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WHRN Gene(Protein Coding)

Whirlin

GCID:
GC09M114403
GIFtS:
41
Genes Participants
UDN Logo

Aliases for WHRN Gene

Aliases for WHRN Gene

  • Whirlin 2 3 3 5
  • Autosomal Recessive Deafness Type 31 Protein 3 4
  • DFNB31 3 4
  • Deafness, Autosomal Recessive 31 2
  • CASK-Interacting Protein CIP98 3
  • KIAA1526 4
  • PDZD7B 3
  • CIP98 3
  • USH2D 3
  • WI 3

External Ids for WHRN Gene

Previous HGNC Symbols for WHRN Gene

  • DFNB31

Summaries for WHRN Gene

Entrez Gene Summary for WHRN Gene

  • This gene is thought to function in the organization and stabilization of sterocilia elongation and actin cystoskeletal assembly, based on studies of the related mouse gene. Mutations in this gene have been associated with autosomal recessive non-syndromic deafness and Usher Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

GeneCards Summary for WHRN Gene

WHRN (Whirlin) is a Protein Coding gene. Diseases associated with WHRN include Usher Syndrome, Type 2D and Deafness, Autosomal Recessive 31. An important paralog of this gene is PDZD7.

UniProtKB/Swiss-Prot for WHRN Gene

  • Necessary for elongation and maintenance of inner and outer hair cell stereocilia in the organ of Corti in the inner ear.

Gene Wiki entry for WHRN Gene

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

Genomics for WHRN Gene

Products:

  1. Regulatory Element

Regulatory Elements for WHRN Gene

Enhancers for WHRN 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
GH09G114586 1.7 FANTOM5 ENCODE dbSUPER 44.4 -84.7 -84739 7.2 HDGF PKNOX1 FOXA2 MLX CREB3L1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 WHRN ENSG00000201749 TMEM268 ATP6V1G1 TNFSF8 AKNA GC09P114598 PIR33481
GH09G114550 1.6 FANTOM5 Ensembl ENCODE 35.7 -46.9 -46949 3.7 PKNOX1 ATF1 SIN3A FEZF1 GLIS2 FOS ZNF263 ZHX2 JUNB TSHZ1 WHRN TNFSF15 ATP6V1G1 TNFSF8 LOC105376229
GH09G114360 2 FANTOM5 Ensembl ENCODE dbSUPER 27.8 +129.4 129374 30.6 HDGF PKNOX1 FOXA2 ZFP64 WRNIP1 SIN3A YBX1 ZNF143 ZNF207 FOS WHRN AKNA TMEM268 ENSG00000201749 ORM1 ORM2 ATP6V1G1 ENSG00000235119
GH09G114483 1.9 FANTOM5 Ensembl ENCODE dbSUPER 25.7 +21.1 21094 2.5 HDGF ATF1 ZNF143 FOS DEK JUNB NCOA1 TBX21 ZNF592 MEF2D WHRN TNFSF15 TNFSF8 ATP6V1G1 LOC100131877 AKNA
GH09G114413 1.2 FANTOM5 Ensembl ENCODE dbSUPER 24.7 +91.0 91013 2.1 NR2F2 TNFSF15 WHRN TMEM268 ENSG00000201749 AKNA ATP6V1G1 LOC100131877
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around WHRN on UCSC Golden Path with GeneCards custom track

Promoters for WHRN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000240277 309 1601 ATF1 AGO1 ARID4B SIN3A ZNF48 ZNF202 SP3 REST ZNF592 CBX8

Genomic Location for WHRN Gene

Chromosome:
9
Start:
114,402,078 bp from pter
End:
114,505,509 bp from pter
Size:
103,432 bases
Orientation:
Minus strand

Genomic View for WHRN Gene

Genes around WHRN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for WHRN Gene

Proteins for WHRN Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    Q9P202-WHRN_HUMAN
    Recommended name:
    Whirlin
    Protein Accession:
    Q9P202
    Secondary Accessions:
    • A5PKU1
    • A5PKZ9
    • Q5TAU9
    • Q5TAV0
    • Q5TAV1
    • Q5TAV2
    • Q96MZ9
    • Q9H9F4
    • Q9UFZ3

