | 89.3 | 0.649 | 0.00000468 | 1092 |
| Missense in Polyphen | 11 | 30.764 | 0.35756 | 373 | ||
| Synonymous | 0.480 | 27 | 30.4 | 0.889 | 0.00000140 | 298 |
| Loss of Function | 1.62 | 5 | 10.7 | 0.467 | 6.05e-7 | 117 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000301 | 0.0000301 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000620 | 0.0000616 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Secreted growth factor that induces neurite outgrowth and which is mitogenic for fibroblasts, epithelial, and endothelial cells (PubMed:1768439, PubMed:1733956). Binds anaplastic lymphoma kinase (ALK) which induces MAPK pathway activation, an important step in the anti-apoptotic signaling of PTN and regulation of cell proliferation (PubMed:11278720). Binds to cell-surface target proteins via their chondroitin sulfate groups (PubMed:26896299). Down-regulates PTPRZ1 activity (PubMed:16814777). {ECO:0000269|PubMed:11278720, ECO:0000269|PubMed:16814777, ECO:0000269|PubMed:1768439, ECO:0000269|PubMed:26896299}.;
- Pathway
- Syndecan-3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.370
Intolerance Scores
- loftool
- 0.496
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 70.87
Haploinsufficiency Scores
- pHI
- 0.289
- hipred
- Y
- hipred_score
- 0.555
- ghis
- 0.531
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptn
- 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); hearing/vestibular/ear phenotype; immune system phenotype; liver/biliary system phenotype; reproductive system phenotype; hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- liver development;transmembrane receptor protein tyrosine phosphatase signaling pathway;nervous system development;heart development;learning;positive regulation of cell population proliferation;regulation of cell shape;regulation of signaling receptor activity;positive regulation of cell-substrate adhesion;positive regulation of neuron projection development;response to activity;negative regulation of angiogenesis;spinal cord development;cerebellum development;thalamus development;bone mineralization;lung development;negative regulation of cell migration;response to estradiol;negative regulation of phosphoprotein phosphatase activity;response to progesterone;cellular response to UV;cellular response to platelet-derived growth factor stimulus;positive regulation of apoptotic process;estrous cycle;endothelial cell differentiation;negative regulation of membrane potential;negative regulation of epithelial cell proliferation;positive regulation of cell division;retinal rod cell differentiation;negative regulation of glial cell proliferation;long-term synaptic potentiation;cellular response to vitamin D;cellular response to hypoxia;negative regulation of mesenchymal cell proliferation;response to kainic acid;rod bipolar cell differentiation;response to ciliary neurotrophic factor;positive regulation of skeletal muscle acetylcholine-gated channel clustering;negative regulation of neuromuscular junction development;response to nerve growth factor;positive regulation of hepatocyte proliferation
- Cellular component
- extracellular region;basement membrane;extracellular space;endoplasmic reticulum;cell surface;membrane;neuromuscular junction;protein-containing complex;perinuclear region of cytoplasm;presynapse;postsynapse
- Molecular function
- protein phosphatase inhibitor activity;growth factor activity;heparin binding;protein kinase binding;chondroitin sulfate proteoglycan binding;chondroitin sulfate binding;vascular endothelial growth factor binding;heparan sulfate binding