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Aliases for USH2A Gene

Aliases for USH2A Gene

  • Usherin 2 3 3 5
  • Usher Syndrome 2A (Autosomal Recessive, Mild) 2 3
  • Usher Syndrome Type IIa Protein 3 4
  • Usher Syndrome Type-2A Protein 3 4
  • Usher Syndrome 2A 3
  • DJ1111A8.1 3
  • RP39 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 (Usherin) is a Protein Coding gene. Diseases associated with USH2A include Usher Syndrome, Type 2A and Retinitis Pigmentosa 39. GO annotations related to this gene include collagen binding and myosin binding. An important paralog of this gene is MEGF9.

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

Regulatory Elements for USH2A Gene

Enhancers for USH2A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F216388 0.2 ENCODE 11 +34.7 34714 0.4 USH2A GC01P216358
GH01F216228 0.3 FANTOM5 6.6 +194.3 194294 0.4 MRPS18BP1 LOC105372918 USH2A GC01P216238
GH01F216462 0.4 ENCODE 0.3 -39.2 -39198 0.2 GATA3 JUND CEBPB USH2A GC01P216682
GH01F216461 0.2 ENCODE 0.3 -38.4 -38359 1.0 USH2A GC01P216682
GH01F216456 0.8 ENCODE 0.3 -33.7 -33668 0.9 JUND FOS MAFK RAD21 TRIM28 USH2A GC01P216682
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around USH2A on UCSC Golden Path with GeneCards custom track

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

Genes around USH2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USH2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USH2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Post-translational modifications for USH2A Gene

  • Glycosylation at Asn 361, Asn 451, Asn 587, Asn 611, Asn 650, Asn 697, Asn 839, Asn 856, Asn 862, Asn 888, Asn 944, Asn 1011, Asn 1071, Asn 1151, Asn 1174, Asn 1379, Asn 1388, Asn 1479, Asn 1635, Asn 1779, Asn 1903, Asn 2011, Asn 2014, Asn 2048, Asn 2130, Asn 2182, Asn 2195, Asn 2258, Asn 2285, Asn 2322, Asn 2377, Asn 2382, Asn 2407, Asn 2413, Asn 2581, Asn 2584, Asn 2656, Asn 2710, Asn 2770, Asn 2788, Asn 2930, Asn 2937, Asn 2970, Asn 3032, Asn 3099, Asn 3217, Asn 3330, Asn 3419, Asn 3433, Asn 3653, Asn 3694, Asn 3733, Asn 3780, Asn 3849, Asn 3984, Asn 4202, Asn 4226, Asn 4317, Asn 4418, Asn 4564, Asn 4583, Asn 4691, Asn 4754, Asn 4800, Asn 4943, and Asn 4950
  • Modification sites at PhosphoSitePlus

Other Protein References for USH2A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for USH2A Gene

Domains & 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 16301216
GO:0005518 collagen binding IEA,IDA 14676276
GO:0017022 myosin binding ISS --
GO:0042803 protein homodimerization activity IEA --
genes like me logo Genes that share ontologies with USH2A: view
genes like me logo Genes that share phenotypes with USH2A: view

Human Phenotype Ontology for USH2A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

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

Clone 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
cytoskeleton 3
endoplasmic reticulum 2
cytosol 1

Gene Ontology (GO) - Cellular Components for USH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001917 photoreceptor inner segment IEA --
GO:0002141 stereocilia ankle link IEA --
GO:0002142 stereocilia ankle link complex ISS --
GO:0005576 extracellular region IEA --
GO:0005604 basement membrane IEA,IDA 12433396
genes like me logo Genes that share ontologies with USH2A: view

Pathways & Interactions 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 IEA,IMP 10090909
GO:0035315 hair cell differentiation ISS --
GO:0045184 establishment of protein localization IEA --
GO:0045494 photoreceptor cell maintenance IEA,IMP 10090909
genes like me logo Genes that share ontologies with USH2A: view

No data available for Pathways by source and SIGNOR curated interactions for USH2A Gene

Transcripts for USH2A Gene

mRNA/cDNA for USH2A Gene

(2) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(8) Selected AceView cDNA sequences:
(4) 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

Clone Products

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 (x15.0) and Testis (x6.8).

Protein differential expression in normal tissues from HIPED for USH2A Gene

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

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for USH2A Gene

NURSA nuclear receptor signaling pathways regulating expression of USH2A Gene:


SOURCE GeneReport for Unigene cluster for USH2A Gene:


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 expression patterns with USH2A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-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
(Pan troglodytes)
Mammalia USH2A 34 35
  • 99.24 (n)
(Canis familiaris)
Mammalia USH2A 34 35
  • 86.69 (n)
(Bos Taurus)
Mammalia USH2A 34 35
  • 86.2 (n)
(Mus musculus)
Mammalia Ush2a 34 16 35
  • 77.92 (n)
(Rattus norvegicus)
Mammalia Ush2a 34
  • 77.34 (n)
(Monodelphis domestica)
Mammalia USH2A 35
  • 74 (a)
(Gallus gallus)
Aves USH2A 34 35
  • 70.95 (n)
(Anolis carolinensis)
Reptilia USH2A 35
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.18151 34
(Danio rerio)
Actinopterygii ush2a 34 35
  • 56.51 (n)
fruit fly
(Drosophila melanogaster)
Insecta LanB1 35
  • 21 (a)
(Caenorhabditis elegans)
Secernentea lam-1 35
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 38 (a)
Species where no ortholog for USH2A was found in the sources mined by GeneCards:
  • 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
rs111033263 Usher syndrome 2A (USH2A) [MIM:276901], Likely pathogenic 215,799,066(-) ATTCC(C/T)GCTGT reference, missense
rs111033264 Usher syndrome 2A (USH2A) [MIM:276901], Pathogenic 215,782,762(-) TAAAC(C/T)GGAGA reference, missense
rs111033273 Usher syndrome 2A (USH2A) [MIM:276901], Pathogenic 216,321,921(-) ATAGA(C/T)GCCTC reference, missense
rs111033275 Retinitis pigmentosa 39 (RP39) [MIM:613809], Usher syndrome 2A (USH2A) [MIM:276901], Likely benign 215,675,568(-) TGAAT(C/T)GTCAG reference, missense
rs121912599 Usher syndrome 2A (USH2A) [MIM:276901], Pathogenic 216,325,492(-) GTACT(A/G)CATTC reference, missense

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

Variant ID Type Subtype PubMed ID
dgv261n106 CNV deletion 24896259
dgv279e59 CNV duplication 20981092
dgv816n54 CNV loss 21841781
dgv817n54 CNV loss 21841781
dgv818n54 CNV loss 21841781
dgv819n54 CNV loss 21841781
esv1292949 CNV deletion 17803354
esv1560943 CNV insertion 17803354
esv1749994 CNV deletion 17803354
esv23405 CNV loss 19812545
esv2496367 CNV deletion 19546169
esv2652396 CNV deletion 19546169
esv2669208 CNV deletion 23128226
esv2674039 CNV deletion 23128226
esv2674123 CNV deletion 23128226
esv2722739 CNV deletion 23290073
esv2722750 CNV deletion 23290073
esv2722761 CNV deletion 23290073
esv2722772 CNV deletion 23290073
esv2722783 CNV deletion 23290073
esv2722794 CNV deletion 23290073
esv2722807 CNV deletion 23290073
esv2762219 CNV loss 21179565
esv2763680 CNV loss 21179565
esv2764185 CNV loss 21179565
esv3302618 CNV tandem duplication 20981092
esv3309838 CNV mobile element insertion 20981092
esv3325216 CNV insertion 20981092
esv3329628 CNV insertion 20981092
esv3422062 CNV insertion 20981092
esv3546533 CNV deletion 23714750
esv3546567 CNV deletion 23714750
esv3546578 CNV deletion 23714750
esv3578428 CNV loss 25503493
esv3578429 CNV loss 25503493
esv3578430 CNV loss 25503493
esv3588816 CNV loss 21293372
esv3588817 CNV loss 21293372
esv3588818 CNV loss 21293372
esv3588819 CNV loss 21293372
esv3588821 CNV loss 21293372
esv3588822 CNV loss 21293372
esv3588823 CNV loss 21293372
esv3588824 CNV loss 21293372
esv6553 CNV gain 19470904
nsv1006028 CNV loss 25217958
nsv1007720 CNV loss 25217958
nsv1012279 CNV loss 25217958
nsv4554 CNV insertion 18451855
nsv468116 CNV loss 19166990
nsv468127 CNV loss 19166990
nsv473278 CNV novel sequence insertion 20440878
nsv474190 CNV novel sequence insertion 20440878
nsv476146 CNV novel sequence insertion 20440878
nsv520724 CNV loss 19592680
nsv523863 CNV loss 19592680
nsv527176 CNV loss 19592680
nsv527827 CNV loss 19592680
nsv549183 CNV loss 21841781
nsv549190 CNV loss 21841781
nsv549191 CNV loss 21841781
nsv549192 CNV loss 21841781
nsv549193 CNV loss 21841781
nsv549194 CNV loss 21841781
nsv549195 CNV loss 21841781
nsv549196 CNV loss 21841781
nsv549199 CNV gain 21841781
nsv832548 CNV gain 17160897
nsv954217 CNV deletion 24416366
nsv998835 CNV loss 25217958
nsv999211 CNV loss 25217958

Variation tolerance for USH2A Gene

Residual Variation Intolerance Score: 99.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.71; 97.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USH2A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for USH2A Gene

MalaCards: The human disease database

(19) MalaCards diseases for USH2A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type 2a
  • retinal disease in usher syndrome type iia, modifier of
retinitis pigmentosa 39
  • rp39
ush2a-related retinitis pigmentosa
  • rp39
usher syndrome type ii
  • ush2
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search USH2A in MalaCards View complete list of genes associated with diseases


  • 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.
  • 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:26377068, ECO:0000269 PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.

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
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with USH2A: view

Publications for USH2A Gene

  1. 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 22 46 64
  2. 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 22 46 64
  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 22 46 64
  4. Comprehensive screening of the USH2A gene in Usher syndrome type II and non-syndromic recessive retinitis pigmentosa. (PMID: 15325563) Seyedahmadi B.J. … Dryja T.P. (Exp. Eye Res. 2004) 3 4 22 46 64
  5. 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 22 64

Products for USH2A Gene

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