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    PLEKHM1 pleckstrin homology and RUN domain containing M1 [ Homo sapiens (human) ]

    Gene ID: 9842, updated on 26-Jul-2021

    Summary

    Official Symbol
    PLEKHM1provided by HGNC
    Official Full Name
    pleckstrin homology and RUN domain containing M1provided by HGNC
    Primary source
    HGNC:HGNC:29017
    See related
    Ensembl:ENSG00000225190 MIM:611466
    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
    B2; AP162; OPTA3; OPTB6
    Summary
    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]
    Expression
    Ubiquitous expression in esophagus (RPKM 12.9), bone marrow (RPKM 10.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PLEKHM1 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (45434262..45490775, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (43513266..43568087, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 455 Neighboring gene Rho GTPase activating protein 27 Neighboring gene microRNA 4315-1 Neighboring gene uncharacterized LOC105369225 Neighboring gene leucine rich repeat containing 37 member A4, pseudogene Neighboring gene ADP ribosylation factor like GTPase 17A pseudogene

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Autosomal recessive osteopetrosis 6
    MedGen: C1969093 OMIM: 611497 GeneReviews: Not available
    Compare labs
    Genome-wide association study confirms SNPs in SNCA and the MAPT region as common risk factors for Parkinson disease.
    GeneReviews: Not available
    Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk.
    GeneReviews: Not available
    Osteopetrosis, autosomal dominant 3
    MedGen: C4748197 OMIM: 618107 GeneReviews: Not available
    Compare labs

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0356

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in autophagosome-lysosome fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in late endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lysosome localization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lysosome localization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of bone resorption ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of ruffle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in autolysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    pleckstrin homology domain-containing family M member 1
    Names
    162 kDa adapter protein
    PH domain-containing family M member 1
    pleckstrin homology domain containing, family M (with RUN domain) member 1

    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_012932.1 RefSeqGene

      Range
      5060..59881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001352825.2NP_001339754.1  pleckstrin homology domain-containing family M member 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks multiple 3' exons, compared to variant 1, and encodes a protein (isoform 2) with a shorter and novel C-terminus, compared to isoform 1.
      Source sequence(s)
      AC091132, AK025379
      Conserved Domains (4) summary
      smart00233
      Location:685777
      PH; Pleckstrin homology domain
      cd13321
      Location:499629
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:49180
      RUN; RUN domain
      pfam12287
      Location:306463
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
    2. NM_014798.3NP_055613.1  pleckstrin homology domain-containing family M member 1 isoform 1

      See identical proteins and their annotated locations for NP_055613.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
      Source sequence(s)
      BC064361, DB064851
      Consensus CDS
      CCDS32671.1
      UniProtKB/Swiss-Prot
      Q9Y4G2
      Related
      ENSP00000389913.3, ENST00000430334.8
      Conserved Domains (5) summary
      smart00233
      Location:685777
      PH; Pleckstrin homology domain
      cd13321
      Location:499629
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:49182
      RUN; RUN domain
      pfam12287
      Location:306463
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:8461048
      zf-RING_9; Putative zinc-RING and/or ribbon

    RNA

    1. NR_027774.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is missing an exon in the 5' coding region compared to variant 1. This variant is represented as non-coding because the use of the translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK299116, BC064361, DB064851
      Related
      ENST00000579197.5
    2. NR_027782.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) is missing an exon in the 5' coding region compared to variant 1. This variant is represented as non-coding because the use of the translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC053848, BC064361, DB064851

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

      Range
      45434262..45490775 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525523.2XP_011523825.1  pleckstrin homology domain-containing family M member 1 isoform X1

      See identical proteins and their annotated locations for XP_011523825.1

      UniProtKB/Swiss-Prot
      Q9Y4G2
      Conserved Domains (5) summary
      smart00233
      Location:685777
      PH; Pleckstrin homology domain
      cd13321
      Location:499629
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:49182
      RUN; RUN domain
      pfam12287
      Location:306463
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:8461048
      zf-RING_9; Putative zinc-RING and/or ribbon
    2. XM_011525526.1XP_011523828.1  pleckstrin homology domain-containing family M member 1 isoform X3

