Gene Gene information from NCBI Gene database.
Entrez ID 7399
Gene name Usherin
Gene symbol USH2A
Synonyms (NCBI Gene)
RP39US2USH2dJ1111A8.1
Chromosome 1
Chromosome location 1q41
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. Mutation
SNPs SNP information provided by dbSNP.
462
SNP ID Visualize variation Clinical significance Consequence
rs730254 C>G,T Conflicting-interpretations-of-pathogenicity, benign-likely-benign Genic downstream transcript variant, coding sequence variant, missense variant
rs34713174 T>- Pathogenic Coding sequence variant, frameshift variant, genic downstream transcript variant
rs35818432 G>C Likely-pathogenic, uncertain-significance, likely-benign Coding sequence variant, missense variant
rs41302239 G>C Uncertain-significance, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant, genic downstream transcript variant
rs41303255 T>A Benign-likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
61
miRTarBase ID miRNA Experiments Reference
MIRT016756 hsa-miR-335-5p Microarray 18185580
MIRT022120 hsa-miR-124-3p Microarray 18668037
MIRT1477231 hsa-miR-3923 CLIP-seq
MIRT1477232 hsa-miR-4459 CLIP-seq
MIRT1477233 hsa-miR-4699-3p CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
51
GO ID Ontology Definition Evidence Reference
GO:0001917 Component Photoreceptor inner segment IEA
GO:0001917 Component Photoreceptor inner segment ISS
GO:0002141 Component Stereocilia ankle link IEA
GO:0002141 Component Stereocilia ankle link ISS
GO:0002142 Component Stereocilia ankle link complex IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608400 12601 ENSG00000042781
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O75445
Protein name Usherin (Usher syndrome type IIa protein) (Usher syndrome type-2A protein)
Protein function Involved in hearing and vision as member of the USH2 complex. In the inner ear, required for the maintenance of the hair bundle ankle formation, which connects growing stereocilia in developing cochlear hair cells. In retina photoreceptors, the
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13385 Laminin_G_3 130 286 Domain
PF00055 Laminin_N 290 516 Laminin N-terminal (Domain VI) Family
PF00053 Laminin_EGF 518 566 Laminin EGF domain Domain
PF00053 Laminin_EGF 575 634 Laminin EGF domain Domain
PF00053 Laminin_EGF 641 691 Laminin EGF domain Domain
PF00053 Laminin_EGF 694 744 Laminin EGF domain Domain
PF00053 Laminin_EGF 747 794 Laminin EGF domain Domain
PF00053 Laminin_EGF 795 844 Laminin EGF domain Domain
PF00053 Laminin_EGF 847 897 Laminin EGF domain Domain
PF00053 Laminin_EGF 900 948 Laminin EGF domain Domain
PF00053 Laminin_EGF 951 999 Laminin EGF domain Domain
PF00053 Laminin_EGF 1002 1050 Laminin EGF domain Domain
PF00041 fn3 1147 1231 Fibronectin type III domain Domain
PF00041 fn3 1243 1351 Fibronectin type III domain Domain
PF00041 fn3 1367 1456 Fibronectin type III domain Domain
PF02210 Laminin_G_2 1548 1681 Laminin G domain Domain
PF02210 Laminin_G_2 1744 1871 Laminin G domain Domain
PF00041 fn3 1956 2044 Fibronectin type III domain Domain
PF00041 fn3 2437 2522 Fibronectin type III domain Domain
PF00041 fn3 2534 2614 Fibronectin type III domain Domain
PF00041 fn3 2628 2712 Fibronectin type III domain Domain
PF00041 fn3 2725 2803 Fibronectin type III domain Domain
PF00041 fn3 2927 3006 Fibronectin type III domain Domain
PF00041 fn3 3592 3670 Fibronectin type III domain Domain
PF00041 fn3 3776 3856 Fibronectin type III domain Domain
PF00041 fn3 3969 4057 Fibronectin type III domain Domain
PF00041 fn3 4159 4253 Fibronectin type III domain Domain
PF00041 fn3 4357 4432 Fibronectin type III domain Domain
PF00041 fn3 4533 4621 Fibronectin type III domain Domain
PF00041 fn3 4827 4921 Fibronectin type III domain Domain
Tissue specificity 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 a
Sequence
MNCPVLSLGSGFLFQVIEMLIFAYFASISLTESRGLFPRLENVGAFKKVSIVPTQAVCGL
PDRSTFCHSSAAAESIQFCTQRFCIQDCPYRSSHPTYTALFSAGLSSCITPDKNDLHPNA
HSNSASFIFGNHKSCFSSPPSPKLMASFTLAVWLKPEQQGVMCVIEKTVDGQIVFKLTIS
EKETMFYYRTVNGLQPPIKVMTLGRILVKKWIHLSVQVHQTKISFFINGVEKDHTPFNAR
TLSGSITDFASGTVQIGQSLNGLEQFVGRMQDFRLYQVALTNREIL
EVFSGDLLRLHAQS
HCRCPGSHPRVHPLAQRYCIPNDAGDTADNRVSRLNPEAHPLSFVNDNDVGTSWVSNVFT
NITQLNQGVTISVDLENGQYQVFYIIIQFFSPQPTEIRIQRKKENSLDWEDWQYFARNCG
AFGMKNNGDLEKPDSVNCLQLSNFTPYSRGNVTFSILTPGPNYRPGYNNFYNTPSLQEFV
KATQIRFHFHGQYYTTETAVNLRHRYYAVDEITISG
RCQCHGHADNCDTTSQPYRCLCSQ
ESFTEGLHCDRCLPLYNDKPFRQGDQ
VYAFNCKPCQCNSHSKSCHYNISVDPFPFEHFRG
GGGVCDDCEHNTTGRNCELCKDYFFRQVGADPSA
IDVCKPCDCDTVGTRNGSILCDQIGG
QCNCKRHVSGRQCNQCQNGFYNLQELDPDGC
SPCNCNTSGTVDGDITCHQNSGQCKCKAN
VIGLRCDHCNFGFKFLRSFNDVGC
EPCQCNLHGSVNKFCNPHSGQCECKKEAKGLQCDTC
RENFYGLDVTNCKA
CDCDTAGSLPGTVCNAKTGQCICKPNVEGRQCNKCLEGNFYLRQNN
SFLC
LPCNCDKTGTINGSLLCNKSTGQCPCKLGVTGLRCNQCEPHRYNLTIDNFQHCQMC
ECDSLGTLPGTICDPISGQCLCVPNRQGRRCNQCQPGFYISPGNATGC
LPCSCHTTGAVN
HICNSLTGQCVCQDASIAGQRCDQCKDHYFGFDPQTGRC
QPCNCHLSGALNETCHLVTGQ
CFCKQFVTGSKCDACVPSASHLDVNNLLGC
SKTPFQQPPPRGQVQSSSAINLSWSPPDSP
NAHWLTYSLLRDGFEIYTTEDQYPYSIQYFLDTDLLPYTKYSYYIETTNVHGSTRSVAVT
YKTKPGVPEGNLTLSYIIPIGSDSVTLTWTTLSNQSGPIEKYILSCAPLAGGQPCVSYEG
HETSATIWNLVPFAKYDFSVQACTSGGCLHS
LPITVTTAQAPPQRLSPPKMQKISSTELH
VEWSPPAELNGIIIRYELYMRRLRSTKETTSEESRVFQSSGWLSPHSFVESANENALKPP
QTMTTITGLEPYTKYEFRVLAVNMAGSVSSA
WVSERTGESAPVFMIPPSVFPLSSYSLNI
SWEKPADNVTRGKVVGYDINMLSEQSPQQSIPMAFSQLLHTAKSQELSYTVEGLKPYRIY
EFTITLCNSVGCVTSA
SGAGQTLAAAPAQLRPPLVKGINSTTIHLRWFPPEELNGPSPIY
QLERRESSLPALMTTMMKGIRFIGNGYCKFPSSTHPVNTDFTGIKASFRTKVPEGLIVFA
ASPGNQEEYFALQLKKGRLYFLFDPQGSPVEVTTTNDHGKQYSDGKWHEIIAIRHQAFGQ
ITLDGIYTGSSAILNGSTVIGDNTGVFLGGLPRSYTILRKDPEIIQKGFVGCLKDVHFMK
N
YNPSAIWEPLDWQSSEEQINVYNSWEGCPASLNEGAQFLGAGFLELHPYMFHGGMNFEI
SFKFRTDQLNGLLLFVYNKDGPDFLAMELKSGILTFRLNTSLAFTQVDLLLGLSYCNGKW
NKVIIKKEGSFISASVNGLMKHASESGDQPLVVNSPVYVGGIPQELLNSYQHLCLEQGFG
GCMKDVKFTRG
AVVNLASVSSGAVRVNLDGCLSTDSAVNCRGNDSILVYQGKEQSVYEGG
LQPFTEYLYRVIASHEGGSVYSDWSRGRTTGAAPQSVPTPSRVRSLNGYSIEVTWDEPVV
RGVIEKYILKAYSEDSTRPPRMPSASAEFVNTSNLTGILTGLLPFKNYAVTLTACTLAGC
TESS
HALNISTPQEAPQEVQPPVAKSLPSSLLLSWNPPKKANGIITQYCLYMDGRLIYSG
SEENYIVTDLAVFTPHQFLLSACTHVGCTNSSWVLLYTAQLPPEHVDSPVLTVLDSRTIH
IQWKQPRKISGILERYVLYMSNHTHDFTIWSVIYNSTELFQDHMLQYVLPGNKYLIKLGA
CTGGGCTVSEASEALTDEDIPEGVPAPKAHSYSPDSFNVSWTEPEYPNGVITSYGLYLDG
ILIHNSSELSYRAYGFAPWSLHSFRVQACTAKGCALGPLVENRTLEAPPEGTVNVFVKTQ
GSRKAHVRWEAPFRPNGLLTHSVLFTGIFYVDPVGNNYTLLNVTKVMYSGEETNLWVLID
GLVPFTNYTVQVNISNSQGSLITDPITIAMPPGAPDGVLPPRLSSATPTSLQVVWSTPAR
NNAPGSPRYQLQMRSGDSTHGFLELFSNPSASLSYEVSDLQPYTEYMFRLVASNGFGSAH
SS
WIPFMTAEDKPGPVVPPILLDVKSRMMLVTWQHPRKSNGVITHYNIYLHGRLYLRTPG
NVTNCTVMHLHPYTAYKFQVEACTSKGCSLSPES
QTVWTLPGAPEGIPSPELFSDTPTSV
IISWQPPTHPNGLVENFTIERRVKGKEEVTTLVTLPRSHSMRFIDKTSALSPWTKYEYRV
LMSTLHGGTNSS
AWVEVTTRPSRPAGVQPPVVTVLEPDAVQVTWKPPLIQNGDILSYEIH
MPDPHITLTNVTSAVLSQKVTHLIPFTNYSVTIVACSGGNGYL
GGCTESLPTYVTTHPTV
PQNVGPLSVIPLSESYVVISWQPPSKPNGPNLRYELLRRKIQQPLASNPPEDLNRWHNIY
SGTQWLYEDKGLSRFTTYEYMLFVHNSVGFTPSREVTVTTLAGLPERGANLTASVLNHTA
IDVRWAKPTVQDLQGEVEYYTLFWSSATSNDSLKILPDVNSHVIGHLKPNTEYWIFISVF
NGVHSI
NSAGLHATTCDGEPQGMLPPEVVIINSTAVRVIWTSPSNPNGVVTEYSIYVNNK
LYKTGMNVPGSFILRDLSPFTIYDIQVEVCTIYACVKSNGTQITTVEDTPSDIPTPTIRG
ITSRSLQIDWVSPRKPNGIILGYDLLWKTWYPCAKTQKLVQDQSDELCKAVRCQKPESIC
GHICYSSEAKVCCNGVLYNPKPGHRCCEEKYIPFVLNSTGVCCGGRIQEAQPNHQCCSGY
YARILPGEVCCPDEQHNRVSVGIGDSCCGRMPYSTSGNQICCAGRLHDGHGQKCCGRQIV
SNDLECCGGEEGVVYNRLPGMFCCGQDYVNMSDTICCSASSGESKAHIKKNDPVPVKCCE
TELIPKSQKCCNGVGYNPLKYVCSDKISTGMMMKETKECRILCPASMEATEHCGRCDFNF
TSHICTVIRGSHNSTGKASIEEMCSSAEETIHTGSVNTYSYTDVNLKPYMTYEYRISAWN
SYGRGLSKAVRARTKEDVPQGVSPPTWTKIDNLEDTIVLNWRKPIQSNGPIIYYILLRNG
IERFRGTSLSFSDKEGIQPFQEYSYQLKACTVAGCATSSKVVAATTQGVPESILPPSITA
LSAVALHLSWSVPEKSNGVIKEYQIRQVGKGLIHTDTTDRRQHTVTGLQPYTNYSFTLTA
CTSAGCTSSE
PFLGQTLQAAPEGVWVTPRHIIINSTTVELYWSLPEKPNGLVSQYQLSRN
GNLLFLGGSEEQNFTDKNLEPNSRYTYKLEVKTGGGSSASDDYIVQTPMSTPEEIYPPYN
ITVIGPYSIFVAWIPPGILIPEIPVEYNVLLNDGSVTPLAFSVGHHQSTLLENLTPFTQY
EIRIQACQNGSCGVSS
RMFVKTPEAAPMDLNSPVLKALGSACIEIKWMPPEKPNGIIINY
FIYRRPAGIEEESVLFVWSEGALEFMDEGDTLRPFTLYEYRVRACNSKGSVESLWSLTQT
LEAPPQDFPAPWAQATSAHSVLLNWTKPESPNGIISHYRVVYQERPDDPTFNSPTVHAFT
VKGTSHQAHLYGLEPFTTYRIGVVAANHAGEILSPWT
LIQTLESSPSGLRNFIVEQKENG
RALLLQWSEPMRTNGVIKTYNIFSDGFLEYSGLNRQFLFRRLDPFTLYTLTLEACTRAGC
AHSAPQPLWTDEAPPDSQLAPTVHSVKSTSVELSWSEPVNPNGKIIRYEVIRRCFEGKAW
GNQTIQADEKIVFTEYNTERNTFMYNDTGLQPWTQCEYKIYTWNSAGHTCSSW
NVVRTLQ
APPEGLSPPVISYVSMNPQKLLISWIPPEQSNGIIQSYRLQRNEMLYPFSFDPVTFNYTD
EELLPFSTYSYALQACTSGGCSTSKPTSITTLEAAPSEVSPPDLWAVSATQMNVCWSPPT
VQNGKITKYLVRYDNKESLAGQGLCLLVSHLQPYSQYNFSLVACTNGGCTAS
VSKSAWTM
EALPENMDSPTLQVTGSESIEITWKPPRNPNGQIRSYELRRDGTIVYTGLETRYRDFTLT
PGVEYSYTVTASNSQGGILSPLVKDRTSPSAPSGMEPPKLQARGPQEILVNWDPPVRTNG
DIINYTLFIRELFERETKIIHINTTHNSFGMQSYIVNQLKPFHRYEIRIQACTTLGCASS
D
WTFIQTPEIAPLMQPPPHLEVQMAPGGFQPTVSLLWTGPLQPNGKVLYYELYRRQIATQ
PRKSNPVLIYNGSSTSFIDSELLPFTEYEYQVWAVNSAGKAPSSWTWCRTGPAPPEGLRA
PTFHVISSTQAVVNISAPGKPNGIVSLYRLFSSSAHGAETVLSEGMATQQTLHGLQAFTN
YSIGVEACTCFNCCSKGPTAELRTHPAPPSGLSSPQIGTLASRTASFRWSPPMFPNGVIH
SYELQFHVACPPDSALPCTPSQIETKYTGLGQKASLGGLQPYTTYKLRVVAHNEVGSTAS
E
WISFTTQKELPQYRAPFSVDSNLSVVCVNWSDTFLLNGQLKEYVLTDGGRRVYSGLDTT
LYIPRTADKTFFFQVICTTDEGSVKTPLIQYDTSTGLGLVLTTPGKKKGSRSKSTEFYSE
LWFIVLMAMLGLILLAIFLSLILQRKIHKEPYIRERPPLVPLQKRMSPLNVYPPGENHMG
LADTKIPRSGTPVSIRSNRSACVLRIPSQNQTSLTYSQGSLHRSVSQLMDIQDKKVLMDN
SLWEAIMGHNSGLYVDEEDLMNAIKDFSSVTKERTTFTDTHL
Sequence length 5202
Interactions View interactions
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
6864
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Abnormal macular morphology Pathogenic rs111033272 RCV000627017
Autosomal dominant nonsyndromic hearing loss 36 Pathogenic; Likely pathogenic rs2464391981, rs111033265, rs1355461608 RCV003155536
RCV003155537
RCV003155539
Autosomal recessive retinitis pigmentosa Pathogenic; Likely pathogenic rs80338902, rs876657731, rs2034900559, rs2036952419, rs2037760415 RCV001257905
RCV001257907
RCV001257906
RCV001257873
RCV001257908
Blindness Pathogenic rs111033272 RCV000627017
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
- no classification for the single variant rs794729203, rs587776538, rs1558028562 -
Acute myeloid leukemia Likely benign; Conflicting classifications of pathogenicity rs75415213, rs45549044 RCV005916115
RCV005890282
Bardet-Biedl syndrome Benign rs41315579 RCV003224127
Childhood onset hearing loss Conflicting classifications of pathogenicity rs148033154, rs140895792 RCV001328024
RCV001543605
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Adenocarcinoma of Lung Associate 30075702
Albinism Associate 39596324
Alzheimer Disease Associate 33794991
Aneurysm Associate 33089500
Arteriovenous Malformations Associate 29932521
Astigmatism Associate 37466950
Autism Spectrum Disorder Associate 31209396
Autistic Disorder Associate 23575222
Bietti Crystalline Dystrophy Associate 35814500
Blindness Associate 36980924