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    EYS eyes shut homolog [ Homo sapiens (human) ]

    Gene ID: 346007, updated on 10-Dec-2024

    Summary

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    Official Symbol
    EYSprovided by HGNC
    Official Full Name
    eyes shut homologprovided by HGNC
    Primary source
    HGNC:HGNC:21555
    See related
    Ensembl:ENSG00000188107 MIM:612424; AllianceGenome:HGNC:21555
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RP25; SPAM; EGFL10; EGFL11; C6orf178; C6orf179; C6orf180; bA74E24.1; dJ22I17.2; bA166P24.2; bA307F22.3; dJ1018A4.2; dJ303F19.1
    Summary
    The product of this gene contains multiple epidermal growth factor (EGF)-like and LamG domains. The protein is expressed in the photoreceptor layer of the retina, and the gene is mutated in autosomal recessive retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    all
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    Genomic context

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    See EYS in Genome Data Viewer
    Location:
    6q12
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (63719980..65707226, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (64866189..66858763, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (64429876..66417119, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene lengsin, lens protein with glutamine synthetase domain Neighboring gene translation initiation factor IF-2-like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282109-64282844 Neighboring gene uncharacterized LOC128125822 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282845-64283580 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64283581-64284316 Neighboring gene Sharpr-MPRA regulatory region 1413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24721 Neighboring gene NANOG hESC enhancer GRCh37_chr6:64344395-64344932 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64345464-64346284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24722 Neighboring gene protein tyrosine phosphatase 4A1 Neighboring gene ribosomal protein L9 pseudogene 18 Neighboring gene platelet activating factor acetylhydrolase 1b regulatory subunit 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24723 Neighboring gene PHD finger protein 3 Neighboring gene uncharacterized LOC105377836 Neighboring gene uncharacterized LOC107986608 Neighboring gene Sharpr-MPRA regulatory region 3621 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:64719266-64719401 Neighboring gene glucosaminyl (N-acetyl) transferase 1 pseudogene 4 Neighboring gene Sharpr-MPRA regulatory region 10142 Neighboring gene S-phase cancer associated transcript 8 Neighboring gene Sharpr-MPRA regulatory region 1709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:65158253-65158752 Neighboring gene Sharpr-MPRA regulatory region 6473 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92402 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92457 Neighboring gene transmembrane protein 98 pseudogene Neighboring gene heterogeneous nuclear ribonucleoprotein D pseudogene 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92499 Neighboring gene uncharacterized LOC105377837 Neighboring gene NANOG hESC enhancer GRCh37_chr6:65716434-65717013 Neighboring gene uncharacterized LOC107986607 Neighboring gene uncharacterized LOC124901559 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92568 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92593 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92629 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92636 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92651 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92656 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92672 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92766 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_92772 and experimental_92778 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92831 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92928 Neighboring gene zinc finger CCCH-type containing 11C Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92954 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:66278733-66279372 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93128 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93271 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr6:66348122-66348622 and GRCh37_chr6:66348623-66349123 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_93370 and experimental_93383 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93446 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93466 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93494 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93502 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93582 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:66481227-66481728 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:66481729-66482228 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93679 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_93689 Neighboring gene SLC25A51 pseudogene 1 Neighboring gene ADH5 pseudogene 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Mutations in the EYS gene account for approximately 5% of autosomal recessive retinitis pigmentosa and cause a fairly homogeneous phenotype. Littink KW, et al. Ophthalmology, 2010 Oct. PMID 20537394
    2. EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa. Abd El-Aziz MM, et al. Nat Genet, 2008 Nov. PMID 18836446, Free PMC Article
    3. EYS Is a Protein Associated with the Ciliary Axoneme in Rods and Cones. Alfano G, et al. PLoS One, 2016. PMID 27846257, Free PMC Article
    4. Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa. Collin RW, et al. Am J Hum Genet, 2008 Nov. PMID 18976725, Free PMC Article
    5. Targeted next-generation sequencing extends the phenotypic and mutational spectrums for EYS mutations. Gu S, et al. Mol Vis, 2016. PMID 27375351, Free PMC Article

