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Aliases for USH1C Gene

Aliases for USH1C Gene

  • USH1 Protein Network Component Harmonin 2 3 5
  • 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
  • Deafness, Autosomal Recessive 18 2
  • Usher Syndrome 1C 2
  • PDZ-73/NY-CO-38 3
  • Protein PDZ-73 4
  • NY-CO-37 3
  • NY-CO-38 3
  • Ush1cpst 3
  • DFNB18A 3
  • AIE-75 3
  • PDZ-45 3
  • PDZ-73 3
  • PDZD7C 3
  • DFNB18 3
  • PDZ73 3
  • AIE75 4

External Ids for USH1C Gene

Previous HGNC Symbols for USH1C Gene

  • DFNB18

Previous GeneCards Identifiers for USH1C Gene

  • GC11U990138
  • GC11M018457
  • GC11M017554
  • GC11M017479
  • GC11M017457
  • GC11M017199

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 (USH1 Protein Network Component Harmonin) is a Protein Coding gene. Diseases associated with USH1C include Usher Syndrome, Type 1C and Deafness, Autosomal Recessive 18A. GO annotations related to this gene include actin filament binding and myosin tail binding. An important paralog of this gene is WHRN.

UniProtKB/Swiss-Prot for USH1C Gene

  • 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 development and maintenance of cochlear hair cell bundles (By similarity). As part of the intermicrovillar adhesion complex/IMAC plays a role in brush border differentiation, controlling microvilli organization and length. Probably plays a central regulatory role in the assembly of the complex, recruiting CDHR2, CDHR5 and MYO7B to the microvilli tips (PubMed:24725409, PubMed:26812018).

Gene Wiki entry for USH1C Gene

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

Genomics for USH1C Gene

Regulatory Elements for USH1C Gene

Enhancers for USH1C 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
GH11G017527 1 ENCODE dbSUPER 35.1 +16.0 15961 2.5 CTCF ESRRA RB1 TAL1 ETV1 MAX RAD21 FOSL1 ZBTB48 ZNF143 USH1C ABCC8
GH11G017540 1.3 Ensembl ENCODE dbSUPER 23.5 +1.7 1656 4.2 ELF3 CTCF ZFP64 ARID4B MAX ZNF644 ZNF48 ZNF7 GATA3 GATA2 USH1C SOX6 ABCC8
GH11G017529 1 ENCODE dbSUPER 22.8 +12.1 12107 4.7 CTCF ZBTB21 JUN KLF17 BRCA1 ZIC2 ZNF121 ZFHX2 GLIS2 RCOR1 USH1C ABCC8
GH11G017546 1.1 Ensembl ENCODE 12.3 -3.2 -3198 1.5 HDGF CTCF PKNOX1 ZNF777 KLF17 ZIC2 ZNF2 ZNF101 ZNF664 E2F1 USH1C OTOG GC11P017559
GH11G017538 0.6 dbSUPER 15.5 +5.2 5234 1.5 BCOR ZNF366 ZNF512 ZMYM3 KDM1A PRDM10 USH1C ABCC8
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USH1C on UCSC Golden Path with GeneCards custom track

Genomic Location for USH1C Gene

Chromosome:
11
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

Genes around USH1C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USH1C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USH1C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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:
    • Part of the IMAC/intermicrovillar adhesion complex/intermicrovillar tip-link complex composed of ANKS4B, MYO7B, USH1C, CDHR2 and CDHR5 (Probable). Part of a complex composed of USH1C, USH1G and MYO7A (PubMed:21709241). Interacts with F-actin (By similarity). Interacts with USH2A (PubMed:16301216). Interacts with SLC4A7 (PubMed:16301216). Interacts (via PDZ1 domain) with the C-terminus of USHBP1 (PubMed:11311560). Interacts (via N-terminus and PDZ 2 domain) with CDH23 (PubMed:19297620). Interacts with USH1G (PubMed:12588794, PubMed:20142502). Interacts with MYO7B (PubMed:24725409, PubMed:26812017). Interacts with CDHR2 and CDHR5; may mediate their interaction with MYO7B at the microvilli tip (PubMed:24725409, PubMed:26812017). Interacts (via PDZ 1 domain) with ANKS4B (PubMed:26812018, PubMed:26812017).
    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

Post-translational modifications for USH1C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for USH1C Gene

Domains & Families for USH1C Gene

Protein Domains for USH1C Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for USH1C Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y6N9

UniProtKB/Swiss-Prot:

USH1C_HUMAN :
  • The PDZ 1 domain mediates interaction with ANKS4B, USHBP1, USH1G, SLC4A7.
Domain:
  • The PDZ 1 domain mediates interaction with ANKS4B, USHBP1, USH1G, SLC4A7.
  • The N-terminal region constitutes an independently folded domain that has structural similarity with the CCM2 C-terminus, despite very low sequence similarity.
genes like me logo Genes that share domains with USH1C: view

Function for USH1C Gene

Molecular function for USH1C Gene

UniProtKB/Swiss-Prot Function:
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 development and maintenance of cochlear hair cell bundles (By similarity). As part of the intermicrovillar adhesion complex/IMAC plays a role in brush border differentiation, controlling microvilli organization and length. Probably plays a central regulatory role in the assembly of the complex, recruiting CDHR2, CDHR5 and MYO7B to the microvilli tips (PubMed:24725409, PubMed:26812018).

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: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

Human Phenotype Ontology for USH1C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for USH1C Gene

MGI Knock Outs for USH1C:

Animal Model Products

miRNA for USH1C Gene

miRTarBase miRNAs that target USH1C

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Localization for USH1C Gene

Subcellular locations from UniProtKB/Swiss-Prot for USH1C Gene

Cytoplasm, cytosol. Cytoplasm, cytoskeleton. Cell projection, microvillus. Note=Colocalizes with F-actin (By similarity). Detected at the tip of cochlear hair cell stereocilia (By similarity). Enriched in microvilli of the intestinal brush border (PubMed:24725409). {ECO:0000250 UniProtKB:Q9ES64, ECO:0000269 PubMed:24725409}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USH1C gene
Compartment Confidence
cytosol 5
plasma membrane 4
cytoskeleton 4
nucleus 2

Gene Ontology (GO) - Cellular Components for USH1C Gene

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

Pathways & Interactions 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 IEA,IMP 11398101
GO:0030046 parallel actin filament bundle assembly ISS --
GO:0030154 cell differentiation IEA --
GO:0032532 regulation of microvillus length ISS --
genes like me logo Genes that share ontologies with USH1C: view

No data available for Pathways by source and SIGNOR curated interactions for USH1C Gene

Transcripts for USH1C Gene

Unigene Clusters for USH1C Gene

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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x10.4), Kidney - Cortex (x9.8), Brain - Spinal cord (cervical c-1) (x7.6), and Small Intestine - Terminal Ileum (x7.4).

Protein differential expression in normal tissues from HIPED for USH1C Gene

This gene is overexpressed in Fetal gut (27.0), Rectum (17.9), Heart (10.2), and Stomach (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for USH1C Gene



Protein tissue co-expression partners for USH1C Gene

NURSA nuclear receptor signaling pathways regulating expression of USH1C Gene:

USH1C

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.

Evidence on tissue expression from TISSUES for USH1C Gene

  • Lung(5)
  • Pancreas(5)
  • Intestine(4.6)
  • Eye(4.4)
  • Kidney(4.4)
  • Liver(4.1)
  • Nervous system(3.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for USH1C Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • immune
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • inner ear
  • middle ear
  • nose
  • outer ear
  • skull
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with USH1C: view

Primer Products

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 34 35
  • 98.85 (n)
cow
(Bos Taurus)
Mammalia USH1C 34 35
  • 91.43 (n)
dog
(Canis familiaris)
Mammalia USH1C 34 35
  • 90.9 (n)
mouse
(Mus musculus)
Mammalia Ush1c 34 16 35
  • 88.36 (n)
oppossum
(Monodelphis domestica)
Mammalia USH1C 35
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USH1C 35
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves USH1C 34 35
  • 68.91 (n)
lizard
(Anolis carolinensis)
Reptilia USH1C 35
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ush1c 34
  • 71.07 (n)
Str.649 34
zebrafish
(Danio rerio)
Actinopterygii ush1c 34 35
  • 68.32 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5921 35
  • 15 (a)
OneToOne
Species where no ortholog for USH1C 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)
  • 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

(2) 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
rs121908370 Pathogenic 17,533,268(-) TGCTG(C/G/T)GAATG nc-transcript-variant, reference, missense, stop-gained
rs138138689 Pathogenic 17,527,222(+) ACTCA(A/C/G/T)GTCTC splice-donor-variant
rs151045328 Pathogenic 17,531,431(+) TATTC(C/T)ACCTG nc-transcript-variant, reference, synonymous-codon
rs397514500 Pathogenic 17,531,233(-) TGTGC(A/C/G/T)TGGTG nc-transcript-variant, reference, missense
rs397515359 Pathogenic 17,531,408(-) CCCCC(-/C)GGCGC nc-transcript-variant, reference, frameshift-variant

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

Variant ID Type Subtype PubMed ID
esv33415 CNV loss 17666407
nsv1040065 CNV gain 25217958
nsv1119862 CNV deletion 24896259
nsv1147405 CNV insertion 26484159
nsv467714 CNV loss 19166990
nsv469895 CNV loss 16826518
nsv553567 CNV gain 21841781
nsv553585 CNV loss 21841781
nsv553586 CNV loss 21841781
nsv7693 CNV deletion 18451855
nsv7694 CNV insertion 18451855

Variation tolerance for USH1C Gene

Residual Variation Intolerance Score: 42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.49; 94.37% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USH1C Gene

Human Gene Mutation Database (HGMD)
USH1C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USH1C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USH1C Gene

Disorders for USH1C Gene

MalaCards: The human disease database

(24) MalaCards diseases for USH1C Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type 1c
  • usher syndrome type 1c
deafness, autosomal recessive 18a
  • autosomal recessive nonsyndromic deafness 18a
usher syndrome, type 1b
  • usher syndrome type 1
dfnb18 nonsyndromic hearing loss and deafness
  • dfnb 18 nonsyndromic hearing loss and deafness
nonsyndromic hearing loss and deafness, autosomal recessive
- elite association - COSMIC cancer census association via MalaCards
Search USH1C in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

USH1C_HUMAN
  • 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.
  • 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.

Relevant External Links for USH1C

Genetic Association Database (GAD)
USH1C
Human Genome Epidemiology (HuGE) Navigator
USH1C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USH1C
genes like me logo Genes that share disorders with USH1C: view

No data available for Genatlas for USH1C Gene

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 22 64
  2. The structure of the harmonin/sans complex reveals an unexpected interaction mode of the two Usher syndrome proteins. (PMID: 20142502) Yan J. … Zhang M. (Proc. Natl. Acad. Sci. U.S.A. 2010) 3 4 22 64
  3. 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 22 64
  4. 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 22 64
  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 22 46 64

Products for USH1C Gene

Sources for USH1C Gene

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