PSD Gene (Protein Coding)

Pleckstrin And Sec7 Domain Containing

GC10M102403
GIFtS:
39
This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012] See more...

Aliases for PSD Gene

Aliases for PSD Gene

  • Pleckstrin And Sec7 Domain Containing 2 3 5
  • EFA6A 2 3 4
  • EFA6 2 3 4
  • PSD1 2 3 4
  • TYL 2 3 4
  • Exchange Factor For ADP-Ribosylation Factor Guanine Nucleotide Factor 6 3 4
  • Pleckstrin Homology And SEC7 Domain-Containing Protein 1 3 4
  • PH And SEC7 Domain-Containing Protein 1 3 4
  • Exchange Factor For ARF6 A 3 4
  • Exchange Factor For ARF6 3 4
  • KIAA2011 2 4
  • Pleckstrin And Sec7 Domain Protein 2
  • Pleckstrin-Sec7 Domains-Containing 3
  • PSD 5

External Ids for PSD Gene

Previous GeneCards Identifiers for PSD Gene

  • GC10M103055
  • GC10M103396
  • GC10M104293
  • GC10M103826
  • GC10M104152
  • GC10M097795

Summaries for PSD Gene

Entrez Gene Summary for PSD Gene

  • This gene encodes a Plekstrin homology and SEC7 domains-containing protein that functions as a guanine nucleotide exchange factor. The encoded protein regulates signal transduction by activating ADP-ribosylation factor 6. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

GeneCards Summary for PSD Gene

PSD (Pleckstrin And Sec7 Domain Containing) is a Protein Coding gene. Diseases associated with PSD include Cone-Rod Dystrophy 1 and Branch Retinal Artery Occlusion. Among its related pathways are Endocytosis. Gene Ontology (GO) annotations related to this gene include obsolete signal transducer activity and ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is PSD2.

UniProtKB/Swiss-Prot Summary for PSD Gene

  • Guanine nucleotide exchange factor for ARF6 (PubMed:23603394). Induces cytoskeletal remodeling (By similarity).

Additional gene information for PSD Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PSD Gene

Genomics for PSD Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PSD 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
GH10J102418 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.6 593 5.1 SP1 HNRNPL GATAD2A CTCF PRDM10 REST ZNF629 TFE3 RFX1 SIX5 FBXL15 PSD lnc-PSD-1 PPRC1 PDCD11 PCGF6 SFXN2 NOLC1 RPEL1 HPS6
GH10J102501 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11 -81.9 -81862 5.2 SP1 CREB1 GATAD2A CTCF TEAD4 PRDM10 ZNF629 REST SIX5 LEF1 ACTR1A SUFU MFSD13A PDCD11 PPRC1 PCGF6 RNU6-43P C10orf95 FBXL15 PSD
GH10J102592 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.5 -178.0 -177990 14.1 HNRNPL GATAD2A CTCF REST TFE3 LEF1 SOX13 IKZF1 NFKBIZ RCOR2 MFSD13A SFXN2 ACTR1A SUFU C10orf95 PSD FBXL15 MIR146B CUEDC2 ARL3
GH10J102462 Promoter/Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas 11.5 -42.0 -41968 1.7 LEF1 IKZF1 ZIC2 MTA1 SP1 HDAC1 SOX6 FOXK2 SCRT2 MGA MFSD13A MIR146B CUEDC2 FBXL15 PSD SUFU RNU6-43P NFKB2 ELOVL3 lnc-SUFU-1
GH10J102239 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 5.8 +177.4 177395 8.5 CEBPG SP1 CREB1 PRDM10 REST ZNF629 TFE3 ZNF512 RFX1 SOX13 PITX3 GBF1 PPRC1 LDB1 PSD BORCS7 RPARP-AS1 KCNIP2 WBP1L lnc-ELOVL3-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PSD on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PSD

Top Transcription factor binding sites by QIAGEN in the PSD gene promoter:
  • COMP1
  • Ik-2
  • Nkx2-5
  • NRSF form 1
  • NRSF form 2
  • PPAR-alpha
  • USF-1
  • USF1
  • Zic3

Genomic Locations for PSD Gene

Genomic Locations for PSD Gene
chr10:102,402,617-102,421,539
(GRCh38/hg38)
Size:
18,923 bases
Orientation:
Minus strand
chr10:104,162,376-104,181,296
(GRCh37/hg19)
Size:
18,921 bases
Orientation:
Minus strand

