PTPRF
protein tyrosine phosphatase receptor type F, the group of Fibronectin type III domain containing|I-set domain containing|Protein tyrosine phosphatases receptor type
Basic information
Region (hg38): 1:43525187-43623666
Previous symbols: [ "LAR" ]
Links
Phenotypes
GenCC
Source:
- breasts and/or nipples, aplasia or hypoplasia of, 2 (Strong), mode of inheritance: AR
- breasts and/or nipples, aplasia or hypoplasia of, 2 (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Breasts and/or nipples, aplasia or hypoplasia of, 2 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Dermatologic; Endocrine | 24781087 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (227 variants)
- not_provided (38 variants)
- PTPRF-related_disorder (28 variants)
- Breasts_and/or_nipples,_aplasia_or_hypoplasia_of,_2 (2 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRF gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002840.5. 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 | 31 | 10 | 41 | |||
| missense | 219 | 14 | 237 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 219 | 45 | 14 |
Highest pathogenic variant AF is 7.75801e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTPRF | protein_coding | protein_coding | ENST00000359947 | 32 | 98486 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 4.68e-8 | 125728 | 0 | 20 | 125748 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.80 | 990 | 1.27e+3 | 0.779 | 0.0000882 | 12310 |
| Missense in Polyphen | 343 | 572.93 | 0.59868 | 5540 | ||
| Synonymous | -0.596 | 555 | 537 | 1.03 | 0.0000401 | 3928 |
| Loss of Function | 7.86 | 10 | 90.8 | 0.110 | 0.00000458 | 955 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000329 | 0.000329 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000622 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Possible cell adhesion receptor. It possesses an intrinsic protein tyrosine phosphatase activity (PTPase) and dephosphorylates EPHA2 regulating its activity.;
- Disease
- DISEASE: Aplasia or hypoplasia of the breasts and/or nipples 2 (BNAH2) [MIM:616001]: A group of congenital deformities encompassing total absence of breasts and nipple (amastia), absence of the nipple (athelia), and absence of the mammary gland (amazia). {ECO:0000269|PubMed:24781087}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Adherens junction - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Insulin Signaling;Neuronal System;Synaptic adhesion-like molecules;EGFR1;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.330
- rvis_EVS
- -3.92
- rvis_percentile_EVS
- 0.2
Haploinsufficiency Scores
- pHI
- 0.309
- hipred
- Y
- hipred_score
- 0.793
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptprf
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; skeleton phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye phenotype; digestive/alimentary 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); renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- ptprfb
- Affected structure
- Rohon-Beard neuron
- Phenotype tag
- abnormal
- Phenotype quality
- subdermal
Gene ontology
- Biological process
- cell adhesion;transmembrane receptor protein tyrosine phosphatase signaling pathway;cell migration;neuron projection regeneration;peptidyl-tyrosine dephosphorylation;regulation of axon regeneration;synaptic membrane adhesion;negative regulation of receptor binding
- Cellular component
- plasma membrane;integral component of plasma membrane;neuron projection;neuronal cell body;extracellular exosome
- Molecular function
- protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;heparin binding;chondroitin sulfate proteoglycan binding;protein-containing complex binding;cell adhesion molecule binding