      See identical proteins and their annotated locations for XP_011523828.1

      Conserved Domains (5) summary
      smart00233
      Location:618710
      PH; Pleckstrin homology domain
      cd13321
      Location:432562
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam12287
      Location:239396
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:779981
      zf-RING_9; Putative zinc-RING and/or ribbon
      cl02689
      Location:49145
      RUN; RUN domain
    3. XM_017025453.1XP_016880942.1  pleckstrin homology domain-containing family M member 1 isoform X5

      UniProtKB/Swiss-Prot
      Q9Y4G2
      Conserved Domains (5) summary
      smart00233
      Location:555647
      PH; Pleckstrin homology domain
      cd13321
      Location:369499
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam12287
      Location:176333
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:716918
      zf-RING_9; Putative zinc-RING and/or ribbon
      cl02689
      Location:152
      RUN; RUN domain
    4. XM_017025454.2XP_016880943.1  pleckstrin homology domain-containing family M member 1 isoform X7

    5. XM_017025452.1XP_016880941.1  pleckstrin homology domain-containing family M member 1 isoform X4

    6. XM_017025451.1XP_016880940.1  pleckstrin homology domain-containing family M member 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9Y4G2
      Conserved Domains (5) summary
      smart00233
      Location:685777
      PH; Pleckstrin homology domain
      cd13321
      Location:499629
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:49182
      RUN; RUN domain
      pfam12287
      Location:306463
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:8461048
      zf-RING_9; Putative zinc-RING and/or ribbon
    7. XM_011525524.1XP_011523826.1  pleckstrin homology domain-containing family M member 1 isoform X1

      See identical proteins and their annotated locations for XP_011523826.1

      UniProtKB/Swiss-Prot
      Q9Y4G2
      Conserved Domains (5) summary
      smart00233
      Location:685777
      PH; Pleckstrin homology domain
      cd13321
      Location:499629
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:49182
      RUN; RUN domain
      pfam12287
      Location:306463
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:8461048
      zf-RING_9; Putative zinc-RING and/or ribbon
    8. XM_011525525.1XP_011523827.1  pleckstrin homology domain-containing family M member 1 isoform X2

      See identical proteins and their annotated locations for XP_011523827.1

      Conserved Domains (5) summary
      smart00233
      Location:634726
      PH; Pleckstrin homology domain
      cd13321
      Location:448578
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam02759
      Location:46131
      RUN; RUN domain
      pfam12287
      Location:255412
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:795997
      zf-RING_9; Putative zinc-RING and/or ribbon
    9. XM_006722201.4XP_006722264.1  pleckstrin homology domain-containing family M member 1 isoform X5

      See identical proteins and their annotated locations for XP_006722264.1

      UniProtKB/Swiss-Prot
      Q9Y4G2
      Conserved Domains (5) summary
      smart00233
      Location:555647
      PH; Pleckstrin homology domain
      cd13321
      Location:369499
      PH_PLEKHM1; Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain
      pfam12287
      Location:176333
      Caprin-1_C; Cytoplasmic activation/proliferation-associated protein-1 C term
      pfam13901
      Location:716918
      zf-RING_9; Putative zinc-RING and/or ribbon
      cl02689
      Location:152
      RUN; RUN domain
    10. XM_011525528.2XP_011523830.1  pleckstrin homology domain-containing family M member 1 isoform X6

      See identical proteins and their annotated locations for XP_011523830.1

      Conserved Domains (3) summary
      smart00233
      Location:164256
      PH; Pleckstrin homology domain
      pfam13901
      Location:325527
      zf-RING_9; Putative zinc-RING and/or ribbon
      cl17171
      Location:4108
      PH-like; Pleckstrin homology-like domain

    RNA

    1. XR_934624.1 RNA Sequence

    2. XR_934625.1 RNA Sequence

    Reference GRCh38.p13 ALT_REF_LOCI_1

    Genomic

    1. NT_167251.2 Reference GRCh38.p13 ALT_REF_LOCI_1

      Range
      126335..181162 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p13 ALT_REF_LOCI_2

    Genomic

    1. NT_187663.1 Reference GRCh38.p13 ALT_REF_LOCI_2

      Range
      126405..180876 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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