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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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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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