Free for academic non-profit institutions. Other users need a Commercial license

Aliases for USH2A Gene

Aliases for USH2A Gene

  • Usher Syndrome 2A (Autosomal Recessive, Mild) 2 3
  • Usher Syndrome Type IIa Protein 3 4
  • Usher Syndrome Type-2A Protein 3 4
  • Usherin 2 3
  • RP39 3 6
  • DJ1111A8.1 3
  • USH2 3
  • US2 3

External Ids for USH2A Gene

Previous HGNC Symbols for USH2A Gene

  • USH2

Previous GeneCards Identifiers for USH2A Gene

  • GC01M215005
  • GC01M212197
  • GC01M9A0069
  • GC01M9A3403
  • GC01M9A2184
  • GC01M212184
  • GC01M213862
  • GC01M215796
  • GC01M186470

Summaries for USH2A Gene

Entrez Gene Summary for USH2A Gene

  • 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]

GeneCards Summary for USH2A Gene

USH2A (Usher Syndrome 2A (Autosomal Recessive, Mild)) is a Protein Coding gene. Diseases associated with USH2A include retinitis pigmentosa 39 and usher syndrome, type 2a. GO annotations related to this gene include collagen binding and myosin binding. An important paralog of this gene is LAMC2.

UniProtKB/Swiss-Prot for USH2A Gene

  • Involved in hearing and vision

Gene Wiki entry for USH2A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USH2A Gene

Genomics for USH2A Gene

Genomic Location for USH2A Gene

215,622,894 bp from pter
216,423,396 bp from pter
800,503 bases
Minus strand

Genomic View for USH2A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for USH2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USH2A Gene

No data available for Regulatory Elements for USH2A Gene

Proteins for USH2A Gene

  • Protein details for USH2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q5VVM9
    • Q6S362
    • Q9NS27

    Protein attributes for USH2A Gene

    5202 amino acids
    Molecular mass:
    575600 Da
    Quaternary structure:
    • Interacts with collagen IV and fibronectin via its laminin EGF-like domains. Interaction with collagen may be required for stable integration into the basement membrane. Interacts with USH1C and WHRN. Interacts with NINL. Interacts with PDZD7.

    Alternative splice isoforms for USH2A Gene


neXtProt entry for USH2A Gene

Proteomics data for USH2A Gene at MOPED

Post-translational modifications for USH2A Gene

  • Glycosylation at Asn361, Asn451, Asn587, Asn611, Asn650, Asn697, Asn839, Asn856, Asn862, Asn888, Asn944, Asn1011, Asn1071, Asn1151, Asn1174, Asn1379, Asn1388, Asn1479, Asn1635, Asn1779, Asn1903, Asn2011, Asn2014, Asn2048, Asn2130, Asn2182, Asn2195, Asn2258, Asn2285, Asn2322, Asn2377, Asn2382, Asn2407, Asn2413, Asn2581, Asn2584, Asn2656, Asn2710, Asn2770, Asn2788, Asn2930, Asn2937, Asn2970, Asn3032, Asn3099, Asn3217, Asn3330, Asn3419, Asn3433, Asn3653, Asn3694, Asn3733, Asn3780, Asn3849, Asn3984, Asn4202, Asn4226, Asn4317, Asn4418, Asn4564, Asn4583, Asn4691, Asn4754, Asn4800, Asn4943, and Asn4950
  • Modification sites at PhosphoSitePlus

Other Protein References for USH2A Gene

No data available for DME Specific Peptides for USH2A Gene

Domains for USH2A Gene

Gene Families for USH2A Gene

Suggested Antigen Peptide Sequences for USH2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The PDZ-binding motif probably mediates the association with some of the PDZ domains of USH1C and WHRN.
  • The PDZ-binding motif probably mediates the association with some of the PDZ domains of USH1C and WHRN.
  • Contains 35 fibronectin type-III domains.
  • Contains 10 laminin EGF-like domains.
  • Contains 2 laminin G-like domains.
  • Contains 1 laminin N-terminal domain.
genes like me logo Genes that share domains with USH2A: view

Function for USH2A Gene

Molecular function for USH2A Gene

GENATLAS Biochemistry:
putative extracellular matrix protein expressed in fetal cochlea,eye,brain,kidney and in adult retina,with homology to laminin mutated in Usher,type IIA
UniProtKB/Swiss-Prot Function:
Involved in hearing and vision

Gene Ontology (GO) - Molecular Function for USH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 20440071
GO:0005518 collagen binding IDA 14676276
GO:0017022 myosin binding ISS --
genes like me logo Genes that share ontologies with USH2A: view
genes like me logo Genes that share phenotypes with USH2A: view

Animal Models for USH2A Gene

MGI Knock Outs for USH2A:

Animal Model Products

miRNA for USH2A Gene

miRTarBase miRNAs that target USH2A

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for USH2A

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for USH2A Gene

Localization for USH2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for USH2A Gene

Cell projection, stereocilium membrane; Single-pass type I membrane protein. Note=Probable component of the interstereocilia ankle links in the inner ear sensory cells.
Isoform 2: Secreted.

Subcellular locations from

Jensen Localization Image for USH2A Gene COMPARTMENTS Subcellular localization image for USH2A gene
Compartment Confidence
extracellular 5
plasma membrane 5
cytosol 2
endoplasmic reticulum 2
nucleus 1

Gene Ontology (GO) - Cellular Components for USH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001917 photoreceptor inner segment IEA --
GO:0002142 stereocilia ankle link complex ISS --
GO:0005604 basement membrane IDA 12433396
GO:0005737 cytoplasm IDA 16434480
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with USH2A: view

Pathways for USH2A Gene

SuperPathways for USH2A Gene

No Data Available

Gene Ontology (GO) - Biological Process for USH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0007605 sensory perception of sound IMP 10090909
GO:0035315 hair cell differentiation ISS --
GO:0045494 photoreceptor cell maintenance IMP 10090909
GO:0048496 maintenance of organ identity IMP 15671307
genes like me logo Genes that share ontologies with USH2A: view

No data available for Pathways by source for USH2A Gene

Transcripts for USH2A Gene

mRNA/cDNA for USH2A Gene

(8) Selected AceView cDNA sequences:
(2) Additional mRNA sequences :
(2) REFSEQ mRNAs :
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for USH2A Gene

Usher syndrome 2A (autosomal recessive, mild):
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for USH2A

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for USH2A Gene

No ASD Table

Relevant External Links for USH2A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USH2A Gene

mRNA expression in normal human tissues for USH2A Gene

mRNA differential expression in normal tissues according to GTEx for USH2A Gene

This gene is overexpressed in Liver (15.0) and Testis (6.8).

Protein differential expression in normal tissues for USH2A Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (63.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for USH2A Gene

SOURCE GeneReport for Unigene cluster for USH2A Gene Hs.655974

mRNA Expression by UniProt/SwissProt for USH2A Gene

Tissue specificity: Present in the basement membrane of many, but not all tissues. Expressed in retina, cochlea, small and large intestine, pancreas, bladder, prostate, esophagus, trachea, thymus, salivary glands, placenta, ovary, fallopian tube, uterus and testis. Absent in many other tissues such as heart, lung, liver, kidney and brain. In the retina, it is present in the basement membranes in the Bruchs layer choroid capillary basement membranes, where it localizes just beneath the retinal pigment epithelial cells (at protein level). Weakly expressed. Isoform 2 is expressed in fetal eye, cochlea and heart, and at very low level in brain, CNS, intestine, skeleton, tongue, kidney and lung. Isoform 2 is not expressed in stomach and liver. In adult tissues, isoform 2 is expressed in neural retina and testis, and at low level in brain, heart, kidney and liver. Isoform 1 displays a similar pattern of expression but is expressed at very low level in fetal cochlea.
genes like me logo Genes that share expressions with USH2A: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Expression partners for USH2A Gene

Orthologs for USH2A Gene

This gene was present in the common ancestor of animals.

Orthologs for USH2A Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia USH2A 35
  • 86.2 (n)
  • 83.54 (a)
USH2A 36
  • 83 (a)
(Canis familiaris)
Mammalia USH2A 35
  • 86.69 (n)
  • 84.03 (a)
USH2A 36
  • 83 (a)
(Mus musculus)
Mammalia Ush2a 35
  • 77.92 (n)
  • 71.57 (a)
Ush2a 16
Ush2a 36
  • 71 (a)
(Pan troglodytes)
Mammalia USH2A 35
  • 99.24 (n)
  • 98.67 (a)
USH2A 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Ush2a 35
  • 77.34 (n)
  • 71.45 (a)
(Monodelphis domestica)
Mammalia USH2A 36
  • 74 (a)
(Gallus gallus)
Aves USH2A 35
  • 70.95 (n)
  • 66.96 (a)
USH2A 36
  • 56 (a)
(Anolis carolinensis)
Reptilia USH2A 36
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.18151 35
(Danio rerio)
Actinopterygii ush2a 35
  • 56.51 (n)
  • 50.58 (a)
ush2a 36
  • 52 (a)
fruit fly
(Drosophila melanogaster)
Insecta LanB1 36
  • 21 (a)
(Caenorhabditis elegans)
Secernentea lam-1 36
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 38 (a)
Species with no ortholog for USH2A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USH2A Gene

Gene Tree for USH2A (if available)
Gene Tree for USH2A (if available)

Paralogs for USH2A Gene

Paralogs for USH2A Gene

(1) SIMAP similar genes for USH2A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with USH2A: view

Variants for USH2A Gene

Sequence variations from dbSNP and Humsavar for USH2A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs301730 -- 216,113,696(+) TTTTT(C/T)AACAA intron-variant
rs301732 -- 216,115,721(+) AAATA(C/T)ATTTC intron-variant
rs301733 -- 216,116,573(+) AATAC(A/G)ATACT intron-variant
rs301738 -- 216,132,803(+) ACATG(A/G)CACTT intron-variant
rs301739 -- 216,134,056(+) TAATA(C/T)AGAGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USH2A Gene

Variant ID Type Subtype PubMed ID
nsv873171 CNV Gain 21882294
esv23405 CNV Loss 19812545
esv2674123 CNV Deletion 23128226
nsv468116 CNV Loss 19166990
esv259592 OTHER Complex 20981092
nsv832548 CNV Gain 17160897
nsv468127 CNV Loss 19166990
nsv520724 CNV Loss 19592680
esv2722739 CNV Deletion 23290073
esv2722750 CNV Deletion 23290073
esv1749994 CNV Deletion 17803354
esv2722761 CNV Deletion 23290073
nsv527176 CNV Loss 19592680
nsv873172 CNV Loss 21882294
dgv528n71 CNV Loss 21882294
esv2652396 CNV Deletion 19546169
esv2722772 CNV Deletion 23290073
esv1292949 CNV Deletion 17803354
nsv873175 CNV Loss 21882294
esv268517 CNV Insertion 20981092
esv273238 CNV Insertion 20981092
esv2669208 CNV Deletion 23128226
nsv873176 CNV Loss 21882294
esv6553 CNV Gain 19470904
esv2496367 CNV Deletion 19546169
esv2674039 CNV Deletion 23128226
esv1560943 CNV Insertion 17803354
nsv4554 CNV Insertion 18451855
esv274110 CNV Insertion 20981092
nsv527827 CNV Loss 19592680
nsv523863 CNV Loss 19592680
esv2722783 CNV Deletion 23290073
esv2722794 CNV Deletion 23290073
esv2722807 CNV Deletion 23290073

Relevant External Links for USH2A Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USH2A Gene

Disorders for USH2A Gene

(2) OMIM Diseases for USH2A Gene (608400)


  • Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269 PubMed:10729113, ECO:0000269 PubMed:10738000, ECO:0000269 PubMed:10909849, ECO:0000269 PubMed:11311042, ECO:0000269 PubMed:12112664, ECO:0000269 PubMed:12525556, ECO:0000269 PubMed:14970843, ECO:0000269 PubMed:15015129, ECO:0000269 PubMed:15025721, ECO:0000269 PubMed:15241801, ECO:0000269 PubMed:15325563, ECO:0000269 PubMed:17085681, ECO:0000269 PubMed:17405132, ECO:0000269 PubMed:18273898, ECO:0000269 PubMed:18452394, ECO:0000269 PubMed:19683999, ECO:0000269 PubMed:19737284, ECO:0000269 PubMed:20309401, ECO:0000269 PubMed:20440071, ECO:0000269 PubMed:20507924, ECO:0000269 PubMed:21593743, ECO:0000269 PubMed:21686329, ECO:0000269 PubMed:22004887, ECO:0000269 PubMed:23737954, ECO:0000269 PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:10775529, ECO:0000269 PubMed:12112664, ECO:0000269 PubMed:12427073, ECO:0000269 PubMed:15325563, ECO:0000269 PubMed:16098008, ECO:0000269 PubMed:17296898, ECO:0000269 PubMed:20507924, ECO:0000269 PubMed:21686329, ECO:0000269 PubMed:22334370, ECO:0000269 PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for USH2A Gene

(8) Novoseek inferred disease relationships for USH2A Gene

Disease -log(P) Hits PubMed IDs
usher syndrome 98 39
retinitis pigmentosa 92.4 11
congenital hearing loss 84.7 1
hearing loss sensorineural 73.6 2
visual impairment 65.4 1

Genatlas disease for USH2A Gene

Usher syndrome,type IIA,congenital,moderate to severe neurosensory deafness,normal vestibular function and retinitis pigmentosa,exhibiting phenotypic variation including atypical cases with vestibular dysfunction

Relevant External Links for USH2A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with USH2A: view

Publications for USH2A Gene

  1. Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa. (PMID: 10729113) Weston M.D. … Kimberling W.J. (Am. J. Hum. Genet. 2000) 2 3 4 23
  2. Mutation of a gene encoding a protein with extracellular matrix motifs in Usher syndrome type IIa. (PMID: 9624053) Eudy J.D. … Sumegi J. (Science 1998) 2 3 4 23
  3. Genetic analysis of 2299delG and C759F mutations (USH2A) in patients with visual and/or auditory impairments. (PMID: 14970843) Aller E. … Beneyto M. (Eur. J. Hum. Genet. 2004) 3 4 23 48
  4. Microarray-based mutation analysis of 183 Spanish families with Usher syndrome. (PMID: 19683999) Jaijo T. … MillA!n J.M. (Invest. Ophthalmol. Vis. Sci. 2010) 3 4 23 48
  5. Four USH2A founder mutations underlie the majority of Usher syndrome type 2 cases among non-Ashkenazi Jews. (PMID: 18452394) Auslender N. … Ben-Yosef T. (Genet. Test. 2008) 3 4 23 48

Products for USH2A Gene

Sources for USH2A Gene

Back to Top