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

Summary

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, Oct 2024]
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

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_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PDZD8 Disruption Causes Cognitive Impairment in Humans, Mice, and Fruit Flies.
Title: PDZD8 Disruption Causes Cognitive Impairment in Humans, Mice, and Fruit Flies.
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.
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.
PDZD8 is not absolutely necessary for HIV-1 infection.
Title: Efficient human immunodeficiency virus (HIV-1) infection of cells lacking PDZD8.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed

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

A009V43 (e-PCR)
- UniSTS:5928

D10S221 (e-PCR)
- UniSTS:35654

D10S221 (e-PCR)
- UniSTS:82800

WI-13732 (e-PCR)
- UniSTS:1479

G32894 (e-PCR)
- UniSTS:117473

STS-H92741 (e-PCR)
- UniSTS:72425

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 more info	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)

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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

117277274..117375440 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047424575.1 → XP_047280531.1 PDZ domain-containing protein 8 isoform X2
XM_011539265.3 → XP_011537567.1 PDZ domain-containing protein 8 isoform X3

See identical proteins and their annotated locations for XP_011537567.1
XM_047424576.1 → XP_047280532.1 PDZ domain-containing protein 8 isoform X3
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)