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Aliases for PDZD7 Gene

Aliases for PDZD7 Gene

  • PDZ Domain Containing 7 2 3 5
  • Deafness, Autosomal Recessive 57 2 3
  • PDZK7 3 4
  • PDZ Domain-Containing Protein 7 3
  • DFNB57 3

External Ids for PDZD7 Gene

Previous HGNC Symbols for PDZD7 Gene

  • PDZK7
  • DFNB57

Previous GeneCards Identifiers for PDZD7 Gene

  • GC10M102758
  • GC10M102767
  • GC10M096407

Summaries for PDZD7 Gene

Entrez Gene Summary for PDZD7 Gene

  • This gene encodes a ciliary protein homologous to proteins which are mutated in Usher syndrome patients, and mutations and translocations involving this gene have been associated with two types of Usher syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

GeneCards Summary for PDZD7 Gene

PDZD7 (PDZ Domain Containing 7) is a Protein Coding gene. Diseases associated with PDZD7 include Usher Syndrome, Type Iia and Usher Syndrome, Type Iic. An important paralog of this gene is WHRN.

Additional gene information for PDZD7 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDZD7 Gene

Genomics for PDZD7 Gene

GeneHancer (GH) Regulatory Elements for PDZD7 Gene

Promoters and enhancers for PDZD7 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
GH10I101030 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 580.2 -2.1 -2090 6.4 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF143 FOS PDZD7 SFXN3 MRPL43 TWNK KAZALD1 TLX1 TLX1NB SEMA4G ENSG00000236662 MIR608
GH10I101028 Enhancer 0.8 ENCODE dbSUPER 550.8 +1.9 1882 1.1 CTCF ZNF3 MAZ ZIC2 RARA TEAD3 ATF4 GATA3 POLR2A VEZF1 SFXN3 PDZD7 TWNK ENSG00000236662 MRPL43 SEMA4G LZTS2
GH10I100986 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 13.1 +43.5 43510 2.5 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF2 SLC30A9 POLR2B MRPL43 GC10M100989 PIR54177 PIR47631 PIR56323 PIR57005 PIR34755 TWNK PHBP9 LZTS2
GH10I101692 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 9.7 -663.2 -663190 3.1 HDGF ARNT ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF143 SP3 SP5 FBXW4 PPRC1 GBF1 MRPL43 LDB1 ENSG00000272572 HPS6 TWNK SUFU LZTS2
GH10I100228 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.7 +801.7 801664 1.8 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B CHUK ENSG00000227492 BLOC1S2 EBAG9P1 MRPL43 CWF19L1 SLC25A28 PHBP9 LZTS2 ENSG00000236308
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDZD7 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDZD7 gene promoter:

Genomic Locations for PDZD7 Gene

Genomic Locations for PDZD7 Gene
chr10:101,007,683-101,031,157
(GRCh38/hg38)
Size:
23,475 bases
Orientation:
Minus strand
chr10:102,767,440-102,790,914
(GRCh37/hg19)

Genomic View for PDZD7 Gene

Genes around PDZD7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDZD7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDZD7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDZD7 Gene

Proteins for PDZD7 Gene

  • Protein details for PDZD7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H5P4-PDZD7_HUMAN
    Recommended name:
    PDZ domain-containing protein 7
    Protein Accession:
    Q9H5P4
    Secondary Accessions:
    • D5FJ77
    • Q8N321

    Protein attributes for PDZD7 Gene

    Size:
    517 amino acids
    Molecular mass:
    55677 Da
    Quaternary structure:
    • Interacts with USH1G. Interacts with GPR98. Interacts with USH2A.

    Three dimensional structures from OCA and Proteopedia for PDZD7 Gene

    Alternative splice isoforms for PDZD7 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDZD7 Gene

Post-translational modifications for PDZD7 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDZD7 Gene

Domains & Families for PDZD7 Gene

Gene Families for PDZD7 Gene

Protein Domains for PDZD7 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PDZD7 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDZD7: view

No data available for UniProtKB/Swiss-Prot for PDZD7 Gene

Function for PDZD7 Gene

Phenotypes From GWAS Catalog for PDZD7 Gene

Gene Ontology (GO) - Molecular Function for PDZD7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19028668
GO:0042803 protein homodimerization activity IEA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with PDZD7: view
genes like me logo Genes that share phenotypes with PDZD7: view

Human Phenotype Ontology for PDZD7 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PDZD7 Gene

MGI Knock Outs for PDZD7:

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for PDZD7 Gene

Localization for PDZD7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDZD7 Gene

Cell projection, cilium. Nucleus.

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 PDZD7 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDZD7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002141 stereocilia ankle link IEA --
GO:0005615 extracellular space IDA,HDA 22664934
GO:0005634 nucleus IDA,IEA 20440071
GO:0005929 cilium IEA,IDA 20440071
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with PDZD7: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDZD7 Gene

Pathways & Interactions for PDZD7 Gene

SuperPathways for PDZD7 Gene

No Data Available

Interacting Proteins for PDZD7 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000359234%0d%0a9606.ENSP00000305941%0d%0a
Selected Interacting proteins: ENSP00000359234 Q9H5P4-PDZD7_HUMAN for PDZD7 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PDZD7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045184 establishment of protein localization IEA --
GO:0050910 detection of mechanical stimulus involved in sensory perception of sound IEA --
GO:0060088 auditory receptor cell stereocilium organization IEA --
GO:0060117 auditory receptor cell development IEA --
genes like me logo Genes that share ontologies with PDZD7: view

No data available for Pathways by source and SIGNOR curated interactions for PDZD7 Gene

Drugs & Compounds for PDZD7 Gene

No Compound Related Data Available

Transcripts for PDZD7 Gene

Unigene Clusters for PDZD7 Gene

PDZ domain containing 7:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDZD7 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: - -
SP2:
SP3:
SP4:

Relevant External Links for PDZD7 Gene

GeneLoc Exon Structure for
PDZD7
ECgene alternative splicing isoforms for
PDZD7

Expression for PDZD7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDZD7 Gene

mRNA differential expression in normal tissues according to GTEx for PDZD7 Gene

This gene is overexpressed in Brain - Cerebellum (x5.6), Brain - Cerebellar Hemisphere (x5.2), and Brain - Cortex (x4.2).

