RYK

receptor like tyrosine kinase, the group of Receptor tyrosine kinases

Basic information

Region (hg38): 3:134065302-134250859

Previous symbols: [ "JTK5A" ]

Links

ENSG00000163785 ∙ NCBI:6259 ∙ OMIM:600524 ∙ HGNC:10481 ∙ Uniprot:P34925 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	1		2
missense			4		2	6
nonsense						0
start loss						0
frameshift					3	3
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding			1		2	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		not specified	Uncertain significance (Apr 03, 2023)
3-134175954-T-C			Benign (Feb 25, 2018)
3-134191843-A-C			Benign (Mar 01, 2023)
3-134191891-T-G		RYK-related disorder • not specified	Conflicting classifications of pathogenicity (Apr 01, 2022)
3-134191925-A-G		RYK-related disorder	Likely benign (Apr 01, 2020)
3-134191929-G-C		not specified	Uncertain significance (Apr 25, 2022)
3-134191957-T-C		not specified	Uncertain significance (Oct 30, 2023)
3-134191982-G-A		not specified	Likely benign (Feb 26, 2024)
3-134195154-G-A		RYK-related disorder	Uncertain significance (Jun 07, 2023)
3-134209709-T-C		RYK-related disorder	Likely benign (Oct 29, 2023)
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		not specified	Uncertain significance (Dec 17, 2021)
3-134250504-G-A			Benign (Dec 31, 2019)
3-134250506-G-A		RYK-related disorder	Likely benign (May 19, 2020)
3-134250508-G-A		RYK-related disorder	Benign (Feb 11, 2021)
3-134250569-A-AGCGGCG		RYK-related disorder	Benign (Dec 20, 2023)
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 • RYK-related disorder	Benign (Nov 04, 2019)
3-134250645-C-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

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: 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
• ghis: 0.600

Essentials

• essential_gene_CRISPR2: S
• 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