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USH2A usherin [ Homo sapiens (human) ]

Gene ID: 7399, updated on 7-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (215622891..216423448, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (214863291..215663779, complement)
105.20220307 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
  • 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. USH2A mutational spectrum causing syndromic and non-syndromic retinal dystrophies in a large cohort of Mexican patients. Ordoñez-Labastida V, et al. Mol Vis, 2023. PMID 37287646, Free PMC Article
  2. Natural Disease Course in Usher Syndrome Patients Harboring USH2A Variant p.Cys870* in Exon 13, Amenable to Exon Skipping Therapy. Čadonič K, et al. Genes (Basel), 2023 Mar 5. PMID 36980924, Free PMC Article
  3. Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review. Lee BJH, et al. Ophthalmic Genet, 2023 Apr. PMID 36856324
  4. Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction. Reurink J, et al. HGG Adv, 2023 Apr 13. PMID 36785559, Free PMC Article
  5. USH2A mutation and specific driver mutation subtypes are associated with clinical efficacy of immune checkpoint inhibitors in lung cancer. Yang D, et al. J Zhejiang Univ Sci B, 2023 Feb 15. PMID 36751700, Free PMC Article

See all (151) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functional Vision in Patients With Biallelic USH2A Variants.
    Title: Functional Vision in Patients With Biallelic USH2A Variants.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Exome sequencing identified five novel USH2A variants in Korean patients with retinitis pigmentosa.
    Title: Exome sequencing identified five novel USH2A variants in Korean patients with retinitis pigmentosa.
  10. Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review.
    Title: Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review.
Submit: New GeneRIF Correction See all GeneRIFs (119)

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 response to stimulus IEA
Inferred from Electronic Annotation
more info
  
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_2023_10

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

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