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Aliases for PLEKHM1 Gene

Aliases for PLEKHM1 Gene

  • Pleckstrin Homology And RUN Domain Containing M1 2 3 5
  • Pleckstrin Homology Domain Containing, Family M (With RUN Domain) Member 1 2 3
  • PH Domain-Containing Family M Member 1 3 4
  • 162 KDa Adapter Protein 3 4
  • AP162 3 4
  • Pleckstrin Homology Domain-Containing Family M Member 1 3
  • KIAA0356 4
  • OPTB6 3
  • B2 3

External Ids for PLEKHM1 Gene

Previous GeneCards Identifiers for PLEKHM1 Gene

  • GC17M043989
  • GC17M040869
  • GC17M043514
  • GC17M043528
  • GC17M043540

Summaries for PLEKHM1 Gene

Entrez Gene Summary for PLEKHM1 Gene

  • The protein encoded by this gene is essential for bone resorption, and may play a critical role in vesicular transport in the osteoclast. Mutations in this gene are associated with autosomal recessive osteopetrosis type 6 (OPTB6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]

GeneCards Summary for PLEKHM1 Gene

PLEKHM1 (Pleckstrin Homology And RUN Domain Containing M1) is a Protein Coding gene. Diseases associated with PLEKHM1 include Osteopetrosis, Autosomal Recessive 6 and Plekhm1-Related Autosomal Recessive Osteopetrosis. An important paralog of this gene is PLEKHM3.

UniProtKB/Swiss-Prot for PLEKHM1 Gene

  • Proposed to act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Required for late stages of endolysosomal maturation, facilitating both endocytosis-mediated degradation of growth factor receptors and autophagosome clearance. Seems to be involved in the terminal maturation of autophagosomes and to mediate autophagosome-lysosome fusion (PubMed:25498145). Involved in vesicular transport in the osteoclast (By similarity). May be involved in negative regulation of endocytic transport from early endosome to late endosome/lysosome implicating its association with Rab7 (PubMed:20943950). May have a role in sialyl-lex-mediated transduction of apoptotic signals (PubMed:12820725). In case of infection contributes to Salmonella typhimurium pathogenesis by supporting the integrity of the Salmonella-containing vacuole (SCV) probably in concert with the HOPS complex and Rab7 (PubMed:25500191).

Gene Wiki entry for PLEKHM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLEKHM1 Gene

Genomics for PLEKHM1 Gene

Regulatory Elements for PLEKHM1 Gene

Enhancers for PLEKHM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F045220 1.6 FANTOM5 ENCODE 17.3 +264.5 264453 12.5 HDGF PKNOX1 CREB3L1 ARNT WRNIP1 ARID4B SIN3A SLC30A9 CBX5 ZNF143 FMNL1 PLEKHM1 ENSG00000233175 NMT1 LRRC37A4P ENSG00000233483 ARHGAP27 SLC25A39 SPATA32 KANSL1-AS1
GH17F045304 1.8 FANTOM5 Ensembl ENCODE 8.4 +177.4 177449 18.0 MLX ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 ZNF263 SP3 LOC102724391 FMNL1 CRHR1-IT1 SPATA32 ENSG00000224505 KANSL1 ARHGAP27 EFTUD2 GPATCH8 DCAKD
GH17F045404 1.5 FANTOM5 ENCODE 6.8 +80.0 79978 13.3 HDGF PKNOX1 ARNT MLX CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 CRHR1-IT1 LRRC37A4P ARHGAP27 FMNL1 ARL17B SPATA32 LOC102724391 GJC1 KANSL1 EFTUD2
GH17F045427 1.3 FANTOM5 ENCODE 7.1 +62.2 62157 1.9 HDGF PKNOX1 ARID4B ZNF48 ZNF2 SLC30A9 GLIS2 ZNF143 SP5 MIER2 ARHGAP27 PLEKHM1 FMNL1 GC17M045407
GH17F045582 1.5 FANTOM5 ENCODE 5.6 -93.8 -93765 4.3 HDGF PKNOX1 WRNIP1 ARID4B SIN3A YBX1 FEZF1 DMAP1 ZNF2 YY1 CRHR1-IT1 LRRC37A4P KANSL1-AS1 LRRC37A2 ARL17B PLEKHM1 ACBD4 FMNL1 DND1P1 PIR53158
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PLEKHM1 on UCSC Golden Path with GeneCards custom track

Genomic Location for PLEKHM1 Gene

Chromosome:
17
Start:
45,434,247 bp from pter
End:
45,490,780 bp from pter
Size:
56,534 bases
Orientation:
Minus strand

