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GeneBe

RYK

receptor like tyrosine kinase, the group of Receptor tyrosine kinases

Basic information

Region (hg38): 3:134065302-134250859

Previous symbols: [ "JTK5A" ]

Links

ENSG00000163785NCBI:6259OMIM:600524HGNC:10481Uniprot:P34925AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RYK gene.

  • not provided (10 variants)
  • Inborn genetic diseases (4 variants)
  • Orofacial cleft 1 (1 variants)
  • RYK-related condition (1 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.

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
1
clinvar
1
clinvar
2
missense
4
clinvar
2
clinvar
6
nonsense
0
start loss
0
frameshift
3
clinvar
3
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
1
clinvar
2
clinvar
3
Total 0 0 6 1 8

Variants in RYK

This is a list of pathogenic ClinVar variants found in the RYK region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
3-134175621-G-C Inborn genetic diseases Uncertain significance (Apr 03, 2023)2532297
3-134175954-T-C Benign (Feb 25, 2018)783406
3-134191843-A-C Benign (Mar 01, 2023)2654162
3-134191891-T-G Inborn genetic diseases • RYK-related condition Conflicting classifications of pathogenicity (Apr 01, 2022)2363166
3-134191925-A-G RYK-related condition Likely benign (Apr 01, 2020)3055004
3-134191929-G-C Inborn genetic diseases Uncertain significance (Apr 25, 2022)2402059
3-134195154-G-A RYK-related condition Uncertain significance (Jun 07, 2023)2632542
3-134209709-T-C RYK-related condition Likely benign (Oct 29, 2023)3048026
3-134209732-G-A Likely benign (Sep 20, 2018)718403
3-134216310-G-C Orofacial cleft 1 Uncertain significance (Jan 19, 2023)2584555
3-134222543-G-C Benign (May 18, 2018)786021
3-134250500-G-C Inborn genetic diseases Uncertain significance (Dec 17, 2021)2268034
3-134250504-G-A Benign (Dec 31, 2019)781973
3-134250506-G-A RYK-related condition Likely benign (May 19, 2020)3034688
3-134250508-G-A RYK-related condition Benign (Feb 11, 2021)3048012
3-134250569-A-AGCGGCG RYK-related condition Benign (Dec 20, 2023)780896
3-134250593-AG-A Benign (Jul 26, 2017)779997
3-134250594-G-G Benign (Dec 31, 2019)767934
3-134250644-GC-G Benign (Jul 26, 2017)779998
3-134250644-G-GC not specified • RYK-related condition Benign (Nov 04, 2019)218478
3-134250645-C-C Benign (Dec 31, 2019)767935

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RYKprotein_codingprotein_codingENST00000296084 16185543
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9890.0108124645031246480.0000120
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.811902740.6930.00001403919
Missense in Polyphen48100.750.476441441
Synonymous1.168498.70.8510.000005401167
Loss of Function4.27326.90.1120.00000139360

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004640.0000464
European (Non-Finnish)0.000008990.00000885
Middle Eastern0.000.00
South Asian0.00003290.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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