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

Gene ID: 23207, updated on 4-Jan-2025

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
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Genomic context

See PLEKHM2 in Genome Data Viewer
Location:
1p36.21
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (15681506..15734769)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (15125588..15179507)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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

General gene information

Clone Names

  • KIAA0842

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables kinesin binding  
enables kinesin binding PubMed 
enables protein binding PubMed 
Process Evidence Code Pubs
involved_in Golgi organization  
involved_in Golgi organization PubMed 
involved_in lysosome localization  
involved_in lysosome localization PubMed 
involved_in lysosome localization PubMed 
involved_in natural killer cell mediated cytotoxicity PubMed 
involved_in regulation of protein localization  
involved_in regulation of protein localization PubMed 
Component Evidence Code Pubs
is_active_in endosome membrane  
located_in endosome membrane PubMed 
located_in lysosomal membrane 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)

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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.

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_2024_08

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

    Related
    ENSP00000520714.1, ENST00000718276.1
    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

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