Genomic View for PLEKHM1 Gene

Genes around PLEKHM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLEKHM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLEKHM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLEKHM1 Gene

Proteins for PLEKHM1 Gene

  • Protein details for PLEKHM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4G2-PKHM1_HUMAN
    Recommended name:
    Pleckstrin homology domain-containing family M member 1
    Protein Accession:
    Q9Y4G2
    Secondary Accessions:
    • Q6P2R5
    • Q8TEL9
    • Q9NPP5
    • Q9NYA0

    Protein attributes for PLEKHM1 Gene

    Size:
    1056 amino acids
    Molecular mass:
    117443 Da
    Quaternary structure:
    • In colon carcinoma and breast carcinoma cells, it interacts with sialyl-lex-positive protein (PubMed:12820725). Interacts with RAB7A (GTP-bound form) (PubMed:20943950, PubMed:25500191). Interacts with VPS41, VPS11 and VPS39; indicative for an association with the HOPS complex; the interaction with VPS41 seems to require RAB7A (PubMed:25500191, PubMed:25498145). Interacts with GABARAP, GABARAPL, GABARAPL2, MAP1LC3A, MAP1LC3B and MAP1LC3C (PubMed:25498145). Interacts with PAFAH1B (By similarity). Interacts with Salmonella typhimurium sifA (PubMed:25500191).
    • In colon carcinoma and breast carcinoma cells, it interacts with sialyl-lex-positive protein (PubMed:12820725). Interacts with RAB7A (GTP-bound form) (PubMed:20943950, PubMed:25500191). Interacts with VPS41, VPS11 and VPS39; indicative for an association with the HOPS complex; the interaction with VPS41 seems to require RAB7A (PubMed:25500191, PubMed:25498145). Interacts with GABARAP, GABARAPL, GABARAPL2, MAP1LC3A, MAP1LC3B and MAP1LC3C (PubMed:25498145). Interacts with PAFAH1B (By similarity). Interacts with Salmonella typhimurium sifA (PubMed:25500191).
    Miscellaneous:
    • Sialyl-lex is a carcinoma associated antigen.
    SequenceCaution:
    • Sequence=BAA20813.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAB91652.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PLEKHM1 Gene

neXtProt entry for PLEKHM1 Gene

Post-translational modifications for PLEKHM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PLEKHM1 Gene

Domains & Families for PLEKHM1 Gene

Gene Families for PLEKHM1 Gene

Protein Domains for PLEKHM1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y4G2

UniProtKB/Swiss-Prot:

PKHM1_HUMAN :
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and LC3A/B/C.
  • Contains 1 phorbol-ester/DAG-type zinc finger.
Domain:
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins GABARAP, GABARAPL, GABARAPL2, and LC3A/B/C.
  • Contains 2 PH domains.
  • Contains 1 RUN domain.
Similarity:
  • Contains 1 phorbol-ester/DAG-type zinc finger.
genes like me logo Genes that share domains with PLEKHM1: view

Function for PLEKHM1 Gene

Molecular function for PLEKHM1 Gene

UniProtKB/Swiss-Prot Function:
Proposed to act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Required for late stages of endolysosomal maturation, facilitating both endocytosis-mediated degradation of growth factor receptors and autophagosome clearance. Seems to be involved in the terminal maturation of autophagosomes and to mediate autophagosome-lysosome fusion (PubMed:25498145). Involved in vesicular transport in the osteoclast (By similarity). May be involved in negative regulation of endocytic transport from early endosome to late endosome/lysosome implicating its association with Rab7 (PubMed:20943950). May have a role in sialyl-lex-mediated transduction of apoptotic signals (PubMed:12820725). In case of infection contributes to Salmonella typhimurium pathogenesis by supporting the integrity of the Salmonella-containing vacuole (SCV) probably in concert with the HOPS complex and Rab7 (PubMed:25500191).

Gene Ontology (GO) - Molecular Function for PLEKHM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PLEKHM1: view
genes like me logo Genes that share phenotypes with PLEKHM1: view

Human Phenotype Ontology for PLEKHM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PLEKHM1 Gene

MGI Knock Outs for PLEKHM1:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLEKHM1

miRNA for PLEKHM1 Gene

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PLEKHM1 Gene

Localization for PLEKHM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLEKHM1 Gene

Cytoplasm. Endosome membrane. Lysosome. Lysosome membrane. Note=Localizes to the external membrane of autolysosomes (PubMed:25498145). In case of infection colocalizes with Salmonella typhimurium sifA in proximity of Salmonella-containing vacuole (SCV) (PubMed:25500191). {ECO:0000269 PubMed:25498145, ECO:0000269 PubMed:25500191}.

