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    USH2A usherin [ Homo sapiens (human) ]

    Gene ID: 7399, updated on 2-Nov-2024

    Summary

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    Official Symbol
    USH2Aprovided by HGNC
    Official Full Name
    usherinprovided by HGNC
    Primary source
    HGNC:HGNC:12601
    See related
    Ensembl:ENSG00000042781 MIM:608400; AllianceGenome:HGNC:12601
    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
    US2; RP39; USH2; dJ1111A8.1
    Summary
    This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
    Expression
    Biased expression in liver (RPKM 1.7), testis (RPKM 0.3) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See USH2A in Genome Data Viewer
    Location:
    1q41
    Exon count:
    72
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (215622891..216423448, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (214863291..215663779, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (215796233..216596790, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904598 Neighboring gene MPRA-validated peak693 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:215677085-215677330 Neighboring gene uncharacterized LOC124904599 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:215740861-215741721 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:215756646-215757845 Neighboring gene MPRA-validated peak696 silencer Neighboring gene small nucleolar RNA SNORD116 Neighboring gene potassium channel tetramerization domain containing 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4139 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:216230868-216232067 Neighboring gene NANOG hESC enhancer GRCh37_chr1:216268639-216269183 Neighboring gene USH2A antisense RNA 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216356256-216356909 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216419825-216420431 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4209 Neighboring gene USH2A antisense RNA 1 Neighboring gene mitochondrial ribosomal protein S18B pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:216566486-216566587 Neighboring gene uncharacterized LOC107985596 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:216659268-216659830 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216771579-216772306 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:216773848-216774416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2536 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4286 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4347 Neighboring gene estrogen related receptor gamma Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4384 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:216913568-216914135 Neighboring gene uncharacterized LOC124904512

    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 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. A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants. Lenassi E, et al. Eur J Hum Genet, 2015 Oct. PMID 25649381, Free PMC Article
    2. [Mutational frequencies in usherin(USH2A gene) in 26 Colombian individuals with Usher syndrome type II]. López G, et al. Biomedica, 2011 Mar. PMID 22159486
    3. A genetic basis for mechanosensory traits in humans. Frenzel H, et al. PLoS Biol, 2012. PMID 22563300, Free PMC Article
    4. Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families. Huang XF, et al. PLoS One, 2013. PMID 23737954, Free PMC Article
    5. Screening for duplications, deletions and a common intronic mutation detects 35% of second mutations in patients with USH2A monoallelic mutations on Sanger sequencing. Steele-Stallard HB, et al. Orphanet J Rare Dis, 2013 Aug 8. PMID 23924366, Free PMC Article

    See all (160) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A large-scale screening identified in USH2A gene the P3272L founder pathogenic variant explaining familial Usher syndrome in Sardinia, Italy.
      Title: A large-scale screening identified in USH2A gene the P3272L founder pathogenic variant explaining familial Usher syndrome in Sardinia, Italy.
    2. High prevalence of exon-13 variants in USH2A-related retinal dystrophies in Taiwanese population.
      Title: High prevalence of exon-13 variants in USH2A-related retinal dystrophies in Taiwanese population.
    3. Functional Vision in Patients With Biallelic USH2A Variants.
      Title: Functional Vision in Patients With Biallelic USH2A Variants.
    4. The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes.
      Title: The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes.
    5. USH2A variants causing retinitis pigmentosa or Usher syndrome provoke differential retinal phenotypes in disease-specific organoids.
      Title: USH2A variants causing retinitis pigmentosa or Usher syndrome provoke differential retinal phenotypes in disease-specific organoids.
    6. Expression of the human usherin c.2299delG mutation leads to early-onset auditory loss and stereocilia disorganization.
      Title: Expression of the human usherin c.2299delG mutation leads to early-onset auditory loss and stereocilia disorganization.
    7. Change in Cone Structure Over 24 Months in USH2A-Related Retinal Degeneration.
      Title: Change in Cone Structure Over 24 Months in USH2A-Related Retinal Degeneration.
    8. USH2A mutational spectrum causing syndromic and non-syndromic retinal dystrophies in a large cohort of Mexican patients.
      Title: USH2A mutational spectrum causing syndromic and non-syndromic retinal dystrophies in a large cohort of Mexican patients.
    9. Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction.
      Title: Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction.
    10. Natural Disease Course in Usher Syndrome Patients Harboring USH2A Variant p.Cys870* in Exon 13, Amenable to Exon Skipping Therapy.
      Title: Natural Disease Course in Usher Syndrome Patients Harboring USH2A Variant p.Cys870* in Exon 13, Amenable to Exon Skipping Therapy.
    Submit: New GeneRIF Correction See all GeneRIFs (121)

