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DFNB59 Gene

protein-coding   GIFtS: 43
GCID: GC02P179316

Deafness, Autosomal Recessive 59

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Deafness, Autosomal Recessive 591 2
PJVK2 3 5
Autosomal Recessive Deafness Type 59 Protein2 3
pejvakin2

External Ids:    HGNC: 295021   Entrez Gene: 4945132   Ensembl: ENSG000002043117   OMIM: 6102195   UniProtKB: Q0ZLH33   

Export aliases for DFNB59 gene to outside databases

Previous GC identifers: GC00U921558 GC02U900985 GC02P179028 GC02P171186


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for DFNB59 Gene:
The protein encoded by this gene is a member of the gasdermin family, a family which is found only in vertebrates.
The encoded protein is required for the proper function of auditory pathway neurons. Defects in this gene are a
cause of non-syndromic sensorineural deafness autosomal recessive type 59 (DFNB59). (provided by RefSeq, Dec
2008)

GeneCards Summary for DFNB59 Gene:
DFNB59 (deafness, autosomal recessive 59) is a protein-coding gene. Diseases associated with DFNB59 include dfnb59 nonsyndromic hearing loss and deafness, and deafness, autosomal recessive 59. An important paralog of this gene is DFNA5.

UniProtKB/Swiss-Prot: PJVK_HUMAN, Q0ZLH3
Function: Essential in the activity of auditory pathway neurons




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000002.12  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the DFNB59 gene promoter:
         ISGF-3   NCX/Ncx   HTF   GATA-1   AREB6   SRY   Sox9   LyF-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DFNB59


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q31.2   Ensembl cytogenetic band:  2q31.2   HGNC cytogenetic band: 2q31.2

DFNB59 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DFNB59 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P179316:  view genomic region     (about GC identifiers)

Start:
179,316,163 bp from pter      End:
179,326,117 bp from pter
Size:
9,955 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PJVK_HUMAN, Q0ZLH3 (See protein sequence)
Recommended Name: Pejvakin  
Size: 352 amino acids; 39913 Da
Miscellaneous: 'Pejvakin' means 'echo' in Persian
Secondary accessions: A0PK14 B9EJE2

Explore the universe of human proteins at neXtProt for DFNB59: NX_Q0ZLH3

Explore proteomics data for DFNB59 at MOPED


See DFNB59 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001036167.1  
ENSEMBL proteins: 
 ENSP00000386647   ENSP00000364271   ENSP00000410776   ENSP00000399579  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR007677 Gasdermin

Graphical View of Domain Structure for InterPro Entry Q0ZLH3

ProtoNet protein and cluster: Q0ZLH3

UniProtKB/Swiss-Prot: PJVK_HUMAN, Q0ZLH3
Similarity: Belongs to the gasdermin family


DFNB59 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: PJVK_HUMAN, Q0ZLH3
Function: Essential in the activity of auditory pathway neurons

Phenotypes:
     1 GenomeRNAi human phenotype for DFNB59:

 Synthetic lethal with Ras 

     3 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Dfnb59):
 behavior/neurological  hearing/vestibular/ear  nervous system 

DFNB59 for phenotypes           About GeneDecksing

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
golgi apparatus1
mitochondrion1
peroxisome1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0043025neuronal cell body IEA--

DFNB59 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Interactions:

    Search GeneGlobe Interaction Network for DFNB59

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007605sensory perception of sound IEA--

DFNB59 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for DFNB59 (PJVK)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for DFNB59 gene: 
NM_001042702.3  

Unigene Cluster for DFNB59:

Deafness, autosomal recessive 59
Hs.87734  [show with all ESTs]
Unigene Representative Sequence: BC020859
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000409117(uc002umi.4 uc002umj.4) ENST00000437056 ENST00000375129
ENST00000442710 ENST00000444615 ENST00000605419
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Additional mRNA sequence: 

BC020859.1 BC127902.1 BC127903.1 BC146938.1 DQ365827.1 

8 DOTS entries:

DT.40233091  DT.100747059  DT.120988744  DT.120988783  DT.120988791  DT.40124215  DT.40274839  DT.91927367 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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DFNB59 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CAGTTCCTTG
DFNB59 Expression
About this image

DFNB59 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

DFNB59 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.87734
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for DFNB59 gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Dfnb591 , 5 deafness, autosomal recessive 59 (human)1, 5 87.69(n)1
96.02(a)1
  2 (45.08 cM)5
3813751  NM_001080711.21  NP_001074180.11 
 766484765 
chicken
(Gallus gallus)
Aves DFNB591 deafness, autosomal recessive 59 73.48(n)
74.72(a)
  429015  XM_426573.4  XP_426573.2 
lizard
(Anolis carolinensis)
Reptilia DFNB596
deafness, autosomal recessive 59
72(a)
1 ↔ 1
GL343320.1(1114410-1125352)
tropical clawed frog
(Xenopus tropicalis)
Amphibia dfnb591 deafness, autosomal recessive 59 71.6(n)
75.21(a)
  100485115  XM_002935682.2  XP_002935728.1 
zebrafish
(Danio rerio)
Actinopterygii dfnb591 deafness, autosomal recessive 59 65.04(n)
66.38(a)
  100006646  XM_001340641.3  XP_001340677.2 


