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    PSD2 pleckstrin and Sec7 domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 84249, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PSD2provided by HGNC
    Official Full Name
    pleckstrin and Sec7 domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:19092
    See related
    Ensembl:ENSG00000146005 MIM:620656; AllianceGenome:HGNC:19092
    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
    EFA6C
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction and regulation of catalytic activity. Predicted to be located in cleavage furrow and ruffle membrane. Predicted to be active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in brain (RPKM 11.2) and testis (RPKM 0.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See PSD2 in Genome Data Viewer
    Location:
    5q31.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (139742475..139844466)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140266708..140369568)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (139175393..139224051)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23248 Neighboring gene uncharacterized LOC124901084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139053795-139054348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139058359-139059081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139064529-139065183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16425 Neighboring gene CXXC finger protein 5 Neighboring gene Sharpr-MPRA regulatory region 3182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139077525-139078494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139079969-139080794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139080795-139081619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139088825-139089815 Neighboring gene uncharacterized LOC124901085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139104350-139104850 Neighboring gene RNA, U6 small nuclear 236, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139117735-139118662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139121544-139122093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139122094-139122642 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139123561-139124154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139125678-139126325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139128271-139128918 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139131846-139131997 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139137793-139138691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139138692-139139589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139141892-139142555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139142556-139143218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139143219-139143882 Neighboring gene PSD2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139169627-139170127 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139174912-139175111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139194145-139194646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139259501-139260264 Neighboring gene neuregulin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23255 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:139364881-139366080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139422349-139423018 Neighboring gene uncharacterized LOC124900193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16442 Neighboring gene mitosis associated long intergenic non-coding RNA 1

    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. Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline. Yu L, et al. JAMA Neurol, 2017 Dec 1. PMID 29084334, Free PMC Article
    2. Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport. Kunkle BW, et al. JAMA Neurol, 2017 Sep 1. PMID 28738127, Free PMC Article
    3. Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2. Cannavo E, et al. J Biol Chem, 2007 Feb 2. PMID 17148452
    4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
    5. Acetylation of ELF5 suppresses breast cancer progression by promoting its degradation and targeting CCND1. Li X, et al. NPJ Precis Oncol, 2021 Mar 19. PMID 33742100, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Brain gene expression of PADI2, ZNF385A, PSD2, and A2ML1 and DNA methylation dysregulations are implicated in the alteration of brain tissue properties associated with late-life cognitive decline above and beyond the influence of common neuropathologic conditions.
      Title: Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline.
    2. PSD2 may be involved in endolysosomal transport-a process known to be important to development of early onset AD.
      Title: Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport.
    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

    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

    Clone Names

    • DKFZp761B0514

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phospholipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of ARF protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cleavage furrow ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ruffle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    PH and SEC7 domain-containing protein 2
    Names
    exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 C
    exchange factor for ARF6 C
    pleckstrin homology and SEC7 domain-containing protein 2

    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_032289.4 → NP_115665.1  PH and SEC7 domain-containing protein 2

      See identical proteins and their annotated locations for NP_115665.1

      Status: VALIDATED

      Source sequence(s)
      AC008667, AL136559, BM663376
      Consensus CDS
      CCDS4216.1
      UniProtKB/Swiss-Prot
      D3DQD3, Q8N3J8, Q9BQI7
      Related
      ENSP00000274710.3, ENST00000274710.4
      Conserved Domains (2) summary
      cd00171
      Location:297 → 464
      Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
      cd13295
      Location:510 → 633
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      139742475..139844466
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417829.1 → XP_047273785.1  PH and SEC7 domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DQD3, Q8N3J8, Q9BQI7

    2. XM_017009976.2 → XP_016865465.1  PH and SEC7 domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DQD3, Q8N3J8, Q9BQI7
      Conserved Domains (2) summary
      cd00171
      Location:297 → 464
      Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
      cd13295
      Location:510 → 633
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    3. XM_017009977.2 → XP_016865466.1  PH and SEC7 domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DQD3, Q8N3J8, Q9BQI7
      Conserved Domains (2) summary
      cd00171
      Location:297 → 464
      Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...
      cd13295
      Location:510 → 633
      PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      140266708..140369568
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353684.1 → XP_054209659.1  PH and SEC7 domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DQD3, Q8N3J8, Q9BQI7

    2. XM_054353685.1 → XP_054209660.1  PH and SEC7 domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      D3DQD3, Q8N3J8, Q9BQI7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQI7.3 GenPept UniProtKB/Swiss-Prot:Q9BQI7

    Gene LinkOut

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

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