RYK
receptor like tyrosine kinase, the group of Receptor tyrosine kinases
Basic information
Region (hg38): 3:134065302-134250859
Previous symbols: [ "JTK5A" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (9 variants)
- Inborn genetic diseases (3 variants)
- not specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RYK gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 3 | 2 | 5 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 4 | 4 | ||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 2 | 2 | ||||
| Total | 0 | 0 | 3 | 1 | 9 |
Variants in RYK
This is a list of pathogenic ClinVar variants found in the RYK region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-134175621-G-C | Inborn genetic diseases | Uncertain significance (Apr 03, 2023) | ||
| 3-134175954-T-C | Benign (Feb 25, 2018) | |||
| 3-134191891-T-G | Inborn genetic diseases | Uncertain significance (Jan 03, 2022) | ||
| 3-134191929-G-C | Inborn genetic diseases | Uncertain significance (Apr 25, 2022) | ||
| 3-134209732-G-A | Likely benign (Sep 20, 2018) | |||
| 3-134216310-G-C | Orofacial cleft 1 | Uncertain significance (Jan 19, 2023) | ||
| 3-134222543-G-C | Benign (May 18, 2018) | |||
| 3-134250500-G-C | Inborn genetic diseases | Uncertain significance (Dec 17, 2021) | ||
| 3-134250504-G-A | Benign (Dec 31, 2019) | |||
| 3-134250569-A-AGCGGCG | Benign (Jun 27, 2018) | |||
| 3-134250593-AG-A | Benign (Jul 26, 2017) | |||
| 3-134250594-G-G | Benign (Dec 31, 2019) | |||
| 3-134250644-GC-G | Benign (Jul 26, 2017) | |||
| 3-134250644-G-GC | not specified | Benign (Jul 15, 2015) | ||
| 3-134250645-C-C | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RYK | protein_coding | protein_coding | ENST00000296084 | 16 | 185543 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.989 | 0.0108 | 124645 | 0 | 3 | 124648 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.81 | 190 | 274 | 0.693 | 0.0000140 | 3919 |
| Missense in Polyphen | 48 | 100.75 | 0.47644 | 1441 | ||
| Synonymous | 1.16 | 84 | 98.7 | 0.851 | 0.00000540 | 1167 |
| Loss of Function | 4.27 | 3 | 26.9 | 0.112 | 0.00000139 | 360 |
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 | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.00000899 | 0.00000885 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be a coreceptor along with FZD8 of Wnt proteins, such as WNT1, WNT3, WNT3A and WNT5A. Involved in neuron differentiation, axon guidance, corpus callosum establishment and neurite outgrowth. In response to WNT3 stimulation, receptor C- terminal cleavage occurs in its transmembrane region and allows the C-terminal intracellular product to translocate from the cytoplasm to the nucleus where it plays a crucial role in neuronal development. {ECO:0000269|PubMed:15454084}.;
- Pathway
- Axon guidance - Homo sapiens (human);WNT-Core;Wnt Signaling Pathway;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;IL-7 signaling;PCP/CE pathway;Beta-catenin independent WNT signaling;JAK STAT pathway and regulation;EPO signaling;VEGF;Wnt signaling network;TCF dependent signaling in response to WNT
(Consensus)
Recessive Scores
- pRec
- 0.189
Haploinsufficiency Scores
- pHI
- 0.281
- hipred
- hipred_score
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.930
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ryk
- 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- ryk
- Affected structure
- retinal inner plexiform layer
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- protein phosphorylation;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;nervous system development;axonogenesis;axon guidance;synapse assembly;Wnt signaling pathway;peptidyl-tyrosine phosphorylation;neurogenesis;corpus callosum development;neuron differentiation;neuron projection development;cell proliferation in midbrain;non-canonical Wnt signaling pathway;chemorepulsion of dopaminergic neuron axon;positive regulation of MAPK cascade;skeletal system morphogenesis;negative regulation of axon extension involved in axon guidance;canonical Wnt signaling pathway;commissural neuron axon guidance;planar cell polarity pathway involved in axon guidance;midbrain dopaminergic neuron differentiation;Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation
- Cellular component
- nucleus;cytoplasm;plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;receptor complex
- Molecular function
- protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;transmembrane signaling receptor activity;frizzled binding;protein binding;ATP binding;Wnt-protein binding;Wnt-activated receptor activity;coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway