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

Gene ID: 9842, updated on 17-Jun-2019

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

Genomic context

See PLEKHM1 in Genome Data Viewer
Location:
17q21.31
Exon count:
17
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (45434262..45490780, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (43513266..43568146, 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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Osteopetrosis autosomal recessive 6
MedGen: C1969093 OMIM: 611497 GeneReviews: Not available
Compare labs
OSTEOPETROSIS, AUTOSOMAL DOMINANT 3
MedGen: CN253817 OMIM: 618107 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Genome-wide association study confirms SNPs in SNCA and the MAPT region as common risk factors for Parkinson disease.
NHGRI GWA Catalog
Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk.
NHGRI GWA Catalog

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
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
autophagy IEA
Inferred from Electronic Annotation
more info
 
intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
 
lysosome localization ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of bone resorption ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ruffle assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
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)

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
    5001..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_027774.1 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_027782.1 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 Annotation Release 109

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..45490780 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..181221 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..180935 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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