    Protein attributes for WHRN Gene

    Size:
    907 amino acids
    Molecular mass:
    96586 Da
    Quaternary structure:
    • Forms homooligomers (By similarity). Interacts with USH2A (PubMed:16434480). Interacts with GPR98/MASS1 (PubMed:16434480). Interacts (via C-terminal PDZ domain) with MPP1/p55 (PubMed:17584769). Interacts with CIB2 (PubMed:23023331). Interacts (via C-terminal PDZ domain) with MYO15A; this interaction is necessary for localization of WHRN to stereocilia tips. Interacts with LRRC4C/NGL1. Interacts with MYO7A. Interacts with RPGR. Interacts with EPS8. Interacts with CASK (By similarity).
    SequenceCaution:
    • Sequence=BAA96050.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for WHRN Gene

    Alternative splice isoforms for WHRN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WHRN Gene

Post-translational modifications for WHRN Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for WHRN Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for WHRN Gene

Domains & Families for WHRN Gene

Gene Families for WHRN Gene

HGNC:

Protein Domains for WHRN Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for WHRN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with WHRN: view

No data available for UniProtKB/Swiss-Prot for WHRN Gene

Function for WHRN Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for WHRN Gene

UniProtKB/Swiss-Prot Function:
Necessary for elongation and maintenance of inner and outer hair cell stereocilia in the organ of Corti in the inner ear.

Gene Ontology (GO) - Molecular Function for WHRN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17584769
GO:0042803 protein homodimerization activity IEA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with WHRN: view
genes like me logo Genes that share phenotypes with WHRN: view

Human Phenotype Ontology for WHRN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for WHRN Gene

MGI Knock Outs for WHRN:

Animal Model Products

miRNA for WHRN Gene

miRTarBase miRNAs that target WHRN

Inhibitory RNA Products

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

Localization for WHRN Gene

Subcellular locations from UniProtKB/Swiss-Prot for WHRN Gene

Cytoplasm. Cell projection, stereocilium. Cell projection, growth cone. Note=Detected at the level of stereocilia in inner outer hair cells of the cochlea and vestibule. Colocalizes with the growing ends of actin filaments (By similarity). Colocalizes with MPP1 in the retina, at the outer limiting membrane (OLM), outer plexifirm layer (OPL), basal bodies and at the connecting cilium (CC). {ECO:0000250, ECO:0000269 PubMed:17584769}.

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 WHRN gene
Compartment Confidence
nucleus 3
cytosol 3
cytoskeleton 2

Gene Ontology (GO) - Cellular Components for WHRN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001917 photoreceptor inner segment IEA --
GO:0002141 stereocilia ankle link IEA --
GO:0002142 stereocilia ankle link complex IEA --
GO:0005737 cytoplasm IDA 16434480
GO:0005884 actin filament IEA --
genes like me logo Genes that share ontologies with WHRN: view

Pathways & Interactions for WHRN Gene

SuperPathways for WHRN Gene

PathCards logo More details on SuperPathways for WHRN
No Data Available

Gene Ontology (GO) - Biological Process for WHRN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001895 retina homeostasis IMP 17171570
GO:0007605 sensory perception of sound IMP 17171570
GO:0010628 positive regulation of gene expression IEA --
GO:0021694 cerebellar Purkinje cell layer formation IEA --
GO:0045184 establishment of protein localization IEA --
genes like me logo Genes that share ontologies with WHRN: view

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

Drugs & Compounds for WHRN Gene

Products:

  1. Drug

(1) Drugs for WHRN Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for WHRN Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with WHRN: view

Transcripts for WHRN Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for WHRN Gene

(14) REFSEQ mRNAs :
(96) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for WHRN Gene

GeneLoc Exon Structure for
WHRN
ECgene alternative splicing isoforms for
WHRN

Expression for WHRN Gene

Products:

  1. Primer

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of WHRN Gene:

WHRN

Evidence on tissue expression from TISSUES for WHRN Gene

  • Nervous system(4.9)

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

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

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for WHRN Gene

Orthologs for WHRN Gene

This gene was present in the common ancestor of animals.

