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PDZD7 PDZ domain containing 7 [ Homo sapiens (human) ]

Gene ID: 79955, updated on 5-Mar-2024

Summary

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Official Symbol
PDZD7provided by HGNC
Official Full Name
PDZ domain containing 7provided by HGNC
Primary source
HGNC:HGNC:26257
See related
Ensembl:ENSG00000186862 MIM:612971; AllianceGenome:HGNC:26257
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDZK7; DFNB57
Summary
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]
Expression
Broad expression in small intestine (RPKM 3.0), duodenum (RPKM 1.7) and 20 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
10q24.31
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (101007679..101031129, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101891054..101914544, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102767436..102790886, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene semaphorin 4G Neighboring gene mitochondrial ribosomal protein L43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102755784-102756653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2712 Neighboring gene twinkle mtDNA helicase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2714 Neighboring gene leucine zipper tumor suppressor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102768034-102768715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102768716-102769396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3906 Neighboring gene sideroflexin 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102810093-102810594 Neighboring gene uncharacterized LOC107984262 Neighboring gene Sharpr-MPRA regulatory region 11881

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Novel homozygous variant in the PDZD7 gene in a family with nonsyndromic sensorineural hearing loss. Du Q, et al. BMC Med Genomics, 2022 Jun 17. PMID 35715776, Free PMC Article
  2. Identification of a Potential Founder Effect of a Novel PDZD7 Variant Involved in Moderate-to-Severe Sensorineural Hearing Loss in Koreans. Lee SY, et al. Int J Mol Sci, 2019 Aug 26. PMID 31454969, Free PMC Article
  3. Novel recessive PDZD7 biallelic mutations associated with hereditary hearing loss in a Chinese pedigree. Luo H, et al. Gene, 2019 Aug 15. PMID 31129248
  4. Novel recessive PDZD7 biallelic mutations in two Chinese families with non-syndromic hearing loss. Guan J, et al. Am J Med Genet A, 2018 Jan. PMID 29048736, Free PMC Article
  5. Confirmation of PDZD7 as a Nonsyndromic Hearing Loss Gene. Vona B, et al. Ear Hear, 2016 Jul-Aug. PMID 26849169

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel homozygous variant in the PDZD7 gene in a family with nonsyndromic sensorineural hearing loss.
    Title: Novel homozygous variant in the PDZD7 gene in a family with nonsyndromic sensorineural hearing loss.
  2. PDZD7 can be an important causative gene for moderate to severe ARNSHL in Koreans. Moreover, at least some, if not all, p.Arg164Trp alleles in Koreans could exert a potential founder effect and arise from diverse haplotypes as a mutational hot spot.
    Title: Identification of a Potential Founder Effect of a Novel PDZD7 Variant Involved in Moderate-to-Severe Sensorineural Hearing Loss in Koreans.
  3. Three mutations in PDZD7 gene linked to autosomal recessive non-syndromic hearing loss (ARNSHL) were identified in a Chinese pedigree. The findings expand not only our knowledge of genetic causes of ARNSHL, but also PDZD7 genes mutation spectrum of the disease. They will aid personalized genetic counseling, molecular diagnostics and clinical management of this condition.
    Title: Novel recessive PDZD7 biallelic mutations associated with hereditary hearing loss in a Chinese pedigree.
  4. Lnc-PDZD7 promotes stemness properties and suppresses chemosensitivity though the miR-101/EZH2/ATOH8 pathway.
    Title: Lnc-PDZD7 contributes to stemness properties and chemosensitivity in hepatocellular carcinoma through EZH2-mediated ATOH8 transcriptional repression.
  5. This is the first report to identify PDZD7 as an ARNSHL-associated gene in the Chinese population. Our finding could expand the pathogenic spectrum and strengthens the clinical diagnostic role of the PDZD7 gene in ARNSHL patients.
    Title: Novel recessive PDZD7 biallelic mutations in two Chinese families with non-syndromic hearing loss.
  6. PDZD7 is confirmed as a bona fide autosomal recessive nonsyndromic hearing loss gene.
    Title: Confirmation of PDZD7 as a Nonsyndromic Hearing Loss Gene.
  7. Mutations in PDZD7 cause autosomal recessive non-syndromic hearing loss.
    Title: PDZD7 and hearing loss: More than just a modifier.
  8. Both WHRN and PDZD7 are required for the complex formation with USH2A and GPR98.
    Title: Whirlin and PDZ domain-containing 7 (PDZD7) proteins are both required to form the quaternary protein complex associated with Usher syndrome type 2.
  9. overexpression of another Usher syndrome protein, PDZD7, decreased the AC inhibition of the VLGR1 beta-subunit
    Title: Constitutive Gαi coupling activity of very large G protein-coupled receptor 1 (VLGR1) and its regulation by PDZD7 protein.
  10. PDZD7 is a scaffolding component of the ankle-link complex in stereocilia and is associated with the Usher syndrome protein network.
    Title: Localization of PDZD7 to the stereocilia ankle-link associates this scaffolding protein with the Usher syndrome protein network.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Hearing loss, autosomal recessive 57
MedGen: C4693893 OMIM: 618003 GeneReviews: Not available
Compare labs
Usher syndrome type 2A
MedGen: C1848634 OMIM: 276901 GeneReviews: Usher Syndrome Type II
Compare labs
Usher syndrome type 2C
MedGen: C2931213 OMIM: 605472 GeneReviews: Usher Syndrome Type II
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within auditory receptor cell development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in auditory receptor cell stereocilium organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within auditory receptor cell stereocilium organization ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in establishment of localization in cell IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within establishment of protein localization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in inner ear receptor cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of USH2 complex ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cilium IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in stereocilia ankle link ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of stereocilia ankle link complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of stereocilia ankle link complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in stereocilium ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in stereocilium tip IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
PDZ domain-containing protein 7
Names
deafness, autosomal recessive 57