ENSEMBL Gene Tree for DFNB59 (if available)
TreeFam Gene Tree for DFNB59 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for DFNB59 gene
DFNA52  

DFNB59 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for DFNB59 (see all 226)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
VAR_0273884
Deafness, autosomal recessive, 59 (DFNB59)4--see VAR_0273882 R W mis40--------
VAR_0688914
Deafness, autosomal recessive, 59 (DFNB59)4--see VAR_0688912 C S mis40--------
VAR_0273874
Deafness, autosomal recessive, 59 (DFNB59)4--see VAR_0273872 T I mis40--------
rs1182039891,2
Cpathogenic1178709861(+) CCACAC/TGACAG 2 R * stg10--------
rs1117066341,2
C,Fpathogenic1178709909(+) CAATGA/C/TGGGTA 2 R W mis12CSA 4
rs1403080481,2
C--171192179(+) GTCTC-/AAAA  
        
AAACA
1 -- int10--------
rs1398165781,2
C--178710036(+) GTTGTA/GTAGGA 1 -- int10--------
rs800820111,2
C--178710073(+) ATATG-/AAAAAA 1 -- int10--------
rs1911504251,2
--178710085(+) AAAACA/CAATCT 1 -- int10--------
rs1811294961,2
--178710145(+) AATTAC/TGTGCA 1 -- int10--------

HapMap Linkage Disequilibrium report for DFNB59 (179316163 - 179326117 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for DFNB59:    About this table    
Variant IDTypeSubtypePubMed ID
nsv834467CNV Loss17160897

Human Gene Mutation Database (HGMD): DFNB59
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing DFNB59
DNA2.0 Custom Variant and Variant Library Synthesis for DFNB59

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 610219   
OMIM disorders: 610220  
UniProtKB/Swiss-Prot: PJVK_HUMAN, Q0ZLH3
  • Deafness, autosomal recessive, 59 (DFNB59) [MIM:610220]: A form of sensorineural hearing impairment with
    absent or severely abnormal auditory brainstem response but normal otoacoustic emissions (auditory neuropathy or
    auditory dys-synchrony). Auditory neuropathies result from a lesion in the area including the inner hair cells,
    connections between the inner hair cells and the cochlear branch of the auditory nerve, the auditory nerve itself
    and auditory pathways of the brainstem. Note=The disease is caused by mutations affecting the gene represented in
    this entry

  • 13 diseases for DFNB59:    
    About MalaCards
    dfnb59 nonsyndromic hearing loss and deafness    deafness, autosomal recessive 59    auditory neuropathy    nonsyndromic hearing loss and deafness, autosomal recessive
    deafness and hereditary hearing loss    nonsyndromic hearing loss and deafness    deafness, autosomal recessive 76    nonsyndromic deafness
    neuropathy    hodgkin's lymphoma    neuronitis    multiple myeloma
    myeloma

    2 diseases from the University of Copenhagen DISEASES database for DFNB59:
    Nonsyndromic deafness     Hodgkin's lymphoma, nodular sclerosis

    DFNB59 for disorders           About GeneDecksing

    Genetic Association Database (GAD): DFNB59
    Human Genome Epidemiology (HuGE) Navigator: DFNB59 (4 documents)

    Export disorders for DFNB59 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for DFNB59 gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with DFNB59)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in the gene encoding pejvakin, a newly identified protein of the afferent auditory pathway, cause DFNB59 auditory neuropathy. (PubMed id 16804542)1, 2, 3 Delmaghani S.... Petit C. (Nat. Genet. 2006)
    2. A p.C343S missense mutation in PJVK causes progressive hearing loss. (PubMed id 22617256)1, 2 Mujtaba G.... Naz S. (Gene 2012)
    3. Genetic causes of nonsyndromic hearing loss in Iran in comparison with other populations. (PubMed id 20739942)1, 4 Mahdieh N....Zeinali S. (J. Hum. Genet. 2010)
    4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. High frequency of autosomal-recessive DFNB59 hearing loss in an isolated Arab population in Israel. (PubMed id 21696384)1 Borck G....Basel-Vanagaite L. (Clin. Genet. 2012)
    7. Variants of OTOF and PJVK genes in Chinese patients with auditory neuropathy spectrum disorder. (PubMed id 21935370)1 Wang J....Qiu J.H. (PLoS ONE 2011)
    8. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (Am. J. Hum. Genet. 2009)
    9. [Sequence analysis of DFNB59 gene in a Chinese family with dominantly inherited auditory neuropathy]. (PubMed id 19160860)1 Xu S....Bu X. (Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2008)
    10. Involvement of DFNB59 mutations in autosomal recessive nonsyndromic hearing impairment. (PubMed id 17373699)1 Collin R.W....Kremer H. (Hum. Mutat. 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 494513 HGNC: 29502 Ensembl:ENSG00000204311 euGenes: HUgn494513 ECgene: DFNB59
    H-InvDB: DFNB59

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for DFNB59 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for DFNB59 gene:
    Search GeneIP for patents involving DFNB59

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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