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DFNB31 Gene(Protein Coding)

Deafness, Autosomal Recessive 31

GCID:
GC09M114402
GIFtS:
54
Genes Participants
UDN Logo

Aliases for DFNB31 Gene

Aliases for DFNB31 Gene

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

External Ids for DFNB31 Gene

Previous GeneCards Identifiers for DFNB31 Gene

  • GC09U990192
  • GC09M112541
  • GC09M114243
  • GC09M116204
  • GC09M117164
  • GC09M086769

Summaries for DFNB31 Gene

Entrez Gene Summary for DFNB31 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 of this gene results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Mar 2010]

GeneCards Summary for DFNB31 Gene

DFNB31 (Deafness, Autosomal Recessive 31) is a Protein Coding gene. Diseases associated with DFNB31 include Usher Syndrome, Type 2D and Deafness, Autosomal Recessive 31. An important paralog of this gene is USH1C.

UniProtKB/Swiss-Prot for DFNB31 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 DFNB31 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DFNB31 Gene

Genomics for DFNB31 Gene

Products:

  1. Regulatory Element

Regulatory Elements for DFNB31 Gene

Enhancers for DFNB31 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around DFNB31 on UCSC Golden Path with GeneCards custom track

Promoters for DFNB31 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around DFNB31 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the DFNB31 gene promoter:

Genomic Location for DFNB31 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 DFNB31 Gene

Genes around DFNB31 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DFNB31 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DFNB31 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DFNB31 Gene

Proteins for DFNB31 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for DFNB31 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 DFNB31 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 DFNB31/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 DFNB31 Gene

    Alternative splice isoforms for DFNB31 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DFNB31 Gene

Proteomics data for DFNB31 Gene at MOPED

Post-translational modifications for DFNB31 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DFNB31 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for DFNB31 Gene

Domains & Families for DFNB31 Gene

Gene Families for DFNB31 Gene

HGNC:

Protein Domains for DFNB31 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for DFNB31 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9P202

UniProtKB/Swiss-Prot:

WHRN_HUMAN :
  • Contains 3 PDZ (DHR) domains.
Domain:
  • Contains 3 PDZ (DHR) domains.
genes like me logo Genes that share domains with DFNB31: view

Function for DFNB31 Gene

Products:

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

Molecular function for DFNB31 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.

Phenotypes for DFNB31 Gene

MGI mutant phenotypes for DFNB31:
inferred from 3 alleles
GenomeRNAi human phenotypes for DFNB31:
genes like me logo Genes that share phenotypes with DFNB31: view

Human Phenotype Ontology for DFNB31 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DFNB31 Gene

MGI Knock Outs for DFNB31:

Animal Model Products

CRISPR Products

miRNA for DFNB31 Gene

miRTarBase miRNAs that target DFNB31

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for DFNB31 Gene

Localization for DFNB31 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DFNB31 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
Jensen Localization Image for DFNB31 Gene COMPARTMENTS Subcellular localization image for DFNB31 gene
Compartment Confidence
cytosol 3
nucleus 3
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for DFNB31 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:0005929 cilium IEA --
GO:0030426 growth cone IEA --
genes like me logo Genes that share ontologies with DFNB31: view

Pathways & Interactions for DFNB31 Gene

SuperPathways for DFNB31 Gene

PathCards logoMore details on SuperPathways for DFNB31
No Data Available

Gene Ontology (GO) - Biological Process for DFNB31 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001895 retina homeostasis IMP 17171570
GO:0010628 positive regulation of gene expression IEA --
GO:0045184 establishment of protein localization IEA --
genes like me logo Genes that share ontologies with DFNB31: view

No data available for Pathways by source and SIGNOR curated interactions for DFNB31 Gene

Drugs & Compounds for DFNB31 Gene

Products:

  1. Drug

(1) Drugs for DFNB31 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for DFNB31 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with DFNB31: view

Transcripts for DFNB31 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for DFNB31 Gene

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

Unigene Clusters for DFNB31 Gene

Deafness, autosomal recessive 31:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DFNB31 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18a ·
SP1: - - - - - - - - -
SP2: -
SP3: - - - - -
SP4: - - - -
SP5: - - - - - -
SP6: - - - - - -
SP7: -
SP8:
SP9:
SP10:
SP11: - - -

ExUns: 18b ^ 19 ^ 20 ^ 21
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for DFNB31 Gene

GeneLoc Exon Structure for
DFNB31
ECgene alternative splicing isoforms for
DFNB31

Expression for DFNB31 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for DFNB31 Gene

mRNA expression in normal human tissues for DFNB31 Gene
mRNA expression by BioGPS for DFNB31 GenemRNA expression by GTEx for DFNB31 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DFNB31 Gene

This gene is overexpressed in Adrenal Gland (x6.7).