Genomic View for PSD Gene

Genes around PSD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PSD Gene

Proteins for PSD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    A5PKW4-PSD1_HUMAN
    Recommended name:
    PH and SEC7 domain-containing protein 1
    Protein Accession:
    A5PKW4
    Secondary Accessions:
    • B1AKX7
    • D3DR87
    • Q15673
    • Q8IVG0

    Protein attributes for PSD Gene

    Size:
    1024 amino acids
    Molecular mass:
    109543 Da
    Quaternary structure:
    • Interacts with ACTN1. Interacts (ARF6-bound form) with KCNK1; does not interact with KCNK1 in the absence of ARF6 (By similarity).
    SequenceCaution:
    • Sequence=BAC23107.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for PSD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PSD Gene

Protein Expression for PSD Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PSD Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PSD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PSD Gene

Domains & Families for PSD Gene

Gene Families for PSD Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PSD Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PSD Gene

GenScript: Design optimal peptide antigens:
  • Pleckstrin homology and SEC7 domain-containing protein 1 (PSD1_HUMAN)
  • PSD protein (Q86YI3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A5PKW4

UniProtKB/Swiss-Prot:

PSD1_HUMAN :
  • Belongs to the PSD family.
Family:
  • Belongs to the PSD family.
genes like me logo Genes that share domains with PSD: view

Function for PSD Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PSD Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor for ARF6 (PubMed:23603394). Induces cytoskeletal remodeling (By similarity).
GENATLAS Biochemistry:
pleckstrin-Sec 7 domains protein,71kDa,with three alternatively spliced forms the larger in the brain,tightly linked to NKF2,in tail to tail orientation

Phenotypes From GWAS Catalog for PSD Gene

Gene Ontology (GO) - Molecular Function for PSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IEA --
GO:0005086 ARF guanyl-nucleotide exchange factor activity IDA 23603394
GO:0005515 protein binding IPI 20339350
GO:0005543 phospholipid binding IEA --
genes like me logo Genes that share ontologies with PSD: view
genes like me logo Genes that share phenotypes with PSD: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PSD

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PSD Gene

Localization for PSD Gene

Subcellular locations from UniProtKB/Swiss-Prot for PSD Gene

Cell membrane. Cell projection, ruffle membrane. Cleavage furrow. Note=Distributed uniformly on the plasma membrane, as well as throughout the cytoplasm during metaphase. Subsequently concentrated at patches in the equatorial region at the onset of cytokinesis, and becomes distributed in the equatorial region concurrent with cleavage furrow ingression. In later cytokinesis phases, fades away from the cleavage furrow and becomes uniformly distributed throughout the plasma membrane. {ECO:0000269 PubMed:23603394}.

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 PSD gene
Compartment Confidence
plasma membrane 5
nucleus 3
endosome 3
cytosol 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
golgi apparatus 2
extracellular 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0014069 postsynaptic density IEA --
GO:0016020 membrane IEA --
GO:0032154 cleavage furrow IEA,IDA 23603394
GO:0032587 ruffle membrane IEA,IDA 23603394
genes like me logo Genes that share ontologies with PSD: view

Pathways & Interactions for PSD Gene

PathCards logo

SuperPathways for PSD Gene

SuperPathway Contained pathways
1 Endocytosis
Endocytosis
-
genes like me logo Genes that share pathways with PSD: view

Pathways by source for PSD Gene

1 KEGG pathway for PSD Gene

Gene Ontology (GO) - Biological Process for PSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction NAS 9417912
GO:0031175 neuron projection development IEA --
GO:0032012 regulation of ARF protein signal transduction IEA --
genes like me logo Genes that share ontologies with PSD: view

No data available for SIGNOR curated interactions for PSD Gene

Drugs & Compounds for PSD Gene

Products:

  1. Drug

(3) Drugs for PSD Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with PSD: view

Transcripts for PSD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PSD Gene

3 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PSD

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

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c · 15d · 15e ^ 16 ^ 17a ·
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - - -
SP5: -
SP6: - -
SP7:
SP8:
SP9: - - - - -
SP10: - - - -
SP11: - - -
SP12: - -
SP13:
SP14:
SP15:

ExUns: 17b ^ 18a · 18b · 18c · 18d ^ 19a · 19b ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5: -
SP6: -
SP7: - -
SP8: - -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for PSD Gene

GeneLoc Exon Structure for
PSD

Expression for PSD Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for PSD Gene
mRNA expression by BioGPS for PSD GenemRNA expression by GTEx for PSD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x5.6), Brain - Hippocampus (x4.8), Brain - Putamen (basal ganglia) (x4.6), Brain - Amygdala (x4.5), Brain - Cortex (x4.4), and Brain - Caudate (basal ganglia) (x4.3).

