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Aliases for PLEKHM2 Gene

Aliases for PLEKHM2 Gene

  • Pleckstrin Homology And RUN Domain Containing M2 2 3 5
  • Pleckstrin Homology Domain Containing, Family M (With RUN Domain) Member 2 2 3
  • PH Domain-Containing Family M Member 2 3 4
  • SKIP 3 4
  • SifA (Salmonella-Induced Filaments A) And Kinesin-Interacting Protein 3
  • Salmonella-Induced Filaments A And Kinesin-Interacting Protein 4
  • Pleckstrin Homology Domain-Containing Family M Member 2 3
  • Novel RUN And PH Domain-Containing Protein 3
  • SifA And Kinesin-Interacting Protein 4
  • KIAA0842 4

External Ids for PLEKHM2 Gene

Previous GeneCards Identifiers for PLEKHM2 Gene

  • GC01P015371
  • GC01P015737
  • GC01P015880
  • GC01P016008
  • GC01P014530
  • GC01P015686
  • GC01P015688

Summaries for PLEKHM2 Gene

Entrez Gene Summary for PLEKHM2 Gene

  • 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]

GeneCards Summary for PLEKHM2 Gene

PLEKHM2 (Pleckstrin Homology And RUN Domain Containing M2) is a Protein Coding gene. Diseases associated with PLEKHM2 include Left Ventricular Noncompaction and Dilated Cardiomyopathy. Among its related pathways are Salmonella infection (KEGG). Gene Ontology (GO) annotations related to this gene include kinesin binding.

UniProtKB/Swiss-Prot for PLEKHM2 Gene

  • May play a role in the regulation of conventional kinesin activity. Required for maintenance of the Golgi apparatus organization. May play a role in membrane tubulation (PubMed:15905402). May play a role in lysosomes movement and localization at the cell periphery (PubMed:25898167).

Gene Wiki entry for PLEKHM2 Gene

Additional gene information for PLEKHM2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLEKHM2 Gene

Genomics for PLEKHM2 Gene

GeneHancer (GH) Regulatory Elements for PLEKHM2 Gene

Promoters and enhancers for PLEKHM2 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
GH01J015678 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 674.9 -1.9 -1910 8 PKNOX1 YBX1 YY1 POLR2B GLIS2 ZNF143 FOS ATF7 RUNX3 JUNB PLEKHM2 ENSG00000271742 SPEN CROCCP3 CASP9 SLC25A34 LINC01772 CROCCP2 ZBTB17 RPL22P3
GH01J015947 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 19.3 +266.9 266912 7.3 HDGF PKNOX1 SMAD1 ARNT SIN3A FEZF1 POLR2B ZNF766 E2F8 FOS SPEN ENSG00000237938 HSPB7 CLCNKA RPL22P3 PLEKHM2 ZBTB17 ENSG00000233078 RPS16P1 CROCC
GH01J015615 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.2 -65.9 -65904 5.4 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 SP3 DDI2 ZBTB17 CROCCP3 ENSG00000237938 LINC01772 SPEN NBPF1 ARHGEF19 PLEKHM2 AGMAT
GH01J015961 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 15.8 +280.3 280330 5.8 HDGF PKNOX1 SMAD1 RB1 STAT5A BMI1 YBX1 BATF KLF5 IRF4 CLCNKA PLEKHM2 ZBTB17 CROCC CLCNKB CASP9 SZRD1 SPEN ENSG00000234607 GC01P015946
GH01J015601 Promoter/Enhancer 1.9 Ensembl ENCODE dbSUPER 10.4 -81.5 -81523 3.3 CLOCK FOXA2 MLX ARID4B SIN3A ZNF2 SLC30A9 ZNF213 ZNF207 FOS CHCHD2P6 ENSG00000237301 GC01P015603 PIR41201 PIR62449 ENSG00000237938 ARHGEF19 CROCCP3 LINC01772 ZBTB17
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLEKHM2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLEKHM2 gene promoter:
  • IRF-7A
  • HSF2
  • Pax-4a
  • STAT1
  • STAT1beta
  • STAT1alpha
  • AhR
  • NF-kappaB1
  • TFIID
  • TBP

Genomic Locations for PLEKHM2 Gene

Genomic Locations for PLEKHM2 Gene
chr1:15,684,267-15,734,769
(GRCh38/hg38)
Size:
50,503 bases
Orientation:
Plus strand
chr1:16,010,827-16,061,264
(GRCh37/hg19)
Size:
50,438 bases
Orientation:
Plus strand