Protein differential expression in normal tissues from HIPED for PDZD7 Gene

This gene is overexpressed in Spleen (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PDZD7 Gene



Protein tissue co-expression partners for PDZD7 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDZD7 Gene:

PDZD7

SOURCE GeneReport for Unigene cluster for PDZD7 Gene:

Hs.438245

mRNA Expression by UniProt/SwissProt for PDZD7 Gene:

Q9H5P4-PDZD7_HUMAN
Tissue specificity: Weakly expressed in the inner ear. Expressed in the retinal pigment epithelium.

Evidence on tissue expression from TISSUES for PDZD7 Gene

  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDZD7 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns with PDZD7: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for PDZD7 Gene

Orthologs for PDZD7 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZD7 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDZD7 34
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LOC511930 33
  • 88.07 (n)
PDZD7 34
  • 41 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LOC486847 33
  • 86 (n)
PDZD7 34
  • 46 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdzd7 33
  • 83.38 (n)
mouse
(Mus musculus)
Mammalia Pdzd7 33 16 34
  • 83.25 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PDZD7 34
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDZD7 34
  • 41 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDZD7 33 34
  • 69.84 (n)
lizard
(Anolis carolinensis)
Reptilia PDZD7 34
  • 30 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100489709 33
  • 58.57 (n)
zebrafish
(Danio rerio)
Actinopterygii pdzd7a 33 34
  • 58.45 (n)
PDZD7 (2 of 2) 34
  • 19 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta dysc 34
  • 10 (a)
OneToMany
Species where no ortholog for PDZD7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 PDZD7 Gene

ENSEMBL:
Gene Tree for PDZD7 (if available)
TreeFam:
Gene Tree for PDZD7 (if available)

Paralogs for PDZD7 Gene

Paralogs for PDZD7 Gene

(2) SIMAP similar genes for PDZD7 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with PDZD7: view

Variants for PDZD7 Gene

Sequence variations from dbSNP and Humsavar for PDZD7 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs587776894 risk-factor, Usher syndrome, type 2A 101,030,054(-) GGGGGGG/GGGGGGGG coding_sequence_variant, frameshift, non_coding_transcript_variant
rs118098246 conflicting-interpretations-of-pathogenicity, not specified 101,022,356(-) A/G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs555444131 conflicting-interpretations-of-pathogenicity, not specified 101,018,271(-) CTCCT/CT coding_sequence_variant, inframe_deletion, non_coding_transcript_variant
rs111750275 likely-benign, not specified 101,010,351(-) C/G/T coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, synonymous_variant
rs112571971 likely-benign, not specified 101,015,772(-) C/T 3_prime_UTR_variant, coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PDZD7 Gene

Variant ID Type Subtype PubMed ID
nsv1137956 CNV deletion 24896259
nsv517698 CNV loss 19592680
nsv7525 CNV insertion 18451855
nsv831965 CNV loss 17160897

Variation tolerance for PDZD7 Gene

Residual Variation Intolerance Score: 53.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.46; 43.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDZD7 Gene

Human Gene Mutation Database (HGMD)
PDZD7
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDZD7

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDZD7 Gene

Disorders for PDZD7 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PDZD7 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
usher syndrome, type iia
  • ush2a
usher syndrome, type iic
  • ush2c
usher syndrome type 2
  • ush2
usher syndrome
  • retinitis pigmentosa-deafness syndrome
usher syndrome, type iid
  • ush2d
- elite association - COSMIC cancer census association via MalaCards
Search PDZD7 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDZD7_HUMAN
  • Note=A chromosomal aberration disrupting PDZD7 has been found in patients with non-syndromic sensorineural deafness. Translocation t(10;11),t(10;11). {ECO:0000269 PubMed:19028668}.
  • Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with 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:20440071}. Note=The gene represented in this entry acts as a disease modifier.
  • Usher syndrome 2C (USH2C) [MIM:605472]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with 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:20440071}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. A PDZD7 mutation has been found in combination with a mutation in GPR98 in a patient affected by Usher syndrome, suggesting PDZD7 mutations contribute to digenic Usher syndrome. {ECO:0000269 PubMed:20440071}.

Additional Disease Information for PDZD7

genes like me logo Genes that share disorders with PDZD7: view

No data available for Genatlas for PDZD7 Gene

Publications for PDZD7 Gene

  1. PDZD7 and hearing loss: More than just a modifier. (PMID: 26416264) Booth KT … Smith RJ (American journal of medical genetics. Part A 2015) 2 3 58
  2. PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome. (PMID: 20440071) Ebermann I … Bolz HJ (The Journal of clinical investigation 2010) 3 4 58
  3. Homozygous disruption of PDZD7 by reciprocal translocation in a consanguineous family: a new member of the Usher syndrome protein interactome causing congenital hearing impairment. (PMID: 19028668) Schneider E … Haaf T (Human molecular genetics 2009) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4 58

Products for PDZD7 Gene

Sources for PDZD7 Gene

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