Protein differential expression in normal tissues from HIPED for PSD Gene

This gene is overexpressed in Plasma (38.7), Fetal Brain (18.2), and Platelet (7.0).

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



Protein tissue co-expression partners for PSD Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PSD

SOURCE GeneReport for Unigene cluster for PSD Gene:

Hs.154658

mRNA Expression by UniProt/SwissProt for PSD Gene:

A5PKW4-PSD1_HUMAN
Tissue specificity: Isoform 2 is expressed in the brain.

Evidence on tissue expression from TISSUES for PSD Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with PSD: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PSD Gene

Orthologs for PSD Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PSD Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PSD 30 31
  • 98.48 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PSD 30 31
  • 93.29 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PSD 30 31
  • 91.98 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Psd 30 17 31
  • 89.74 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Psd 30
  • 89.47 (n)
Oppossum
(Monodelphis domestica)
 Mammalia PSD 31
  • 79 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia PSD 31
  • 69 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PSD 30 31
  • 67.37 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PSD 31
  • 60 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia psd 30
  • 62.06 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.33589 30
Zebrafish
(Danio rerio)
 Actinopterygii LOC570918 30
  • 65.08 (n)
PSD (1 of 3) 31
  • 54 (a)
 OneToMany
PSD (2 of 3) 31
  • 29 (a)
 OneToMany
CABZ01075947.1 31
  • 23 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta Efa6 31
  • 19 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea Y55D9A.1a 32
  • 37 (a)
Y55D9A.1b 32
  • 37 (a)
efa-6 31
  • 26 (a)
 OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes GEA2 31
  • 8 (a)
 ManyToMany
GEA1 31
  • 7 (a)
 ManyToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 24 (a)
 OneToMany
Species where no ortholog for PSD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 Vase (Ciona intestinalis)
  • 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)

Evolution for PSD Gene

ENSEMBL:
Gene Tree for PSD (if available)
TreeFam:
Gene Tree for PSD (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PSD: view image

Paralogs for PSD Gene

Paralogs for PSD Gene

(3) SIMAP similar genes for PSD Gene using alignment to 3 proteins:

  • PSD1_HUMAN
  • L0R6N0_HUMAN
  • Q86YI3_HUMAN
genes like me logo Genes that share paralogs with PSD: view

Variants for PSD Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PSD Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
721837 Benign: not provided 102,403,234(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
730323 Benign: not provided 102,416,559(-) G/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
739565 Likely Benign: not provided 102,411,109(-) G/A SYNONYMOUS_VARIANT
744259 Likely Benign: not provided 102,417,009(-) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT
746061 Likely Benign: not provided 102,410,909(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for PSD Gene

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

Variant ID Type Subtype PubMed ID
nsv1159761 CNV deletion 26073780
nsv525546 CNV loss 19592680
nsv552058 CNV loss 21841781
nsv951006 CNV deletion 24416366

Variation tolerance for PSD Gene

Residual Variation Intolerance Score: 31.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.31; 53.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PSD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSD

SNP Genotyping and Copy Number Assay Products

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

Disorders for PSD Gene

MalaCards: The human disease database

(2) MalaCards diseases for PSD Gene - From: DISEASES

Disorder Aliases PubMed IDs
cone-rod dystrophy 1
  • retinitis pigmentosa 1
branch retinal artery occlusion
  • arterial retinal branch occlusion
- elite association - COSMIC cancer census association via MalaCards
Search PSD in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PSD

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PSD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PSD Gene

Publications for PSD Gene

  1. Identification of a novel gene, PSD, adjacent to NFKB2/lyt-10, which contains Sec7 and pleckstrin-homology domains. (PMID: 9417912) Perletti L … Neri A (Genomics 1997) 2 3 4
  2. EFA6 activates Arf6 and participates in its targeting to the Flemming body during cytokinesis. (PMID: 23603394) Ueda T … Nakayama K (FEBS letters 2013) 3 4
  3. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. (PMID: 19773279) Hosgood HD … Lan Q (Occupational and environmental medicine 2009) 3 41
  4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 41
  5. EFA6 proteins regulate lumen formation through α-actinin 1. (PMID: 29246944) Milanini J … Luton F (Journal of cell science 2018) 3

ExternalLinks

View latest publications for PSD gene in Mastermind

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