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Phototoxicity avoidance is a potential therapeutic approach for retinal dystrophy caused by EYS dysfunction.
      Title: Phototoxicity avoidance is a potential therapeutic approach for retinal dystrophy caused by EYS dysfunction.
    2. RETINITIS PIGMENTOSA ASSOCIATED WITH THE EYS C2139Y VARIANT : An Important Cause of Blindness in East Asian Populations.
      Title: RETINITIS PIGMENTOSA ASSOCIATED WITH THE EYS C2139Y VARIANT : An Important Cause of Blindness in East Asian Populations.
    3. Genotypic and phenotypic profiles of EYS gene-related retinitis pigmentosa: a retrospective study.
      Title: Genotypic and phenotypic profiles of EYS gene-related retinitis pigmentosa: a retrospective study.
    4. Likely pathogenic structural variants in genetically unsolved patients with retinitis pigmentosa revealed by long-read sequencing.
      Title: Likely pathogenic structural variants in genetically unsolved patients with retinitis pigmentosa revealed by long-read sequencing.
    5. Genotypic spectrum and phenotype correlations of EYS-associated disease in a Chinese cohort.
      Title: Genotypic spectrum and phenotype correlations of EYS-associated disease in a Chinese cohort.
    6. Investigation of genotype-phenotype relationship in Turkish patients with inherited retinal disease by next generation sequencing.
      Title: Investigation of genotype-phenotype relationship in Turkish patients with inherited retinal disease by next generation sequencing.
    7. EYS mutations and implementation of minigene assay for variant classification in EYS-associated retinitis pigmentosa in northern Sweden.
      Title: EYS mutations and implementation of minigene assay for variant classification in EYS-associated retinitis pigmentosa in northern Sweden.
    8. A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa.
      Title: A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa.
    9. ""Genetic and clinical findings in an ethnically diverse retinitis pigmentosa cohort associated with pathogenic variants in EYS"".
      Title: "Genetic and clinical findings in an ethnically diverse retinitis pigmentosa cohort associated with pathogenic variants in EYS".
    10. Identification of Novel EYS Mutations by Targeted Sequencing Analysis.
      Title: Identification of Novel EYS Mutations by Targeted Sequencing Analysis.
    Submit: New GeneRIF Correction See all GeneRIFs (50)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Retinitis pigmentosa 25
    MedGen: C1864446 OMIM: 602772 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Identification of a melanoma susceptibility locus and somatic mutation in TET2.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0663

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in detection of light stimulus involved in visual perception IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in skeletal muscle tissue regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in interphotoreceptor matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in photoreceptor outer segment IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein eyes shut homolog
    Names
    EGF-like-domain, multiple 10
    EGF-like-domain, multiple 11
    epidermal growth factor-like protein 10
    epidermal growth factor-like protein 11
    protein spacemaker homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_023443.2 RefSeqGene

      Range
      5000..1992246
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142800.2 → NP_001136272.1  protein eyes shut homolog isoform 1 precursor

      See identical proteins and their annotated locations for NP_001136272.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AL450319, BX537914, FJ416331
      Consensus CDS
      CCDS47445.1
      UniProtKB/Swiss-Prot
      Q5T1H1
      Related
      ENSP00000424243.1, ENST00000503581.6
      Conserved Domains (5) summary
      smart00282
      Location:2719 → 2856
      LamG; Laminin G domain
      cd00054
      Location:1161 → 1197
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:2149 → 2315
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam02210
      Location:2461 → 2582
      Laminin_G_2; Laminin G domain
      pfam06247
      Location:195 → 283
      Plasmod_Pvs28; Plasmodium ookinete surface protein Pvs28

    2. NM_001142801.2 → NP_001136273.1  protein eyes shut homolog isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks several 3' exons but contains an alternate 3' terminal exon, and it thus differs in its 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a substantially shorter and unique C-terminus, compared to isoform 1.
      Source sequence(s)
      AL365217, AL450319, BX537914, FJ416331
      Consensus CDS
      CCDS47446.1
      UniProtKB/TrEMBL
      F1T0I0
      Related
      ENSP00000377042.2, ENST00000393380.6
      Conserved Domains (1) summary
      pfam06247
      Location:195 → 283
      Plasmod_Pvs28; Plasmodium ookinete surface protein Pvs28

    3. NM_001292009.2 → NP_001278938.1  protein eyes shut homolog isoform 4 precursor

      See identical proteins and their annotated locations for NP_001278938.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an additional in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (4) that is longer than isoform 1.
      Source sequence(s)
      AL450319, FJ416331, FM209056
      Consensus CDS
      CCDS78156.1
      UniProtKB/Swiss-Prot
      A2RUR2, A8MVE7, B7TYK8, B7UUQ3, B7ZBE7, B7ZBE8, B7ZBR3, B9ZVD2, Q5SZM4, Q5T1H1, Q5T3C8, Q5T669, Q5TEL3, Q5TEL4, Q5VVG4, Q6UY05, Q9H557, Q9NQ15
      Related
      ENSP00000359655.3, ENST00000370621.7
      Conserved Domains (5) summary
      smart00282
      Location:2740 → 2877
      LamG; Laminin G domain
      cd00054
      Location:1161 → 1197
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:2149 → 2315
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam02210
      Location:2461 → 2582
      Laminin_G_2; Laminin G domain
      pfam06247
      Location:195 → 283
      Plasmod_Pvs28; Plasmodium ookinete surface protein Pvs28

    4. NM_198283.2 → NP_938024.1  protein eyes shut homolog isoform 3 precursor

      See identical proteins and their annotated locations for NP_938024.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several exons but contains alternate 5' and 3' exon structure, and it thus differs in its 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (3) has a substantially shorter and unique C-terminus, compared to isoform 1.
      Source sequence(s)
      AL365217, AY358133
      Consensus CDS
      CCDS4967.1
      UniProtKB/TrEMBL
      F1T0I0
      Related
      ENSP00000341818.5, ENST00000342421.9
      Conserved Domains (1) summary
      pfam06247
      Location:195 → 283
      Plasmod_Pvs28; Plasmodium ookinete surface protein Pvs28

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      63719980..65707226 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      64866189..66858763 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T1H1.5 GenPept UniProtKB/Swiss-Prot:Q5T1H1

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