    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

    EBI GWAS Catalog

    Description
    Dissecting the genetics of chronic mucus hypersecretion in smokers with and without COPD.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables collagen binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables myosin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within establishment of protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in hair cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in inner ear auditory receptor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inner ear receptor cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in inner ear receptor cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in maintenance of animal organ identity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sensory perception of light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of USH2 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary basal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in periciliary membrane compartment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    colocalizes_with photoreceptor connecting cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    colocalizes_with photoreceptor inner segment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in stereocilia ankle link ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of stereocilia ankle link complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in stereocilium bundle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in stereocilium membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    colocalizes_with terminal bouton ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    usherin
    Names
    Usher syndrome 2A (autosomal recessive, mild)
    usher syndrome type IIa protein
    usher syndrome type-2A protein

    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_009497.2 RefSeqGene

      Range
      5001..805558
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_007123.6 → NP_009054.6  usherin isoform A precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses a different splice site in its 3' coding region when compared to variant 2. The resulting protein (isoform A) has a shorter and distinct C-terminus, compared to isoform B.
      Source sequence(s)
      AC138024, AF055580, AL358858, AL445650
      Consensus CDS
      CCDS1516.1
      Related
      ENSP00000355909.3, ENST00000366942.3
      Conserved Domains (8) summary
      smart00060
      Location:1368 → 1451
      FN3; Fibronectin type 3 domain
      smart00180
      Location:847 → 897
      EGF_Lam; Laminin-type epidermal growth factor-like domai
      smart00560
      Location:146 → 283
      LamGL; LamG-like jellyroll fold domain
      cd00055
      Location:900 → 948
      EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
      cd00063
      Location:1242 → 1357
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00041
      Location:1058 → 1132
      fn3; Fibronectin type III domain
      pfam00053
      Location:641 → 691
      Laminin_EGF; Laminin EGF domain
      cl02806
      Location:291 → 516
      Laminin_N; Laminin N-terminal (Domain VI)

    2. NM_206933.4 → NP_996816.3  usherin isoform B precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is the longer transcript and it encodes the longer isoform (B).
      Source sequence(s)
      AC092799, AL445650, AY481573
      Consensus CDS
      CCDS31025.1
      UniProtKB/Swiss-Prot
      O75445, Q5VVM9, Q6S362, Q9NS27
      UniProtKB/TrEMBL
      A0A0K1P7S2
      Related
      ENSP00000305941.3, ENST00000307340.8
      Conserved Domains (9) summary
      smart00060
      Location:1368 → 1451
      FN3; Fibronectin type 3 domain
      smart00180
      Location:847 → 897
      EGF_Lam; Laminin-type epidermal growth factor-like domai
      smart00560
      Location:146 → 283
      LamGL; LamG-like jellyroll fold domain
      cd00055
      Location:900 → 948
      EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
      cd00063
      Location:2533 → 2619
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd00110
      Location:1716 → 1868
      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 ...
      pfam00041
      Location:1150 → 1227
      fn3; Fibronectin type III domain
      pfam00053
      Location:641 → 691
      Laminin_EGF; Laminin EGF domain
      cl02806
      Location:291 → 516
      Laminin_N; Laminin N-terminal (Domain VI)

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      215622891..216423448 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      214863291..215663779 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75445.3 GenPept UniProtKB/Swiss-Prot:O75445

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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