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

Gene ID: 118987, updated on 2-Nov-2024

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, Nov 2024]
Expression
Broad expression in bone marrow (RPKM 51.5), testis (RPKM 17.7) and 24 other tissues See more
Orthologs
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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: HPA RNA-seq normal tissues 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. Efficient human immunodeficiency virus (HIV-1) infection of cells lacking PDZD8. Zhang S, et al. Virology, 2015 Jul. PMID 25771112, Free PMC Article
  2. 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
  3. 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
  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 (59) 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)

Genotypes

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

    See identical proteins and their annotated locations for NP_776152.1

    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

    See identical proteins and their annotated locations for XP_011537567.1

  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

    See identical proteins and their annotated locations for XP_011537568.1

    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

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