Genomic View for PLEKHM2 Gene

Genes around PLEKHM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLEKHM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLEKHM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLEKHM2 Gene

Proteins for PLEKHM2 Gene

  • Protein details for PLEKHM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IWE5-PKHM2_HUMAN
    Recommended name:
    Pleckstrin homology domain-containing family M member 2
    Protein Accession:
    Q8IWE5
    Secondary Accessions:
    • O94928
    • Q5VT65
    • Q6NUH9
    • Q7L8G1
    • Q8IVT7
    • Q8N2T4
    • Q96AY0
    • Q9NTF7

    Protein attributes for PLEKHM2 Gene

    Size:
    1019 amino acids
    Molecular mass:
    112780 Da
    Quaternary structure:
    • Interacts with KIF5B (PubMed:15905402). Interacts with BORCS5 (PubMed:25898167).
    • (Microbial infection) Interacts with the S.typhimurium sifA protein; required for S.typhimurium infection.
    SequenceCaution:
    • Sequence=AAH40441.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA74865.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PLEKHM2 Gene

neXtProt entry for PLEKHM2 Gene

Post-translational modifications for PLEKHM2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PLEKHM2 Gene

No data available for DME Specific Peptides for PLEKHM2 Gene

Domains & Families for PLEKHM2 Gene

Gene Families for PLEKHM2 Gene

Protein Domains for PLEKHM2 Gene

Suggested Antigen Peptide Sequences for PLEKHM2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PLEKHM2: view

No data available for UniProtKB/Swiss-Prot for PLEKHM2 Gene

Function for PLEKHM2 Gene

Molecular function for PLEKHM2 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the regulation of conventional kinesin activity. Required for maintenance of the Golgi apparatus organization. May play a role in membrane tubulation (PubMed:15905402). May play a role in lysosomes movement and localization at the cell periphery (PubMed:25898167).

Phenotypes From GWAS Catalog for PLEKHM2 Gene

Gene Ontology (GO) - Molecular Function for PLEKHM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15905402
GO:0019894 kinesin binding IDA 15905402
genes like me logo Genes that share ontologies with PLEKHM2: view
genes like me logo Genes that share phenotypes with PLEKHM2: view

Animal Models for PLEKHM2 Gene

MGI Knock Outs for PLEKHM2:
  • Plekhm2 Plekhm2<tm1a(EUCOMM)Wtsi>

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLEKHM2 Gene

Localization for PLEKHM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLEKHM2 Gene

Cytoplasm.

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 PLEKHM2 gene
Compartment Confidence
endosome 4
nucleus 2
cytosol 2
lysosome 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for PLEKHM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0010008 endosome membrane IDA 18996344
genes like me logo Genes that share ontologies with PLEKHM2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLEKHM2 Gene

Pathways & Interactions for PLEKHM2 Gene

SuperPathways for PLEKHM2 Gene

SuperPathway Contained pathways
1 Salmonella infection (KEGG)
genes like me logo Genes that share pathways with PLEKHM2: view

Pathways by source for PLEKHM2 Gene

1 KEGG pathway for PLEKHM2 Gene

Gene Ontology (GO) - Biological Process for PLEKHM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007030 Golgi organization IMP 15905402
GO:0032418 lysosome localization IMP 25898167
GO:0032880 regulation of protein localization IMP 18787122
GO:1903527 positive regulation of membrane tubulation IDA 18996344
genes like me logo Genes that share ontologies with PLEKHM2: view

No data available for SIGNOR curated interactions for PLEKHM2 Gene

Drugs & Compounds for PLEKHM2 Gene

No Compound Related Data Available

Transcripts for PLEKHM2 Gene

Unigene Clusters for PLEKHM2 Gene

Pleckstrin homology domain containing, family M (with RUN domain) member 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLEKHM2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19a · 19b · 19c ·
SP1: -
SP2: - - -
SP3: -
SP4: -
SP5: - -
SP6: -
SP7:

ExUns: 19d ^ 20 ^ 21a · 21b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for PLEKHM2 Gene

GeneLoc Exon Structure for
PLEKHM2
ECgene alternative splicing isoforms for
PLEKHM2

Expression for PLEKHM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLEKHM2 Gene

Protein differential expression in normal tissues from HIPED for PLEKHM2 Gene

This gene is overexpressed in Lymph node (14.4), Peripheral blood mononuclear cells (13.9), Testis (11.4), Blymphocyte (8.0), and Spleen (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PLEKHM2 Gene



Protein tissue co-expression partners for PLEKHM2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PLEKHM2 Gene:

PLEKHM2

SOURCE GeneReport for Unigene cluster for PLEKHM2 Gene:

Hs.646775

Evidence on tissue expression from TISSUES for PLEKHM2 Gene

  • Nervous system(4.7)
  • Kidney(4.2)
  • Bone(4)
  • Skin(2.6)
  • Eye(2.5)
  • Muscle(2.5)
genes like me logo Genes that share expression patterns with PLEKHM2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLEKHM2 Gene

Orthologs for PLEKHM2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLEKHM2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLEKHM2 34 33
  • 99.54 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PLEKHM2 34 33
  • 89.37 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLEKHM2 34 33
  • 89.16 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Plekhm2 16 34 33
  • 86.84 (n)
rat
(Rattus norvegicus)
Mammalia Plekhm2 33
  • 86.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PLEKHM2 34
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PLEKHM2 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLEKHM2 34 33
  • 76.87 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 67 (a)
OneToMany
-- 34
  • 59 (a)
OneToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.3098 33
zebrafish
(Danio rerio)
Actinopterygii plekhm2 34 33
  • 63.73 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG17360 34
  • 14 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
OneToOne
Species where no ortholog for PLEKHM2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PLEKHM2 Gene

ENSEMBL:
Gene Tree for PLEKHM2 (if available)
TreeFam:
Gene Tree for PLEKHM2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLEKHM2: view image

Paralogs for PLEKHM2 Gene

No data available for Paralogs for PLEKHM2 Gene

Variants for PLEKHM2 Gene

Sequence variations from dbSNP and Humsavar for PLEKHM2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs115985482 benign, Dilated Cardiomyopathy, Recessive 15,719,829(+) C/G/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, synonymous_variant, upstream_transcript_variant
rs116455686 benign, Dilated Cardiomyopathy, Recessive 15,730,534(+) A/G coding_sequence_variant, synonymous_variant
rs116565708 benign, Dilated Cardiomyopathy, Recessive 15,731,198(+) G/T coding_sequence_variant, synonymous_variant
rs138211346 benign, Dilated Cardiomyopathy, Recessive 15,727,011(+) C/T intron_variant
rs143372200 benign, Dilated Cardiomyopathy, Recessive 15,727,132(+) C/G/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PLEKHM2 Gene

Variant ID Type Subtype PubMed ID
dgv11n27 CNV gain 19166990
dgv147n54 CNV gain+loss 21841781
dgv148n54 CNV gain 21841781
dgv149n54 CNV loss 21841781
dgv150n54 CNV gain 21841781
dgv151n54 CNV gain 21841781
esv2674903 CNV deletion 23128226
esv28978 CNV gain 19812545
esv3585317 CNV gain 21293372
esv3585319 CNV gain 21293372
nsv1006877 CNV gain 25217958
nsv1076156 CNV deletion 25765185
nsv1143439 CNV deletion 24896259
nsv508925 CNV insertion 20534489
nsv524044 CNV loss 19592680
nsv545612 CNV gain 21841781
nsv545613 CNV loss 21841781
nsv545617 CNV loss 21841781
nsv954825 CNV deletion 24416366

Variation tolerance for PLEKHM2 Gene

Residual Variation Intolerance Score: 76.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.11; 90.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLEKHM2 Gene

Human Gene Mutation Database (HGMD)
PLEKHM2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLEKHM2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLEKHM2 Gene

Disorders for PLEKHM2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PLEKHM2 Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
left ventricular noncompaction
  • left ventricular hypertrabeculation
dilated cardiomyopathy
  • cardiomyopathy, familial idiopathic
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLEKHM2

genes like me logo Genes that share disorders with PLEKHM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLEKHM2 Gene

Publications for PLEKHM2 Gene

  1. The intracellular fate of Salmonella depends on the recruitment of kinesin. (PMID: 15905402) Boucrot E … Méresse S (Science (New York, N.Y.) 2005) 3 4 22 58
  2. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  3. BORC, a multisubunit complex that regulates lysosome positioning. (PMID: 25898167) Pu J … Bonifacino JS (Developmental cell 2015) 3 4 58
  4. The Salmonella virulence protein SifA is a G protein antagonist. (PMID: 18787122) Jackson LK … Haldar K (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 22 58
  5. Structure and function of Salmonella SifA indicate that its interactions with SKIP, SseJ, and RhoA family GTPases induce endosomal tubulation. (PMID: 18996344) Ohlson MB … Miller SI (Cell host & microbe 2008) 3 4 58

Products for PLEKHM2 Gene

Sources for PLEKHM2 Gene

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