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 PLEKHM1 gene
Compartment Confidence
nucleus 5
lysosome 4
endosome 4
cytosol 2

Gene Ontology (GO) - Cellular Components for PLEKHM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
GO:0010008 endosome membrane IEA --
genes like me logo Genes that share ontologies with PLEKHM1: view

Pathways & Interactions for PLEKHM1 Gene

SuperPathways for PLEKHM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PLEKHM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006914 autophagy IEA --
GO:0015031 protein transport IEA --
GO:0035556 intracellular signal transduction IEA --
genes like me logo Genes that share ontologies with PLEKHM1: view

No data available for Pathways by source and SIGNOR curated interactions for PLEKHM1 Gene

Drugs & Compounds for PLEKHM1 Gene

(4) Additional Compounds for PLEKHM1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Diglycerides Group A
  • 1,2-Dimyristoyl-rac-glycerol
  • DAG(14:0/14:0)
  • DAG(28:0)
  • DG(14:0/14:0)
  • DG(28:0)
Diglycerides Group B
  • 1-Palmitoleoyl-2-arachidonyl-sn-glycerol
  • DAG(16:1/20:0)
  • DAG(16:1n7/20:0)
  • DAG(16:1w7/20:0)
  • DAG(36:1)
Diglycerides Group C
  • 1-Myristoyl-3-stearoyl-sn-glycerol
  • 1-Tetradecanoyl-3-octadecanoyl-sn-glycerol
  • DAG(14:0/0:0/18:0)
  • DAG(32:0)
  • DG(32:0)
Diglycerides Group D
  • 1,2-Didocosahexaenoyl-rac-glycerol
  • DAG(22:6/22:6)
  • DAG(22:6n3/22:6n3)
  • DAG(22:6w3/22:6w3)
  • DAG(44:12)
genes like me logo Genes that share compounds with PLEKHM1: view

Transcripts for PLEKHM1 Gene

Unigene Clusters for PLEKHM1 Gene

Pleckstrin homology domain containing, family M (with RUN domain) member 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLEKHM1 Gene

No ASD Table

Relevant External Links for PLEKHM1 Gene

GeneLoc Exon Structure for
PLEKHM1
ECgene alternative splicing isoforms for
PLEKHM1

Expression for PLEKHM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLEKHM1 Gene

mRNA differential expression in normal tissues according to GTEx for PLEKHM1 Gene

This gene is overexpressed in Whole Blood (x4.6).

Protein differential expression in normal tissues from HIPED for PLEKHM1 Gene

This gene is overexpressed in Spleen (48.8) and Cerebrospinal fluid (10.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLEKHM1 Gene



Protein tissue co-expression partners for PLEKHM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PLEKHM1 Gene:

PLEKHM1

SOURCE GeneReport for Unigene cluster for PLEKHM1 Gene:

Hs.514242

mRNA Expression by UniProt/SwissProt for PLEKHM1 Gene:

Q9Y4G2-PKHM1_HUMAN
Tissue specificity: Expressed in placenta, liver, prostate, thymus, spleen, ovary, colon, colon carcinoma and peripheral blood lymphocytes (PBL). Weakly expressed in brain, lung, kidney, and testis. No expression in heart, skeletal muscle, pancreas and small intestine. Predominantly expressed in the breast carcinoma cell line MCF-7.
genes like me logo Genes that share expression patterns with PLEKHM1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for PLEKHM1 Gene

Orthologs for PLEKHM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLEKHM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLEKHM1 34 35
  • 99.56 (n)
cow
(Bos Taurus)
Mammalia PLEKHM1 34 35
  • 84.58 (n)
mouse
(Mus musculus)
Mammalia Plekhm1 34 16 35
  • 83.98 (n)
rat
(Rattus norvegicus)
Mammalia Plekhm1 34
  • 83.78 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PLEKHM1 35
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PLEKHM1 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLEKHM1 34 35
  • 68.79 (n)
lizard
(Anolis carolinensis)
Reptilia PLEKHM1 35
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plekhm1 34
  • 55.4 (n)
zebrafish
(Danio rerio)
Actinopterygii plekhm1 34 35
  • 57.12 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12729 34
worm
(Caenorhabditis elegans)
Secernentea Y56A3A.16 35
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.897 35
  • 37 (a)
OneToMany
Species where no ortholog for PLEKHM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PLEKHM1 Gene

ENSEMBL:
Gene Tree for PLEKHM1 (if available)
TreeFam:
Gene Tree for PLEKHM1 (if available)

Paralogs for PLEKHM1 Gene

Paralogs for PLEKHM1 Gene