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GIPC3 Gene(Protein Coding)

GIPC PDZ Domain Containing Family Member 3

GCID:
GC19P003585
GIFtS:
47
Genes Participants
UDN Logo

Aliases for GIPC3 Gene

Aliases for GIPC3 Gene

  • GIPC PDZ Domain Containing Family Member 3 2 3 5
  • C19orf64 3 4
  • GIPC PDZ Domain Containing Family, Member 3 2
  • Chromosome 19 Open Reading Frame 64 2
  • PDZ Domain-Containing Protein GIPC3 3
  • Deafness, Autosomal Recessive 72 2
  • Deafness, Autosomal Recessive 15 2
  • DFNB95 3
  • DFNB15 3
  • DFNB72 3

External Ids for GIPC3 Gene

Previous HGNC Symbols for GIPC3 Gene

  • C19orf64
  • DFNB72
  • DFNB15

Previous GeneCards Identifiers for GIPC3 Gene

  • GC19P003677
  • GC19P003654
  • GC19P003525
  • GC19P003536
  • GC19P003351

Summaries for GIPC3 Gene

Entrez Gene Summary for GIPC3 Gene

  • The protein encoded by this gene belongs to the GIPC family. Studies in mice suggest that this gene is required for postnatal maturation of the hair bundle and long-term survival of hair cells and spiral ganglion in the ear. Mutations in this gene are associated with autosomal recessive deafness. [provided by RefSeq, Dec 2011]

GeneCards Summary for GIPC3 Gene

GIPC3 (GIPC PDZ Domain Containing Family Member 3) is a Protein Coding gene. Diseases associated with GIPC3 include Deafness, Autosomal Recessive 15 and Nonsyndromic Deafness. An important paralog of this gene is GIPC1.

UniProtKB/Swiss-Prot for GIPC3 Gene

  • Required for postnatal maturation of the hair bundle and long-term survival of hair cells and spiral ganglion.

Gene Wiki entry for GIPC3 Gene

Additional gene information for GIPC3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GIPC3 Gene

Genomics for GIPC3 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for GIPC3 Gene

Promoters and enhancers for GIPC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH19I003585 Promoter 1.4 EPDnew Ensembl 550.8 +0.2 154 0.2 ZNF148 NCOA6 RB1 GMEB1 ZFX MGA ZNF592 ZBTB5 EZH2 GIPC3 TBXA2R
GH19I003579 Enhancer 1.3 Ensembl ENCODE dbSUPER 17.5 -5.3 -5291 2.2 HDGF ATF1 PKNOX1 ARNT ARID2 FOS ATF7 MCM3 ZNF592 GMEB1 GIPC3 CACTIN-AS1 HMG20B MATK MFSD12
GH19I003625 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 7.3 +41.0 41038 2.3 HDGF PKNOX1 CLOCK MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CACTIN GNA11 ZNF77 TLE2 ZNF555 MRPL54 GIPC3 GC19M003615
GH19I003605 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 7.1 +22.1 22062 4.6 HDGF PKNOX1 ARNT SIN3A YBX1 ZNF2 POLR2B ZNF766 SP3 MCM5 CACTIN-AS1 TBXA2R ZNF77 CACTIN CCDC94 ENSG00000267030 ZNF555 ENSG00000267769 APBA3 GNA11
GH19I003570 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.9 -10.9 -10913 8 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A ZNF2 ZNF143 FOS MFSD12 HMG20B CACTIN ZNF77 CCDC94 CACTIN-AS1 ENSG00000267980 GIPC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GIPC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GIPC3 gene promoter:

Genomic Locations for GIPC3 Gene

Genomic Locations for GIPC3 Gene
chr19:3,585,541-3,593,541
(GRCh38/hg38)
Size:
8,001 bases
Orientation:
Plus strand
chr19:3,585,551-3,593,539
(GRCh37/hg19)

Genomic View for GIPC3 Gene

Genes around GIPC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GIPC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GIPC3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GIPC3 Gene

Proteins for GIPC3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for GIPC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TF64-GIPC3_HUMAN
    Recommended name:
    PDZ domain-containing protein GIPC3
    Protein Accession:
    Q8TF64
    Secondary Accessions:
    • O75227

    Protein attributes for GIPC3 Gene

    Size:
    312 amino acids
    Molecular mass:
    33982 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC24304.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for GIPC3 Gene

Protein Expression for GIPC3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for GIPC3 Gene

No Post-translational modifications

Other Protein References for GIPC3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GIPC3 Gene

Domains & Families for GIPC3 Gene

Gene Families for GIPC3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for GIPC3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GIPC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TF64

UniProtKB/Swiss-Prot:

GIPC3_HUMAN :
  • Belongs to the GIPC family.
Family:
  • Belongs to the GIPC family.
genes like me logo Genes that share domains with GIPC3: view

Function for GIPC3 Gene

Products:

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

Molecular function for GIPC3 Gene

UniProtKB/Swiss-Prot Function:
Required for postnatal maturation of the hair bundle and long-term survival of hair cells and spiral ganglion.

Phenotypes for GIPC3 Gene

MGI mutant phenotypes for GIPC3:
inferred from 2 alleles
GenomeRNAi human phenotypes for GIPC3:
genes like me logo Genes that share phenotypes with GIPC3: view

Human Phenotype Ontology for GIPC3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GIPC3 Gene

MGI Knock Outs for GIPC3:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targets and HOMER Transcription for GIPC3 Gene

Localization for GIPC3 Gene

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 GIPC3 gene
Compartment Confidence
cytosol 3
nucleus 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GIPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031982 colocalizes_with vesicle IBA --
genes like me logo Genes that share ontologies with GIPC3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for GIPC3 Gene

Pathways & Interactions for GIPC3 Gene

SuperPathways for GIPC3 Gene

PathCards logo More details on SuperPathways for GIPC3
No Data Available

Gene Ontology (GO) - Biological Process for GIPC3 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for GIPC3 Gene

Drugs & Compounds for GIPC3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for GIPC3 Gene

Products:

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

mRNA/cDNA for GIPC3 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(17) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for GIPC3 Gene

GIPC PDZ domain containing family, member 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GIPC3 Gene

No ASD Table

Relevant External Links for GIPC3 Gene

GeneLoc Exon Structure for
GIPC3
ECgene alternative splicing isoforms for
GIPC3

Expression for GIPC3 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GIPC3 Gene

mRNA expression in normal human tissues for GIPC3 Gene
mRNA expression by BioGPS for GIPC3 GenemRNA expression by GTEx for GIPC3 Gene

mRNA differential expression in normal tissues according to GTEx for GIPC3 Gene

This gene is overexpressed in Esophagus - Muscularis (x5.2).

Protein differential expression in normal tissues from HIPED for GIPC3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (33.0), Platelet (11.8), and Adrenal (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GIPC3 Gene



NURSA nuclear receptor signaling pathways regulating expression of GIPC3 Gene:

GIPC3

SOURCE GeneReport for Unigene cluster for GIPC3 Gene:

Hs.266873

mRNA Expression by UniProt/SwissProt for GIPC3 Gene:

Q8TF64-GIPC3_HUMAN
Tissue specificity: Widely expressed in adult and fetal tissues. Highest levels are found in jejunum, lymph node, parietal lobe, fetal spleen and fetal thymus. Expressed in cervical, melanoma, chronic myelogenous and gastric cancer cell lines.

Phenotype-based relationships between genes and organs from Gene ORGANizer for GIPC3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • 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 GIPC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Evidence on tissue expression from TISSUES for GIPC3 Gene

Orthologs for GIPC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for GIPC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia GIPC3 33 34
  • 92.79 (n)
dog
(Canis familiaris)
 Mammalia GIPC3 33 34
  • 89.96 (n)
cow
(Bos Taurus)
 Mammalia GIPC3 33
  • 89.1 (n)
oppossum
(Monodelphis domestica)
 Mammalia GIPC3 34
  • 84 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Gipc3 33 16 34
  • 83.82 (n)
rat
(Rattus norvegicus)
 Mammalia Gipc3 33
  • 83.57 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia GIPC3 34
  • 67 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LOC100857667 33
  • 77.7 (n)
GIPC3 34
  • 71 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia gipc3 33
  • 69.74 (n)
zebrafish
(Danio rerio)
 Actinopterygii zgc:136839 33
  • 71.96 (n)
GIPC3 34
  • 64 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta kermit 33 34
  • 61.76 (n)
l(2)02045 35
  • 54 (a)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP007674 33
  • 58.76 (n)
worm
(Caenorhabditis elegans)
 Secernentea C35D10.2 35
  • 34 (a)
F44D12.4 35
  • 34 (a)
gipc-2 34
  • 28 (a)
 ManyToMany
gipc-1 34
  • 27 (a)
 ManyToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 47 (a)
 OneToMany
Species where no ortholog for GIPC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 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)

Evolution for GIPC3 Gene

ENSEMBL:
Gene Tree for GIPC3 (if available)
TreeFam:
Gene Tree for GIPC3 (if available)

Paralogs for GIPC3 Gene

Paralogs for GIPC3 Gene

(2) SIMAP similar genes for GIPC3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with GIPC3: view

Variants for GIPC3 Gene

Sequence variations from dbSNP and Humsavar for GIPC3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs387906999 pathogenic, Deafness, autosomal recessive 15, Deafness, autosomal recessive, 15 (DFNB15) [MIM:601869] 3,589,910(+) T/G coding_sequence_variant, missense_variant
rs387907000 pathogenic, Deafness, autosomal recessive 15 3,590,154(+) G/A coding_sequence_variant, missense_variant, stop_gained
rs387907001 pathogenic, Deafness, autosomal recessive 15, Deafness, autosomal recessive, 15 (DFNB15) [MIM:601869] 3,589,892(+) G/A coding_sequence_variant, missense_variant
rs387907002 pathogenic, Deafness, autosomal recessive 15, Deafness, autosomal recessive, 15 (DFNB15) [MIM:601869] 3,586,967(+) C/A/T coding_sequence_variant, missense_variant
rs727503062 likely-pathogenic, Nonsyndromic hearing loss and deafness, not provided 3,585,719(+) C/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for GIPC3 Gene

Variant ID Type Subtype PubMed ID
esv3366545 CNV duplication 20981092
nsv1146030 CNV deletion 26484159
nsv470114 CNV loss 18288195
nsv833713 CNV loss 17160897
nsv953948 CNV deletion 24416366

Variation tolerance for GIPC3 Gene

Residual Variation Intolerance Score: 55.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.33; 26.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GIPC3 Gene

Human Gene Mutation Database (HGMD)
GIPC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GIPC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GIPC3 Gene

Disorders for GIPC3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for GIPC3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 15
  • dfnb15
nonsyndromic deafness
  • nonsyndromic hearing loss
non-syndromic genetic deafness
  • isolated genetic deafness
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
audiogenic seizures
  • audiogenic seizure
- elite association - COSMIC cancer census association via MalaCards
Search GIPC3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GIPC3_HUMAN
  • Deafness, autosomal recessive, 15 (DFNB15) [MIM:601869]: A form of non-syndromic sensorineural hearing loss with prelingual onset. 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:21326233, ECO:0000269 PubMed:21660509}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GIPC3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GIPC3: view

No data available for Genatlas for GIPC3 Gene

Publications for GIPC3 Gene

  1. Molecular cloning and characterization of human GIPC3, a novel gene homologous to human GIPC1 and GIPC2. (PMID: 11836571) Saitoh T … Katoh M (International journal of oncology 2002) 2 3 4 22 58
  2. Gipc3 mutations associated with audiogenic seizures and sensorineural hearing loss in mouse and human. (PMID: 21326233) Charizopoulou N … Noben-Trauth K (Nature communications 2011) 2 3 4 58
  3. Mutations of GIPC3 cause nonsyndromic hearing loss DFNB72 but not DFNB81 that also maps to chromosome 19p. (PMID: 21660509) Rehman AU … Friedman TB (Human genetics 2011) 3 4 58
  4. Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: a two-stage Spanish case-control study. (PMID: 18950845) Vega A … Carracedo A (Gynecologic oncology 2009) 3 44 58
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 58

Products for GIPC3 Gene

Sources for GIPC3 Gene

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