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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
  • 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 intermediate osteopetrosis. An important paralog of this gene is KIAA0226L.

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

Promoters for PLEKHM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs 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).
    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};

neXtProt entry for PLEKHM1 Gene

Proteomics data for PLEKHM1 Gene at MOPED

Post-translational modifications for PLEKHM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

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).
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

CRISPR Products

miRNA for PLEKHM1 Gene

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for PLEKHM1 Gene COMPARTMENTS Subcellular localization image for PLEKHM1 gene
Compartment Confidence
endosome 4
lysosome 4
vacuole 4
cytosol 2
nucleus 2

Gene Ontology (GO) - Cellular Components for PLEKHM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005765 lysosomal 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

Interacting Proteins for PLEKHM1 Gene

Gene Ontology (GO) - Biological Process for PLEKHM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy 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:

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 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, MOPED, and MaxQB for PLEKHM1 Gene



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

Protein tissue co-expression partners for PLEKHM1 Gene

Primer Products

In Situ Assay 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
cow
(Bos Taurus)
Mammalia PLEKHM1 35
  • 84.58 (n)
  • 83.57 (a)
PLEKHM1 36
  • 79 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plekhm1 35
  • 83.98 (n)
  • 84.3 (a)
Plekhm1 16
Plekhm1 36
  • 82 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PLEKHM1 35
  • 99.56 (n)
  • 99.43 (a)
PLEKHM1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Plekhm1 35
  • 83.78 (n)
  • 84.38 (a)
oppossum
(Monodelphis domestica)
Mammalia PLEKHM1 36
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PLEKHM1 36
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLEKHM1 35
  • 68.79 (n)
  • 63.96 (a)
PLEKHM1 36
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLEKHM1 36
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plekhm1 35
  • 55.4 (n)
  • 49.2 (a)
zebrafish
(Danio rerio)
Actinopterygii plekhm1 35
  • 57.12 (n)
  • 49.34 (a)
plekhm1 36
  • 42 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12729 35
worm
(Caenorhabditis elegans)
Secernentea Y56A3A.16 36
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.897 36
  • 37 (a)
OneToMany
Species with no ortholog for PLEKHM1:
  • 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

(2) SIMAP similar genes for PLEKHM1 Gene using alignment to 9 proteins:

Pseudogenes.org Pseudogenes for PLEKHM1 Gene

genes like me logo Genes that share paralogs with PLEKHM1: view

Variants for PLEKHM1 Gene

Sequence variations from dbSNP and Humsavar for PLEKHM1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1859059 - 45,468,387(-) GCCGC(A/G)TCCCC intron-variant, nc-transcript-variant, reference, missense
rs9730 -- 45,436,185(-) GGCTT(C/G)GGCCT intron-variant, nc-transcript-variant, utr-variant-3-prime
rs11012 -- 45,436,075(-) TTCCC(A/G)CCTCC intron-variant, nc-transcript-variant, utr-variant-3-prime
rs1554464 -- 45,464,552(+) CATGA(C/G)CTGGC intron-variant
rs1574127 -- 45,490,361(-) CCCCA(C/T)TTTAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PLEKHM1 Gene

Variant ID Type Subtype PubMed ID
nsv428342 CNV Gain 18775914
dgv964e1 CNV Complex 17122850
esv627 CNV CNV 17122850
nsv511056 CNV Complex 20534489
dgv965e1 CNV Complex 17122850
nsv908304 CNV Loss 21882294
dgv123e55 CNV Loss 17911159
nsv9562 CNV Gain 18304495
esv2715974 CNV Deletion 23290073
dgv966e1 CNV Complex 17122850
dgv124e55 CNV Loss 17911159
dgv967e1 CNV Complex 17122850
nsv509659 CNV Insertion 20534489

Variation tolerance for PLEKHM1 Gene

Residual Variation Intolerance Score: 32.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.08; 38.04% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLEKHM1 Gene

HapMap Linkage Disequilibrium report
PLEKHM1
Human Gene Mutation Database (HGMD)
PLEKHM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLEKHM1 Gene

Disorders for PLEKHM1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PLEKHM1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
osteopetrosis, autosomal recessive 6
  • osteopetrosis autosomal recessive 6
intermediate osteopetrosis
  • autosomal recessive intermediate osteopetrosis
plekhm1-related autosomal recessive osteopetrosis
  • osteopetrosis, autosomal recessive 6
osteopetrosis
  • albers-schonberg disease
dandy-walker syndrome
  • atresia of foramina of magendie and luschka
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PKHM1_HUMAN
  • Osteopetrosis, autosomal recessive 6 (OPTB6) [MIM:611497]: A rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. Osteopetrosis occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Recessive osteopetrosis commonly manifests in early infancy with macrocephaly, feeding difficulties, evolving blindness and deafness, bone marrow failure, severe anemia, and hepatosplenomegaly. Deafness and blindness are generally thought to represent effects of pressure on nerves. {ECO:0000269 PubMed:17404618}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PLEKHM1

Genetic Association Database (GAD)
PLEKHM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLEKHM1
genes like me logo Genes that share disorders with PLEKHM1: view

No data available for Genatlas for PLEKHM1 Gene

Publications for PLEKHM1 Gene

  1. Novel adapter protein AP162 connects a sialyl-Le(x)-positive mucin with an apoptotic signal transduction pathway. (PMID: 12820725) Hartel-Schenk S. … Hanski C. (Glycoconj. J. 2001) 2 3 4 23 67
  2. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T. … Ohara O. (DNA Res. 1997) 2 3
  3. PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins. (PMID: 25498145) McEwan D.G. … Dikic I. (Mol. Cell 2015) 3
  4. PLEKHM1 regulates Salmonella-containing vacuole biogenesis and infection. (PMID: 25500191) McEwan D.G. … Dikic I. (Cell Host Microbe 2015) 3
  5. Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk. (PMID: 23544013) Couch F.J. … Antoniou A.C. (PLoS Genet. 2013) 3

Products for PLEKHM1 Gene

Sources for PLEKHM1 Gene

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