Orthologs for WHRN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia DFNB31 34 35
  • 99.05 (n)
cow
(Bos Taurus)
 Mammalia DFNB31 34 35
  • 89.11 (n)
dog
(Canis familiaris)
 Mammalia DFNB31 34 35
  • 87.4 (n)
rat
(Rattus norvegicus)
 Mammalia Dfnb31 34
  • 85.71 (n)
mouse
(Mus musculus)
 Mammalia Whrn 34 16 35
  • 85.65 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia DFNB31 35
  • 74 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia DFNB31 35
  • 69 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves DFNB31 34 35
  • 73.45 (n)
lizard
(Anolis carolinensis)
 Reptilia DFNB31 35
  • 60 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia dfnb31 34
  • 61.17 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.32716 34
zebrafish
(Danio rerio)
 Actinopterygii LOC100334777 34
  • 64.65 (n)
dfnb31a 35
  • 58 (a)
 OneToMany
dfnb31b 35
  • 50 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta dysc 35
  • 21 (a)
 OneToMany
Species where no ortholog for WHRN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 WHRN Gene

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

Paralogs for WHRN Gene

Paralogs for WHRN Gene

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

Variants for WHRN Gene

Sequence variations from dbSNP and Humsavar for WHRN Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs137852839 Pathogenic 114,403,982(-) CAGGC(C/T)GAGGA nc-transcript-variant, reference, stop-gained
rs137852840 Pathogenic 114,504,495(-) CCGAC(C/T)AGCTG nc-transcript-variant, upstream-variant-2KB, reference, stop-gained
rs397517255 Pathogenic 114,424,483(-) AGACA(C/T)GAGTG nc-transcript-variant, reference, stop-gained, utr-variant-5-prime
rs397517258 Pathogenic 114,478,747(-) AGCTG(-/G)TGCTG nc-transcript-variant, reference, frameshift-variant, utr-variant-5-prime
rs779760634 Pathogenic 114,423,524(+) GAGAA(C/T)TGGAG intron-variant, splice-acceptor-variant

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

Variant ID Type Subtype PubMed ID
dgv12859n54 CNV gain 21841781
dgv33e196 CNV duplication 17116639
dgv7706n100 CNV gain 25217958
dgv948n27 CNV gain 19166990
esv2677969 CNV deletion 23128226
esv27525 CNV gain 19812545
esv2762830 CNV loss 21179565
esv3573365 CNV loss 25503493
esv3621558 CNV loss 21293372
esv3621559 CNV loss 21293372
nsv1110055 CNV deletion 24896259
nsv615233 CNV gain 21841781
nsv615248 CNV loss 21841781
nsv6678 CNV insertion 18451855
nsv831693 CNV gain 17160897

Variation tolerance for WHRN Gene

Residual Variation Intolerance Score: 98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.57; 91.23% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for WHRN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
WHRN

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

Disorders for WHRN Gene

MalaCards: The human disease database

(13) MalaCards diseases for WHRN Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type 2d
  • usher syndrome type 2d
deafness, autosomal recessive 31
  • autosomal recessive nonsyndromic deafness 31
usher syndrome type 2
  • ush2
dfnb31 nonsyndromic hearing loss and deafness
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
- elite association - COSMIC cancer census association via MalaCards
Search WHRN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

WHRN_HUMAN
  • Deafness, autosomal recessive, 31 (DFNB31) [MIM:607084]: 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:11973626, ECO:0000269 PubMed:12833159, ECO:0000269 PubMed:15841483}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Usher syndrome 2D (USH2D) [MIM:611383]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa and 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). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269 PubMed:17171570}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for WHRN

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
WHRN
genes like me logo Genes that share disorders with WHRN: view

No data available for Genatlas for WHRN Gene

Publications for WHRN Gene

  1. A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss. (PMID: 17171570) Ebermann I. … Bolz H. (Hum. Genet. 2007) 2 3 4 22 64
  2. Defects in whirlin, a PDZ domain molecule involved in stereocilia elongation, cause deafness in the whirler mouse and families with DFNB31. (PMID: 12833159) Mburu P. … Brown S.D. (Nat. Genet. 2003) 2 3 4 22 64
  3. The DFNB31 gene product whirlin connects to the Usher protein network in the cochlea and retina by direct association with USH2A and VLGR1. (PMID: 16434480) van Wijk E. … Kremer H. (Hum. Mol. Genet. 2006) 3 4 22 64
  4. Alterations of the CIB2 calcium- and integrin-binding protein cause Usher syndrome type 1J and nonsyndromic deafness DFNB48. (PMID: 23023331) Riazuddin S. … Ahmed Z.M. (Nat. Genet. 2012) 3 4 64
  5. Sequence variants of the DFNB31 gene among Usher syndrome patients of diverse origin. (PMID: 20352026) Aller E. … MillA!n J.M. (Mol. Vis. 2010) 3 22 64

Products for WHRN Gene

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