YES1

YES proto-oncogene 1, Src family tyrosine kinase, the group of Src family tyrosine kinases|SH2 domain containing

Basic information

Region (hg38): 18:721587-812546

Links

ENSG00000176105 ∙ NCBI:7525 ∙ OMIM:164880 ∙ HGNC:12841 ∙ Uniprot:P07947 ∙ 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 YES1 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YES1 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						0
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in YES1

This is a list of pathogenic ClinVar variants found in the YES1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-724497-T-C		not specified	Uncertain significance (Sep 01, 2021)
18-732908-G-A		not specified	Uncertain significance (Dec 18, 2023)
18-736862-C-T		not specified	Uncertain significance (Dec 08, 2023)
18-736867-T-C		not specified	Uncertain significance (Feb 06, 2023)
18-736939-A-G		not specified	Uncertain significance (Dec 17, 2021)
18-742950-G-C		not specified	Uncertain significance (Oct 16, 2023)
18-742972-A-G		not specified	Uncertain significance (Oct 25, 2022)
18-743007-A-C		not specified	Uncertain significance (Sep 20, 2023)
18-743319-C-T		not specified	Uncertain significance (Jun 22, 2023)
18-745710-G-C		not specified	Uncertain significance (Feb 15, 2023)
18-745746-T-C		not specified	Uncertain significance (Jun 24, 2022)
18-745776-T-C		not specified	Uncertain significance (Dec 12, 2023)
18-745837-G-A		not specified	Uncertain significance (Dec 07, 2021)
18-747947-G-A		not specified	Uncertain significance (Nov 13, 2023)
18-747990-T-C		not specified	Uncertain significance (Nov 14, 2023)
18-751739-T-G			Likely benign (Jul 01, 2023)
18-751793-T-C		not specified	Uncertain significance (Sep 16, 2021)
18-756587-C-T		not specified	Uncertain significance (Oct 14, 2023)
18-756596-A-G		not specified	Uncertain significance (Dec 18, 2023)
18-756629-C-T		not specified	Uncertain significance (Jan 26, 2022)
18-756721-G-A		not specified	Uncertain significance (Oct 20, 2021)
18-756733-T-C		not specified	Uncertain significance (Jul 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YES1	protein_coding	protein_coding	ENST00000584307	11	90960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000401	1.00	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	232	287	0.807	0.0000141	3517
Missense in Polyphen		66	113.87	0.57961		1391
Synonymous	-0.0900	101	99.9	1.01	0.00000503	1041
Loss of Function	3.09	13	31.8	0.409	0.00000186	378

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000164	0.000163
South Asian	0.000120	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-receptor protein tyrosine kinase that is involved in the regulation of cell growth and survival, apoptosis, cell-cell adhesion, cytoskeleton remodeling, and differentiation. Stimulation by receptor tyrosine kinases (RTKs) including EGRF, PDGFR, CSF1R and FGFR leads to recruitment of YES1 to the phosphorylated receptor, and activation and phosphorylation of downstream substrates. Upon EGFR activation, promotes the phosphorylation of PARD3 to favor epithelial tight junction assembly. Participates in the phosphorylation of specific junctional components such as CTNND1 by stimulating the FYN and FER tyrosine kinases at cell-cell contacts. Upon T-cell stimulation by CXCL12, phosphorylates collapsin response mediator protein 2/DPYSL2 and induces T-cell migration. Participates in CD95L/FASLG signaling pathway and mediates AKT-mediated cell migration. Plays a role in cell cycle progression by phosphorylating the cyclin-dependent kinase 4/CDK4 thus regulating the G1 phase. Also involved in G2/M progression and cytokinesis. {ECO:0000269|PubMed:11901164, ECO:0000269|PubMed:18479465, ECO:0000269|PubMed:19276087, ECO:0000269|PubMed:21566460, ECO:0000269|PubMed:21713032}.
• Pathway: Adherens junction - Homo sapiens (human);Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;Interleukin-11 Signaling Pathway;Developmental Biology;RUNX2 regulates osteoblast differentiation;RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Signal Transduction;Gene expression (Transcription);Signaling by Interleukins;Generic Transcription Pathway;Cytokine Signaling in Immune system;Alpha6Beta4Integrin;CD28 co-stimulation;CTLA4 inhibitory signaling;Costimulation by the CD28 family;RNA Polymerase II Transcription;EPH-Ephrin signaling;EPHA-mediated growth cone collapse;Immune System;EPHB-mediated forward signaling;EPH-ephrin mediated repulsion of cells;Adaptive Immune System;KitReceptor;Regulation of KIT signaling;PECAM1 interactions;CXCR4-mediated signaling events;Cell surface interactions at the vascular wall;Hemostasis;Thromboxane A2 receptor signaling;Noncanonical Wnt signaling pathway;Ephrin B reverse signaling;Class I PI3K signaling events;Axon guidance;Signaling by SCF-KIT;Signaling by ERBB2;Wnt;Signaling by Receptor Tyrosine Kinases;CDC42 signaling events;Glypican 1 network;Netrin-mediated signaling events;Signaling events mediated by focal adhesion kinase;Regulation of p38-alpha and p38-beta;Alpha-synuclein signaling;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B;EPHA forward signaling;Regulation of signaling by CBL;Interleukin-3, 5 and GM-CSF signaling (Consensus)

Recessive Scores

• pRec: 0.513

Intolerance Scores

• loftool: 0.451
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.927
• hipred: Y
• hipred_score: 0.746
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Yes1
• Phenotype: respiratory system phenotype; hematopoietic system phenotype; normal 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); 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); immune system phenotype; skeleton phenotype; renal/urinary system 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); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: yes1
• Affected structure: epiboly
• Phenotype tag: abnormal
• Phenotype quality: arrested

Gene ontology

• Biological process: cellular protein modification process;transmembrane receptor protein tyrosine kinase signaling pathway;regulation of glucose transmembrane transport;cell differentiation;T cell costimulation;cellular response to platelet-derived growth factor stimulus;peptidyl-tyrosine autophosphorylation;Fc-gamma receptor signaling pathway involved in phagocytosis;regulation of vascular permeability;positive regulation of transcription by RNA polymerase II;ephrin receptor signaling pathway;positive regulation of peptidyl-tyrosine phosphorylation;leukocyte migration;cellular response to retinoic acid;cellular response to transforming growth factor beta stimulus
• Cellular component: Golgi apparatus;microtubule organizing center;cytosol;actin filament;plasma membrane;focal adhesion;extrinsic component of cytoplasmic side of plasma membrane;extracellular exosome;glutamatergic synapse;postsynaptic specialization, intracellular component
• Molecular function: phosphotyrosine residue binding;protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;signaling receptor binding;epidermal growth factor receptor binding;protein binding;ATP binding;enzyme binding;ion channel binding