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    PDZD8 PDZ domain containing 8 [ Homo sapiens (human) ]

    Gene ID: 118987, updated on 4-Jan-2025

    Summary

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    Official Symbol
    PDZD8provided by HGNC
    Official Full Name
    PDZ domain containing 8provided by HGNC
    Primary source
    HGNC:HGNC:26974
    See related
    Ensembl:ENSG00000165650 MIM:614235; AllianceGenome:HGNC:26974
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PDZK8; IDDADF
    Summary
    Predicted to enable lipid binding activity and metal ion binding activity. Involved in several processes, including mitochondrial calcium ion homeostasis; mitochondrion-endoplasmic reticulum membrane tethering; and regulation of cell morphogenesis. Located in endoplasmic reticulum membrane and mitochondria-associated endoplasmic reticulum membrane contact site. [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Broad expression in bone marrow (RPKM 51.5), testis (RPKM 17.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDZD8 in Genome Data Viewer
    Location:
    10q25.3-q26.11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (117277274..117375440, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (118171771..118269881, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (119036785..119134951, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118975364-118975881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118976399-118976916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:118982213-118982713 Neighboring gene potassium two pore domain channel subfamily K member 18 Neighboring gene SLC18A2 antisense RNA 1 Neighboring gene solute carrier family 18 member A2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4099 Neighboring gene CRISPRi-validated cis-regulatory element chr10.4281 Neighboring gene CRISPRi-validated cis-regulatory element chr10.4282 Neighboring gene uncharacterized LOC105378502 Neighboring gene Sharpr-MPRA regulatory region 14976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2861 Neighboring gene EMX2 opposite strand/antisense RNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:119294387-119295350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:119303472-119304094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:119304095-119304717 Neighboring gene empty spiracles homeobox 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Efficient human immunodeficiency virus (HIV-1) infection of cells lacking PDZD8. Zhang S, et al. Virology, 2015 Jul. PMID 25771112, Free PMC Article
    2. PDZD8 mediates a Rab7-dependent interaction of the ER with late endosomes and lysosomes. Guillén-Samander A, et al. Proc Natl Acad Sci U S A, 2019 Nov 5. PMID 31636202, Free PMC Article
    3. Contribution of PDZD8 to stabilization of the human immunodeficiency virus type 1 capsid. Guth CA, et al. J Virol, 2014 May. PMID 24554657, Free PMC Article
    4. PDZD8 is a novel moesin-interacting cytoskeletal regulatory protein that suppresses infection by herpes simplex virus type 1. Henning MS, et al. Virology, 2011 Jul 5. PMID 21549406
    5. PDZD8 is a novel Gag-interacting factor that promotes retroviral infection. Henning MS, et al. J Virol, 2010 Sep. PMID 20573829, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDZD8 Disruption Causes Cognitive Impairment in Humans, Mice, and Fruit Flies.
      Title: PDZD8 Disruption Causes Cognitive Impairment in Humans, Mice, and Fruit Flies.
    2. Protrudin and PDZD8 contribute to neuronal integrity by promoting lipid extraction required for endosome maturation.
      Title: Protrudin and PDZD8 contribute to neuronal integrity by promoting lipid extraction required for endosome maturation.
    3. PDZD8 tethers the endoplasmic reticulum to late endosomes and lysosomes via an interaction with Rab7.
      Title: PDZD8 mediates a Rab7-dependent interaction of the ER with late endosomes and lysosomes.
    4. PDZD8 is not absolutely necessary for HIV-1 infection.
      Title: Efficient human immunodeficiency virus (HIV-1) infection of cells lacking PDZD8.
    5. The PDZD8 coiled-coil domain is sufficient for HIV-1 capsid binding, but other parts of the protein, including the PDZ domain, are apparently required for stabilizing the capsid and supporting HIV-1 infection.
      Title: Contribution of PDZD8 to stabilization of the human immunodeficiency virus type 1 capsid.
    6. PDZD8 is a novel moesin-interacting protein that suppresses infection by herpes simplex virus type 1.
      Title: PDZD8 is a novel moesin-interacting cytoskeletal regulatory protein that suppresses infection by herpes simplex virus type 1.
    7. A mutant of PDZD8 lacking the coiled-coil domain in its Gag-interacting region failed to bind Gag and promote HIV-1 infection.
      Title: PDZD8 is a novel Gag-interacting factor that promotes retroviral infection.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    Submit: New GeneRIF Correction

