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Aliases for USH1C Gene

Aliases for USH1C Gene

  • Usher Syndrome 1C (Autosomal Recessive, Severe) 2 3
  • Autoimmune Enteropathy-Related Antigen AIE-75 3 4
  • Renal Carcinoma Antigen NY-REN-3 3 4
  • Usher Syndrome Type-1C Protein 3 4
  • Antigen NY-CO-38/NY-CO-37 3 4
  • Harmonin 2 3
  • DFNB18A 3 6
  • Deafness, Autosomal Recessive 18 2
  • PDZ-73/NY-CO-38 3
  • Protein PDZ-73 4
  • NY-CO-37 3
  • NY-CO-38 3
  • Ush1cpst 3
  • AIE-75 3
  • PDZ-45 3
  • PDZ-73 3
  • PDZD7C 3
  • DFNB18 3
  • PDZ73 3
  • AIE75 4

External Ids for USH1C Gene

Previous Symbols for USH1C Gene

  • DFNB18

Summaries for USH1C Gene

Entrez Gene Summary for USH1C Gene

  • This gene encodes a scaffold protein that functions in the assembly of Usher protein complexes. The protein contains PDZ domains, a coiled-coil region with a bipartite nuclear localization signal and a PEST degradation sequence. Defects in this gene are the cause of Usher syndrome type 1C and non-syndromic sensorineural deafness autosomal recessive type 18. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

GeneCards Summary for USH1C Gene

USH1C (Usher Syndrome 1C (Autosomal Recessive, Severe)) is a Protein Coding gene. Diseases associated with USH1C include usher syndrome, type 1c and autoimmune enteropathy. An important paralog of this gene is DFNB31.

UniProtKB/Swiss-Prot for USH1C Gene

  • Required for normal development and maintenance of cochlear hair cell bundles. Anchoring/scaffolding protein that is a part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A that mediates mechanotransduction in cochlear hair cells. Required for normal hearing (By similarity).

Gene Wiki entry for USH1C Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USH1C Gene

Genomics for USH1C Gene

Genomic Location for USH1C Gene

Start:
17,493,895 bp from pter
End:
17,544,416 bp from pter
Size:
50,522 bases
Orientation:
Minus strand

Genomic View for USH1C Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for USH1C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USH1C Gene

Regulatory Elements for USH1C Gene

Proteins for USH1C Gene

  • Protein details for USH1C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y6N9-USH1C_HUMAN
    Recommended name:
    Harmonin
    Protein Accession:
    Q9Y6N9
    Secondary Accessions:
    • A8K423
    • Q7RTU8
    • Q96B29
    • Q9UM04
    • Q9UM17
    • Q9UPC3

    Protein attributes for USH1C Gene

    Size:
    552 amino acids
    Molecular mass:
    62211 Da
    Quaternary structure:
    • Interacts with F-actin. Interacts with HARP (By similarity). Interacts with USH1G/SANS, USH2A and SLC4A7. Interacts (via the first PDZ domain) with the C-terminus of USHBP1. Interacts (via N-terminus and second PDZ domain) with CDH23. Part of a complex composed of USH1C, USH1G and MYO7A.
    SequenceCaution:
    • Sequence=AAC18049.1; Type=Frameshift; Positions=552; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for USH1C Gene

    Alternative splice isoforms for USH1C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USH1C Gene

Proteomics data for USH1C Gene at MOPED

Post-translational modifications for USH1C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for USH1C Gene

No data available for DME Specific Peptides for USH1C Gene

Domains for USH1C Gene

Protein Domains for USH1C Gene

InterPro:
Blocks:
ProtoNet:

UniProtKB/Swiss-Prot:

USH1C_HUMAN
Domain:
  • The PDZ domain 1 mediates interactions with USH1G/SANS and SLC4A7.:
    • Q9Y6N9
  • The N-terminal region constitutes an independently folded domain that has structural similarity with the CCM2 C-terminus, despite very low sequence similarity.:
    • Q9Y6N9
  • Contains 3 PDZ (DHR) domains.:
    • Q9Y6N9
genes like me logo Genes that share domains with USH1C: view

No data available for Gene Families for USH1C Gene

Function for USH1C Gene

Molecular function for USH1C Gene

UniProtKB/Swiss-Prot Function: Required for normal development and maintenance of cochlear hair cell bundles. Anchoring/scaffolding protein that is a part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A that mediates mechanotransduction in cochlear hair cells. Required for normal hearing (By similarity).

Gene Ontology (GO) - Molecular Function for USH1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 11311560
GO:0030507 spectrin binding IDA 23704327
GO:0032029 myosin tail binding IEA --
GO:0051015 actin filament binding IEA --
genes like me logo Genes that share ontologies with USH1C: view
genes like me logo Genes that share phenotypes with USH1C: view

Animal Models for USH1C Gene

MGI Knock Outs for USH1C:

miRNA for USH1C Gene

miRTarBase miRNAs that target USH1C

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for USH1C Gene

Localization for USH1C Gene

Subcellular locations from UniProtKB/Swiss-Prot for USH1C Gene

Cytoplasm, cytosol. Cytoplasm, cytoskeleton. Note=Colocalizes with F-actin (By similarity). Detected at the tip of cochlear hair cell stereocilia. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for USH1C Gene COMPARTMENTS Subcellular localization image for USH1C gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 2
plasma membrane 2

Gene Ontology (GO) - Cellular Components for USH1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment IEA --
GO:0001917 photoreceptor inner segment IEA --
GO:0005737 cytoplasm IDA 10209257
GO:0005829 cytosol IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with USH1C: view

Pathways for USH1C Gene

SuperPathways for USH1C Gene

No Data Available

Gene Ontology (GO) - Biological Process for USH1C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle IMP 15219944
GO:0007605 sensory perception of sound IMP 11398101
GO:0030046 parallel actin filament bundle assembly IEA --
GO:0042472 inner ear morphogenesis IEA --
GO:0042491 auditory receptor cell differentiation IEA --
genes like me logo Genes that share ontologies with USH1C: view

No data available for Pathways by source for USH1C Gene

Transcripts for USH1C Gene

Unigene Clusters for USH1C Gene

Usher syndrome 1C (autosomal recessive, severe):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USH1C Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b · 23c
SP1: - - -
SP2: -
SP3: - - - -
SP4: - - - -
SP5: -
SP6:

Relevant External Links for USH1C Gene

GeneLoc Exon Structure for
USH1C
ECgene alternative splicing isoforms for
USH1C

Expression for USH1C Gene

mRNA expression in normal human tissues for USH1C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for USH1C Gene

This gene is overexpressed in Colon - Transverse (10.4), Kidney - Cortex (9.8), Brain - Spinal cord (cervical c-1) (7.6), and Small Intestine - Terminal Ileum (7.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for USH1C Gene

SOURCE GeneReport for Unigene cluster for USH1C Gene Hs.502072

mRNA Expression by UniProt/SwissProt for USH1C Gene

Q9Y6N9-USH1C_HUMAN
Tissue specificity: Expressed in small intestine, colon, kidney, eye and weakly in pancreas. Expressed also in vestibule of the inner ear.
genes like me logo Genes that share expressions with USH1C: view

Orthologs for USH1C Gene

This gene was present in the common ancestor of animals.

Orthologs for USH1C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia USH1C 36
  • 98.85 (n)
  • 98.66 (a)
USH1C 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia USH1C 36
  • 91.43 (n)
  • 96.19 (a)
USH1C 37
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia USH1C 36
  • 90.9 (n)
  • 94.76 (a)
USH1C 37
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ush1c 36
  • 88.36 (n)
  • 92.86 (a)
Ush1c 16
Ush1c 37
  • 91 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USH1C 37
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USH1C 37
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves USH1C 36
  • 68.91 (n)
  • 72.65 (a)
USH1C 37
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USH1C 37
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.649 36
ush1c 36
  • 71.07 (n)
  • 71.93 (a)
zebrafish
(Danio rerio)
Actinopterygii ush1c 36
  • 68.32 (n)
  • 70.69 (a)
ush1c 37
  • 70 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5921 37
  • 15 (a)
OneToOne
Species with no ortholog for USH1C:
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for USH1C Gene

ENSEMBL:
Gene Tree for USH1C (if available)
TreeFam:
Gene Tree for USH1C (if available)

Paralogs for USH1C Gene

Paralogs for USH1C Gene

Selected SIMAP similar genes for USH1C Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with USH1C: view

Variants for USH1C Gene

Sequence variations from dbSNP and Humsavar for USH1C Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs16770 -- 17,517,225(+) CCTGT(C/T)GTCTA intron-variant
rs732983 -- 17,532,080(+) AAGTC(C/T)ACTCT intron-variant
rs733126 -- 17,530,773(+) CTCTT(C/T)GGCAT intron-variant
rs733874 -- 17,510,284(+) TGGAC(A/T)GTGGA intron-variant
rs878208 -- 17,500,539(+) GGCTC(C/T)TACCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USH1C Gene

Variant ID Type Subtype PubMed ID
nsv469895 CNV Loss 16826518
nsv467714 CNV Loss 19166990
esv33415 CNV Loss 17666407
nsv7693 CNV Loss 18451855
nsv7694 CNV Insertion 18451855

Relevant External Links for USH1C Gene

HapMap Linkage Disequilibrium report
USH1C
Human Gene Mutation Database (HGMD)
USH1C
Locus Specific Mutation Databases (LSDB)
USH1C

Disorders for USH1C Gene

(2) OMIM Diseases for USH1C Gene (605242)

UniProtKB/Swiss-Prot

USH1C_HUMAN
  • Usher syndrome 1C (USH1C) [MIM:276904]: 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). USH1 is characterized by profound congenital sensorineural deafness, absent vestibular function and prepubertal onset of progressive retinitis pigmentosa leading to blindness. {ECO:0000269 PubMed:10973247}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Deafness, autosomal recessive, 18A (DFNB18A) [MIM:602092]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269 PubMed:12107438}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) Novoseek inferred disease relationships for USH1C Gene

Disease -log(P) Hits PubMed IDs
dfnb18 97.2 5
usher syndrome 97.1 15
retinal degeneration 66.9 2

Relevant External Links for USH1C

GeneTests
USH1C
GeneReviews
USH1C
Genetic Association Database (GAD)
USH1C
Human Genome Epidemiology (HuGE) Navigator
USH1C
genes like me logo Genes that share disorders with USH1C: view

Publications for USH1C Gene

  1. A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C. (PMID: 10973247) Verpy E. … Petit C. (Nat. Genet. 2000) 2 3 4 23
  2. Identification of an autoimmune enteropathy-related 75-kilodalton antigen. (PMID: 10500064) Kobayashi I. … Kobayashi K. (Gastroenterology 1999) 3 4 23
  3. Scaffold protein harmonin (USH1C) provides molecular links between Usher syndrome type 1 and type 2. (PMID: 16301216) Reiners J. … Wolfrum U. (Hum. Mol. Genet. 2005) 3 4 23
  4. Assembling stable hair cell tip link complex via multidentate interactions between harmonin and cadherin 23. (PMID: 19297620) Pan L. … Zhang M. (Proc. Natl. Acad. Sci. U.S.A. 2009) 3 4 23
  5. Characterization of Usher syndrome type I gene mutations in an Usher syndrome patient population. (PMID: 15660226) Ouyang X.M. … Liu X.Z. (Hum. Genet. 2005) 3 23 49

Products for USH1C Gene

Sources for USH1C Gene

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