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    USH1C USH1 protein network component harmonin [ Homo sapiens (human) ]

    Gene ID: 10083, updated on 11-Apr-2024

    Summary

    Official Symbol
    USH1Cprovided by HGNC
    Official Full Name
    USH1 protein network component harmoninprovided by HGNC
    Primary source
    HGNC:HGNC:12597
    See related
    Ensembl:ENSG00000006611 MIM:605242; AllianceGenome:HGNC:12597
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PDZ73; AIE-75; DFNB18; PDZ-45; PDZ-73; PDZD7C; DFNB18A; NY-CO-37; NY-CO-38; ush1cpst; PDZ-73/NY-CO-38
    Summary
    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]
    Expression
    Biased expression in small intestine (RPKM 13.7), duodenum (RPKM 13.0) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See USH1C in Genome Data Viewer
    Location:
    11p15.1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (17493900..17544416, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (17591495..17642149, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (17515447..17565963, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATP binding cassette subfamily C member 8 Neighboring gene succinate dehydrogenase complex subunit C pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17497048-17497604 Neighboring gene uncharacterized LOC124902641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17514781-17515280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17516552-17517052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17517053-17517553 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:17550891-17551094 Neighboring gene otogelin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17623679-17624178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17626113-17626614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17666796-17667296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17667297-17667797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:17672009-17672509 Neighboring gene long intergenic non-protein coding RNA 2729

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables spectrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G2/M transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in actin filament bundle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in auditory receptor cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in brush border assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in brush border assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in brush border assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in equilibrioception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in inner ear auditory receptor cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in inner ear receptor cell stereocilium organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in inner ear receptor cell stereocilium organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in parallel actin filament bundle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in photoreceptor cell maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to microvillus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to microvillus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of microvillus length ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in retinal cone cell development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sensory perception of light stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in apical part of cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in brush border IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in microvillus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in photoreceptor inner segment IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in photoreceptor inner segment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in photoreceptor outer segment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of stereocilia ankle link complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in stereocilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in stereocilium TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in stereocilium tip IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    harmonin
    Names
    Usher syndrome 1C (autosomal recessive, severe)
    antigen NY-CO-38/NY-CO-37
    autoimmune enteropathy-related antigen AIE-75
    renal carcinoma antigen NY-REN-3
    usher syndrome type-1C protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011883.2 RefSeqGene

      Range
      5001..55517
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001297764.2NP_001284693.1  harmonin isoform c

      See identical proteins and their annotated locations for NP_001284693.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant b3, one of which results in a translational frameshift. The resulting protein (isoform c) has a distinct C-terminus and is shorter than isoform b3.
      Source sequence(s)
      AB018687, AF039699, AK225614, BC016057
      Consensus CDS
      CCDS73265.1
      UniProtKB/TrEMBL
      A0A0S2Z4V1, B4DV53
      Related
      ENSP00000436934.1, ENST00000527020.5
      Conserved Domains (4) summary
      cd00992
      Location:85165
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd07353
      Location:280
      harmonin_N; N-terminal protein-binding module of harmonin
      TIGR02794
      Location:283364
      tolA_full; TolA protein
      pfam03879
      Location:297339
      Cgr1; Cgr1 family
    2. NM_005709.4NP_005700.2  harmonin isoform a

      See identical proteins and their annotated locations for NP_005700.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) has multiple differences in the coding region, compared to variant b3, one of which results in a translational frameshift. The resulting protein (isoform a) has a distinct C-terminus and is shorter than isoform b3.
      Source sequence(s)
      AC124799, KF455327
      Consensus CDS
      CCDS31438.1
      UniProtKB/Swiss-Prot
      A8K423, Q7RTU8, Q96B29, Q9UM04, Q9UM17, Q9UPC3, Q9Y6N9
      UniProtKB/TrEMBL
      A0A0S2Z4U9, B4DV53
      Related
      ENSP00000317018.4, ENST00000318024.9
      Conserved Domains (4) summary
      cd00992
      Location:85165
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd07353
      Location:280
      harmonin_N; N-terminal protein-binding module of harmonin
      TIGR02794
      Location:302383
      tolA_full; TolA protein
      pfam03879
      Location:316358
      Cgr1; Cgr1 family
    3. NM_153676.4NP_710142.1  harmonin isoform b3

      See identical proteins and their annotated locations for NP_710142.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b3) encodes the longest isoform (b3).
      Source sequence(s)
      AC124799, KF455327
      Consensus CDS
      CCDS7825.1
      UniProtKB/Swiss-Prot
      Q9Y6N9
      Related
      ENSP00000005226.7, ENST00000005226.12
      Conserved Domains (4) summary
      cd00992
      Location:85165
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd07353
      Location:280
      harmonin_N; N-terminal protein-binding module of harmonin
      TIGR02794
      Location:302383
      tolA_full; TolA protein
      pfam03879
      Location:316358
      Cgr1; Cgr1 family

    RNA

    1. NR_123738.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences compared to variant b3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB018687, AC124799, AF039699, AK225614
      Related
      ENST00000526313.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      17493900..17544416 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011519832.4XP_011518134.1  harmonin isoform X3

      UniProtKB/TrEMBL
      B4DV53
      Conserved Domains (4) summary
      cd00992
      Location:85165
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd07353
      Location:280
      harmonin_N; N-terminal protein-binding module of harmonin
      TIGR02794
      Location:302383
      tolA_full; TolA protein
      pfam03879
      Location:309358
      Cgr1; Cgr1 family
    2. XM_017017075.2XP_016872564.1  harmonin isoform X10

    3. XM_047426221.1XP_047282177.1  harmonin isoform X8

    4. XM_047426219.1XP_047282175.1  harmonin isoform X5

    5. XM_017017073.1XP_016872562.1  harmonin isoform X2

    6. XM_017017074.1XP_016872563.1  harmonin isoform X4

    7. XM_017017072.1XP_016872561.1  harmonin isoform X1

    8. XM_047426222.1XP_047282178.1  harmonin isoform X9

    9. XM_047426220.1XP_047282176.1  harmonin isoform X7

    10. XM_011519834.3XP_011518136.1  harmonin isoform X6

      Conserved Domains (4) summary
      cd00992
      Location:85165
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd07353
      Location:280
      harmonin_N; N-terminal protein-binding module of harmonin
      TIGR02794
      Location:302383
      tolA_full; TolA protein
      pfam03879
      Location:316358
      Cgr1; Cgr1 family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      17591495..17642149 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367419.1XP_054223394.1  harmonin isoform X3

    2. XM_054367426.1XP_054223401.1  harmonin isoform X10

    3. XM_054367424.1XP_054223399.1  harmonin isoform X8

    4. XM_054367421.1XP_054223396.1  harmonin isoform X5

    5. XM_054367418.1XP_054223393.1  harmonin isoform X2

    6. XM_054367420.1XP_054223395.1  harmonin isoform X4

    7. XM_054367417.1XP_054223392.1  harmonin isoform X1

    8. XM_054367425.1XP_054223400.1  harmonin isoform X9

    9. XM_054367423.1XP_054223398.1  harmonin isoform X7

    10. XM_054367422.1XP_054223397.1  harmonin isoform X6