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    PLEKHM2 pleckstrin homology and RUN domain containing M2 [ Homo sapiens (human) ]

    Gene ID: 23207, updated on 6-Jun-2024

    Summary

    Official Symbol
    PLEKHM2provided by HGNC
    Official Full Name
    pleckstrin homology and RUN domain containing M2provided by HGNC
    Primary source
    HGNC:HGNC:29131
    See related
    Ensembl:ENSG00000116786 MIM:609613; AllianceGenome:HGNC:29131
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SKIP
    Summary
    This gene encodes a protein that binds the plus-end directed microtubule motor protein kinesin, together with the lysosomal GTPase Arl8, and is required for lysosomes to distribute away from the microtubule-organizing center. The encoded protein belongs to the multisubunit BLOC-one-related complex that regulates lysosome positioning. It binds a Salmonella effector protein called Salmonella induced filament A and is a critical host determinant in Salmonella pathogenesis. It has a domain architecture consisting of an N-terminal RPIP8, UNC-14, and NESCA (RUN) domain that binds kinesin-1 as well as the lysosomal GTPase Arl8, and a C-terminal pleckstrin homology domain that binds the Salmonella induced filament A effector protein. Naturally occurring mutations in this gene lead to abnormal localization of lysosomes, impaired autophagy flux and are associated with recessive dilated cardiomyopathy and left ventricular noncompaction. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in bone marrow (RPKM 21.8), testis (RPKM 21.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PLEKHM2 in Genome Data Viewer
    Location:
    1p36.21
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (15681506..15734769)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (15125588..15179507)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16010815..16061264)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 309 Neighboring gene CD24 molecule pseudogene 1 Neighboring gene DNA damage inducible 1 homolog 2 Neighboring gene MPRA-validated peak82 silencer Neighboring gene regulator of solute carriers 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:16005129-16005676 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16006379-16006879 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 244 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:16051023-16051299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16051819-16052339 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16061087-16061852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16061853-16062619 Neighboring gene SLC25A34 and TMEM82 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16068575-16069355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16070316-16070829 Neighboring gene solute carrier family 25 member 34 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16070830-16071342 Neighboring gene transmembrane protein 82

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of pleckstrin homology domain containing, family M (with RUN domain) member 2 (PLEKHM2) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0842

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables kinesin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables kinesin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Golgi organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysosome localization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lysosome localization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lysosome localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in natural killer cell mediated cytotoxicity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein localization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    pleckstrin homology domain-containing family M member 2
    Names
    PH domain-containing family M member 2
    SifA (Salmonella-induced filaments A) and kinesin-interacting protein
    novel RUN and PH domain-containing protein
    pleckstrin homology domain containing, family M (with RUN domain) member 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_053033.1 RefSeqGene

      Range
      7815..58264
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001410755.1NP_001397684.1  pleckstrin homology domain-containing family M member 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL121992, AL450998, AL606758
      Consensus CDS
      CCDS90868.1
      UniProtKB/TrEMBL
      A0A2R8Y575
      Related
      ENSP00000364950.2, ENST00000375793.2
    2. NM_015164.4NP_055979.2  pleckstrin homology domain-containing family M member 2 isoform 1

      See identical proteins and their annotated locations for NP_055979.2

      Status: REVIEWED

      Source sequence(s)
      AB020649, AL121992, BC040441, HY056873
      Consensus CDS
      CCDS44063.1
      UniProtKB/Swiss-Prot
      O94928, Q5VT65, Q5VVD7, Q6NUH9, Q7L8G1, Q8IVT7, Q8IWE5, Q8N2T4, Q96AY0, Q9NTF7
      UniProtKB/TrEMBL
      A0A2R8Y575
      Related
      ENSP00000364956.3, ENST00000375799.8
      Conserved Domains (3) summary
      smart00593
      Location:93156
      RUN; domain involved in Ras-like GTPase signaling
      cd13309
      Location:773875
      PH_SKIP; SifA and kinesin-interacting protein Pleckstrin homology (PH) domain
      pfam00169
      Location:772873
      PH; 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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      15681506..15734769
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000757.1XP_016856246.1  pleckstrin homology domain-containing family M member 2 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y575
    2. XM_017000758.1XP_016856247.1  pleckstrin homology domain-containing family M member 2 isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y575
    3. XM_005245791.5XP_005245848.1  pleckstrin homology domain-containing family M member 2 isoform X3

      Conserved Domains (2) summary
      cd13309
      Location:570672
      PH_SKIP; SifA and kinesin-interacting protein Pleckstrin homology (PH) domain
      pfam00169
      Location:569670
      PH; PH domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      15125588..15179507
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335373.1XP_054191348.1  pleckstrin homology domain-containing family M member 2 isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y575
    2. XM_054335374.1XP_054191349.1  pleckstrin homology domain-containing family M member 2 isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y575
    3. XM_054335375.1XP_054191350.1  pleckstrin homology domain-containing family M member 2 isoform X3

    RNA

    1. XR_008485964.1 RNA Sequence