SOURCE GeneReport for Unigene cluster for DFNB31 Gene Hs.93836

genes like me logo Genes that share expression patterns with DFNB31: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for DFNB31 Gene

Orthologs for DFNB31 Gene

This gene was present in the common ancestor of animals.

Orthologs for DFNB31 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia DFNB31 35
  • 89.11 (n)
  • 90.94 (a)
DFNB31 36
  • 90 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia DFNB31 35
  • 87.4 (n)
  • 88.24 (a)
DFNB31 36
  • 84 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Whrn 35
  • 85.65 (n)
  • 88.26 (a)
Whrn 16
Whrn 36
  • 87 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia DFNB31 35
  • 99.05 (n)
  • 98.51 (a)
DFNB31 36
  • 98 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Dfnb31 35
  • 85.71 (n)
  • 87.79 (a)
oppossum
(Monodelphis domestica)
 Mammalia DFNB31 36
  • 69 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia DFNB31 36
  • 74 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves DFNB31 35
  • 73.45 (n)
  • 71.65 (a)
DFNB31 36
  • 67 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia DFNB31 36
  • 60 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia dfnb31 35
  • 61.17 (n)
  • 62.07 (a)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.32716 35
zebrafish
(Danio rerio)
 Actinopterygii LOC100334777 35
  • 64.65 (n)
  • 68.97 (a)
dfnb31a 36
  • 58 (a)
 OneToMany
dfnb31b 36
  • 50 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta dysc 36
  • 21 (a)
 OneToMany
Species with no ortholog for DFNB31:
  • 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 DFNB31 Gene

ENSEMBL:
Gene Tree for DFNB31 (if available)
TreeFam:
Gene Tree for DFNB31 (if available)

Paralogs for DFNB31 Gene

Paralogs for DFNB31 Gene

(3) SIMAP similar genes for DFNB31 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with DFNB31: view

Variants for DFNB31 Gene

Sequence variations from dbSNP and Humsavar for DFNB31 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs4978584 - 114,424,432(+) GGTGG(C/T)GTGTT intron-variant, nc-transcript-variant, reference, missense, utr-variant-5-prime
rs2274159 - 114,403,966(+) TGGAC(A/G)CCGAC nc-transcript-variant, reference, missense
rs2274158 - 114,403,926(+) CTCTC(C/G/T)TTCCG nc-transcript-variant, reference, missense
rs942519 -, - 114,406,753(+) AAGGC(A/G)TGGAG nc-transcript-variant, downstream-variant-500B, reference, missense
rs10817610 - 114,426,286(+) GGGCA(C/T)GGGGC intron-variant, nc-transcript-variant, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for DFNB31 Gene

Variant ID Type Subtype PubMed ID
nsv893750 CNV Loss 21882294
dgv33e196 CNV Duplication 17116639
dgv948n27 CNV Gain 19166990
nsv831693 CNV Gain 17160897
nsv6678 CNV Insertion 18451855
esv2677969 CNV Deletion 23128226
esv27525 CNV Gain 19812545

Variation tolerance for DFNB31 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 DFNB31 Gene

Human Gene Mutation Database (HGMD)
DFNB31

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DFNB31 Gene

Disorders for DFNB31 Gene

MalaCards: The human disease database

(12) MalaCards diseases for DFNB31 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
  • deafness, autosomal recessive, 31
usher syndrome type ii
  • ush2
dfnb31 nonsyndromic hearing loss and deafness
  • dfnb 31 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

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 DFNB31

Genetic Association Database (GAD)
DFNB31
Human Genome Epidemiology (HuGE) Navigator
DFNB31
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DFNB31
genes like me logo Genes that share disorders with DFNB31: view

No data available for Genatlas for DFNB31 Gene

Publications for DFNB31 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 23 67
  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 23
  3. 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 23
  4. Overexpression of the signal peptide whirlin isoform 2 is related to disease progression in colorectal cancer patients. (PMID: 19724906) Toiyama Y. … Kusunoki M. (Int. J. Oncol. 2009) 3 23
  5. 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 23

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