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_028030.1 RefSeqGene

    Range
    5029..28479
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001195263.2 → NP_001182192.1  PDZ domain-containing protein 7 isoform 1

    See identical proteins and their annotated locations for NP_001182192.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK026862, AL133215, DA197280, FJ617449
    Consensus CDS
    CCDS73182.1
    UniProtKB/Swiss-Prot
    D5FJ77, Q8N321, Q9H5P4
    Related
    ENSP00000480489.1, ENST00000619208.6
    Conserved Domains (2) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd07358
    Location:554 → 630
    HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins

  2. NM_001351044.2 → NP_001337973.1  PDZ domain-containing protein 7 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the coding region, which results in a frameshift, lacks multiple exons in the 3' coding region, and has a distinct 3' terminal exon, resulting in a distinct 3' coding region and 3' UTR compared to variant 1. It encodes isoform 3, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK026862, AL133215, AW058493, DA197280, FJ617449
    Conserved Domains (1) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  3. NM_024895.5 → NP_079171.1  PDZ domain-containing protein 7 isoform 2

    See identical proteins and their annotated locations for NP_079171.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1 and is also known as PDZD7-A.
    Source sequence(s)
    AK026862, AL133215, DA197280
    Consensus CDS
    CCDS31269.1
    UniProtKB/Swiss-Prot
    Q9H5P4
    Related
    ENSP00000359234.3, ENST00000370215.7
    Conserved Domains (1) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    101007679..101031129 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011540178.4 → XP_011538480.1  PDZ domain-containing protein 7 isoform X2

    Conserved Domains (2) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd07358
    Location:553 → 629
    HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins

  2. XM_011540177.4 → XP_011538479.1  PDZ domain-containing protein 7 isoform X1

    See identical proteins and their annotated locations for XP_011538479.1

    UniProtKB/Swiss-Prot
    D5FJ77, Q8N321, Q9H5P4
    Conserved Domains (2) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd07358
    Location:554 → 630
    HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins

  3. XM_047425767.1 → XP_047281723.1  PDZ domain-containing protein 7 isoform X1

    UniProtKB/Swiss-Prot
    D5FJ77, Q8N321, Q9H5P4

  4. XM_011540179.4 → XP_011538481.1  PDZ domain-containing protein 7 isoform X4

    Conserved Domains (2) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    cd07358
    Location:554 → 630
    HN_PDZD7_like; harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins

  5. XM_047425768.1 → XP_047281724.1  PDZ domain-containing protein 7 isoform X3

  6. XM_005270165.4 → XP_005270222.1  PDZ domain-containing protein 7 isoform X6

    UniProtKB/TrEMBL
    A0A2R8Y892
    Related
    ENSP00000496747.1, ENST00000644782.1
    Conserved Domains (1) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  7. XM_011540181.4 → XP_011538483.1  PDZ domain-containing protein 7 isoform X7

    Conserved Domains (1) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  8. XM_011540183.4 → XP_011538485.1  PDZ domain-containing protein 7 isoform X8

    Conserved Domains (1) summary
    cd00992
    Location:84 → 164
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

  9. XM_017016667.3 → XP_016872156.1  PDZ domain-containing protein 7 isoform X5

    UniProtKB/TrEMBL
    A0A2R8YFN1
    Related
    ENSP00000495283.1, ENST00000645349.1

  10. XM_017016668.3 → XP_016872157.1  PDZ domain-containing protein 7 isoform X9

  11. XM_047425769.1 → XP_047281725.1  PDZ domain-containing protein 7 isoform X5

    UniProtKB/TrEMBL
    A0A2R8YFN1

  12. XM_047425771.1 → XP_047281727.1  PDZ domain-containing protein 7 isoform X10

RNA

  1. XR_945816.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    101891054..101914544 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054366764.1 → XP_054222739.1  PDZ domain-containing protein 7 isoform X1

    UniProtKB/Swiss-Prot
    D5FJ77, Q8N321, Q9H5P4

  2. XM_054366765.1 → XP_054222740.1  PDZ domain-containing protein 7 isoform X2

  3. XM_054366763.1 → XP_054222738.1  PDZ domain-containing protein 7 isoform X1

    UniProtKB/Swiss-Prot
    D5FJ77, Q8N321, Q9H5P4

  4. XM_054366766.1 → XP_054222741.1  PDZ domain-containing protein 7 isoform X4

  5. XM_054366769.1 → XP_054222744.1  PDZ domain-containing protein 7 isoform X6

    UniProtKB/TrEMBL
    A0A2R8Y892

  6. XM_054366770.1 → XP_054222745.1  PDZ domain-containing protein 7 isoform X7

  7. XM_054366771.1 → XP_054222746.1  PDZ domain-containing protein 7 isoform X8

  8. XM_054366767.1 → XP_054222742.1  PDZ domain-containing protein 7 isoform X5

    UniProtKB/TrEMBL
    A0A2R8YFN1

  9. XM_054366772.1 → XP_054222747.1  PDZ domain-containing protein 7 isoform X9

  10. XM_054366768.1 → XP_054222743.1  PDZ domain-containing protein 7 isoform X5

    UniProtKB/TrEMBL
    A0A2R8YFN1

  11. XM_054366773.1 → XP_054222748.1  PDZ domain-containing protein 7 isoform X10

RNA

  1. XR_008488266.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H5P4.2 GenPept UniProtKB/Swiss-Prot:Q9H5P4

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