PTK7
protein tyrosine kinase 7 (inactive), the group of I-set domain containing|Receptor tyrosine kinases
Basic information
Region (hg38): 6:43076307-43161719
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (99 variants)
- not_provided (12 variants)
- PTK7-related_disorder (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTK7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002821.5. 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 | 10 | |||||
| missense | 94 | 104 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 95 | 12 | 7 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PTK7 | protein_coding | protein_coding | ENST00000481273 | 20 | 85452 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00279 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.24 | 508 | 671 | 0.757 | 0.0000415 | 7023 |
| Missense in Polyphen | 172 | 288.12 | 0.59697 | 3034 | ||
| Synonymous | -0.552 | 282 | 270 | 1.04 | 0.0000165 | 2164 |
| Loss of Function | 5.69 | 8 | 52.5 | 0.152 | 0.00000249 | 573 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000868 | 0.0000868 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000883 | 0.0000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inactive tyrosine kinase involved in Wnt signaling pathway. Component of both the non-canonical (also known as the Wnt/planar cell polarity signaling) and the canonical Wnt signaling pathway. Functions in cell adhesion, cell migration, cell polarity, proliferation, actin cytoskeleton reorganization and apoptosis. Has a role in embryogenesis, epithelial tissue organization and angiogenesis. {ECO:0000269|PubMed:18471990, ECO:0000269|PubMed:20558616, ECO:0000269|PubMed:20837484, ECO:0000269|PubMed:21103379, ECO:0000269|PubMed:21132015}.;
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.0972
- rvis_EVS
- -0.77
- rvis_percentile_EVS
- 13.18
Haploinsufficiency Scores
- pHI
- 0.646
- hipred
- Y
- hipred_score
- 0.639
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.600
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptk7
- Phenotype
- embryo phenotype; respiratory 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); 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); 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; limbs/digits/tail phenotype; vision/eye phenotype; skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; craniofacial phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- ptk7b
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- increased width
Gene ontology
- Biological process
- establishment of planar polarity;ventricular septum development;axis elongation;protein phosphorylation;cell adhesion;signal transduction;positive regulation of neuron projection development;cell migration;actin cytoskeleton reorganization;wound healing;establishment of epithelial cell apical/basal polarity;convergent extension;lung-associated mesenchyme development;coronary vasculature development;cellular response to retinoic acid;cochlea morphogenesis;planar cell polarity pathway involved in neural tube closure;positive regulation of canonical Wnt signaling pathway
- Cellular component
- integral component of plasma membrane;cell-cell junction;focal adhesion
- Molecular function
- protein kinase activity;protein binding;ATP binding;coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway