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USH1C Usher syndrome 1C (autosomal recessive, severe) [ Homo sapiens (human) ]

Gene ID: 10083, updated on 23-Mar-2015
Official Symbol
USH1Cprovided by HGNC
Official Full Name
Usher syndrome 1C (autosomal recessive, severe)provided by HGNC
Primary source
HGNC:HGNC:12597
See related
Ensembl:ENSG00000006611; HPRD:09241; MIM:605242; Vega:OTTHUMG00000166323
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]
Orthologs
See USH1C in MapViewer
Location:
11p14.3
Exon count:
29
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 11 NC_000011.10 (17493895..17544416, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (17515442..17565963, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene natural killer cell cytotoxicity receptor 3 ligand 1 Neighboring gene potassium channel, inwardly rectifying subfamily J, member 11 Neighboring gene ATP-binding cassette, sub-family C (CFTR/MRP), member 8 Neighboring gene succinate dehydrogenase complex, subunit C pseudogene 4 Neighboring gene otogelin Neighboring gene uncharacterized LOC102723330

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin filament binding IEA
Inferred from Electronic Annotation
more info
 
myosin tail binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
spectrin binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
auditory receptor cell differentiation IEA
Inferred from Electronic Annotation
more info
 
equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
parallel actin filament bundle assembly IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
apical part of cell IDA
Inferred from Direct Assay
more info
PubMed 
brush border IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
photoreceptor inner segment IEA
Inferred from Electronic Annotation
more info
 
photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
stereocilium TAS
Traceable Author Statement
more info
PubMed 
synapse IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
harmonin
Names
harmonin
antigen NY-CO-38/NY-CO-37
autoimmune enteropathy-related antigen AIE-75
renal carcinoma antigen NY-REN-3
usher syndrome type-1C protein

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_011883.1 RefSeqGene

    Range
    5001..55522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001297764.1NP_001284693.1  harmonin isoform c

    See proteins identical to 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/Swiss-Prot
    Q9Y6N9
    Related
    ENSP00000436934, OTTHUMP00000232615, ENST00000527020, OTTHUMT00000389149
    Conserved Domains (3) 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) ...
    pfam00769
    Location:275416
    ERM; Ezrin/radixin/moesin family
    cd07353
    Location:280
    harmonin_N; N-terminal protein-binding module of harmonin
  2. NM_005709.3NP_005700.2  harmonin isoform a

    See proteins identical to 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
    Q9Y6N9
    Related
    ENSP00000317018, OTTHUMP00000232613, ENST00000318024, OTTHUMT00000389146
    Conserved Domains (3) 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) ...
    pfam00769
    Location:294435
    ERM; Ezrin/radixin/moesin family
    cd07353
    Location:280
    harmonin_N; N-terminal protein-binding module of harmonin
  3. NM_153676.3NP_710142.1  harmonin isoform b3

    See proteins identical to 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, OTTHUMP00000232616, ENST00000005226, OTTHUMT00000389153
    Conserved Domains (3) summary
    TIGR02794
    Location:302383
    tolA_full; TolA protein
    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

RNA

  1. NR_123738.1 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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p2 Primary Assembly

    Range
    17493895..17544416
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519832.1XP_011518134.1  

    Conserved Domains (3) 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
    Protein_TolA; TolA protein
  2. XM_011519831.1XP_011518133.1  

    Conserved Domains (3) 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
    Protein_TolA; TolA protein
  3. XM_011519833.1XP_011518135.1  

    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
    Protein_TolA; TolA protein
    cl21478
    Location:301355
    Mt_ATP-synt_B; Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
  4. XM_011519834.1XP_011518136.1  

    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
    Protein_TolA; TolA protein
    cl21478
    Location:301355
    Mt_ATP-synt_B; Mitochondrial ATP synthase B chain precursor (ATP-synt_B)

RNA

  1. XR_930842.1 RNA Sequence

  2. XR_930841.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018922.2 Alternate CHM1_1.1

    Range
    17515265..17565784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)