    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
    Intellectual developmental disorder with autism and dysmorphic facies
    MedGen: C5774206 OMIM: 620021 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    A meta-analysis of genome-wide association studies of the electrocardiographic early repolarization pattern.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag PDZD8 binds to HIV-1 Gag and promotes HIV-1 infection. The C-terminal coiled-coil domain (amino acids 1028-1155) of PDZD8 interacts with Gag and is required for enhancement of HIV-1 infection PubMed
    capsid gag The putative coiled-coil motif (residues 1017-1063) of PDZD8 is both necessary and sufficient for HIV-1 CA-NC binding and the PDZ domain (residues 366-450) contributes to the function of PDZD8 as an HIV-1 cofactor for infectivity PubMed
    gag Human PDZD8 is an important contributor to the in vitro stabilization of HIV-1 CA-NC complexes by cell lysates PubMed
    matrix gag The putative coiled-coil motif (residues 1017-1063) of PDZD8 is both necessary and sufficient for HIV-1 CA-NC binding and the PDZ domain (residues 366-450) contributes to the function of PDZD8 as an HIV-1 cofactor for infectivity PubMed
    gag Human PDZD8 is an important contributor to the in vitro stabilization of HIV-1 CA-NC complexes by cell lysates PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25412, FLJ34427

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitochondrial calcium ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial calcium ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrion-endoplasmic reticulum membrane tethering IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrion-endoplasmic reticulum membrane tethering IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    is_active_in mitochondria-associated endoplasmic reticulum membrane contact site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondria-associated endoplasmic reticulum membrane contact site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PDZ domain-containing protein 8
    Names
    sarcoma antigen NY-SAR-84/NY-SAR-104

    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.

    mRNA and Protein(s)

    1. NM_173791.5 → NP_776152.1  PDZ domain-containing protein 8

      Status: VALIDATED

      Source sequence(s)
      AL359836, AL391988
      Consensus CDS
      CCDS7600.1
      UniProtKB/Swiss-Prot
      Q86WE0, Q86WE5, Q8NEN9, Q9UFF1
      Related
      ENSP00000334642.5, ENST00000334464.7
      Conserved Domains (3) summary
      cd00029
      Location:841 → 883
      C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
      cd00992
      Location:364 → 441
      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) ...
      cl26464
      Location:517 → 635
      Atrophin-1; Atrophin-1 family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      117277274..117375440 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005269518.5 → XP_005269575.1  PDZ domain-containing protein 8 isoform X1

      Conserved Domains (3) summary
      cd00029
      Location:800 → 842
      C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
      cd00992
      Location:323 → 400
      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) ...
      pfam15264
      Location:522 → 633
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    2. XM_047424575.1 → XP_047280531.1  PDZ domain-containing protein 8 isoform X2

    3. XM_011539265.3 → XP_011537567.1  PDZ domain-containing protein 8 isoform X3

    4. XM_047424576.1 → XP_047280532.1  PDZ domain-containing protein 8 isoform X3

    5. XM_011539266.4 → XP_011537568.1  PDZ domain-containing protein 8 isoform X3

      Conserved Domains (1) summary
      pfam10296
      Location:99 → 206
      DUF2404; Putative integral membrane protein conserved region (DUF2404)

    RNA

    1. XR_945602.3 RNA Sequence

    2. XR_007061943.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      118171771..118269881 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364738.1 → XP_054220713.1  PDZ domain-containing protein 8 isoform X1

    2. XM_054364739.1 → XP_054220714.1  PDZ domain-containing protein 8 isoform X2

    3. XM_054364740.1 → XP_054220715.1  PDZ domain-containing protein 8 isoform X3

    4. XM_054364741.1 → XP_054220716.1  PDZ domain-containing protein 8 isoform X3

    RNA

    1. XR_008488165.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NEN9.1 GenPept UniProtKB/Swiss-Prot:Q8NEN9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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