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PLEKHM3 pleckstrin homology domain containing M3 [ Homo sapiens (human) ]

Gene ID: 389072, updated on 3-Apr-2024

Summary

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Official Symbol
PLEKHM3provided by HGNC
Official Full Name
pleckstrin homology domain containing M3provided by HGNC
Primary source
HGNC:HGNC:34006
See related
Ensembl:ENSG00000178385 MIM:619186; AllianceGenome:HGNC:34006
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DAPR; PLEKHM1L
Summary
Predicted to enable metal ion binding activity. Predicted to be involved in myoblast differentiation. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 3.2), thyroid (RPKM 2.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2q33.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (207821288..208025527, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (208295515..208499792, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (208686012..208890251, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene cyclin Y like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208631909-208632465 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208632466-208633023 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208635695-208636515 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:208636987-208637462 Neighboring gene microRNA 4775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208647704-208648204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208660472-208661457 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208661458-208662442 Neighboring gene frizzled class receptor 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208666419-208666920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208666921-208667420 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208675729-208676550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17048 Neighboring gene HNF1 motif-containing MPRA enhancer 152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208713897-208714396 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:208772908-208774107 Neighboring gene Sharpr-MPRA regulatory region 2767 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:208835249-208835782 Neighboring gene RNA, U6 small nuclear 360, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17049 Neighboring gene ribosomal protein L9 pseudogene 14 Neighboring gene RNA, 5S ribosomal pseudogene 116

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. CircPLEKHM3 acts as a tumor suppressor through regulation of the miR-9/BRCA1/DNAJB6/KLF4/AKT1 axis in ovarian cancer. Zhang L, et al. Mol Cancer, 2019 Oct 17. PMID 31623606, Free PMC Article
  2. Identification and characterization of a novel gene, dapr, involved in skeletal muscle differentiation and protein kinase B signaling. Virtanen C, et al. J Biol Chem, 2009 Jan 16. PMID 19028694
  3. C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy. Yan BR, et al. Autophagy, 2022 Apr. PMID 34432599, Free PMC Article
  4. A central chaperone-like role for 14-3-3 proteins in human cells. Segal D, et al. Mol Cell, 2023 Mar 16. PMID 36931259
  5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircPLEKHM3 is down-regulated in ovarian cancer. Patients with a lower circPLEKHM3 expression have a worse prognosis. CircPLEKHM3 was found to act as a tumor suppressor that inhibits cell proliferation.
    Title: CircPLEKHM3 acts as a tumor suppressor through regulation of the miR-9/BRCA1/DNAJB6/KLF4/AKT1 axis in ovarian cancer.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. DAPR is a novel gene that binds to PKB/AKT and is a critical component for the differentiation of skeletal muscle myoblast cells into myotubes.
    Title: Identification and characterization of a novel gene, dapr, involved in skeletal muscle differentiation and protein kinase B signaling.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ41210, AC083900.1, DKFZp686O04200

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in myoblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
pleckstrin homology domain-containing family M member 3
Names
PH domain-containing family M member 3
differentiation associated protein

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001080475.3 → NP_001073944.1  pleckstrin homology domain-containing family M member 3

    See identical proteins and their annotated locations for NP_001073944.1

    Status: VALIDATED

    Source sequence(s)
    AC083900, AC093698, AC096772
    Consensus CDS
    CCDS42808.1
    UniProtKB/Swiss-Prot
    B9EKV2, Q6ZWE6, Q8WW68
    UniProtKB/TrEMBL
    C9J119
    Related
    ENSP00000417003.2, ENST00000427836.8
    Conserved Domains (4) summary
    cd13327
    Location:364 → 451
    PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
    cd14674
    Location:214 → 303
    PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
    pfam00169
    Location:362 → 454
    PH; PH domain
    pfam13901
    Location:529 → 729
    zf-RING_9; Putative zinc-RING and/or ribbon

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    207821288..208025527 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004073.2 → XP_016859562.1  pleckstrin homology domain-containing family M member 3 isoform X6

  2. XM_005246545.4 → XP_005246602.1  pleckstrin homology domain-containing family M member 3 isoform X4

    UniProtKB/TrEMBL
    C9J119
    Conserved Domains (4) summary
    cd13327
    Location:364 → 451
    PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
    cd14674
    Location:214 → 303
    PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
    pfam00169
    Location:362 → 454
    PH; PH domain
    pfam13901
    Location:529 → 651
    zf-RING_9; Putative zinc-RING and/or ribbon

  3. XM_011511160.3 → XP_011509462.1  pleckstrin homology domain-containing family M member 3 isoform X1

    See identical proteins and their annotated locations for XP_011509462.1

    UniProtKB/Swiss-Prot
    B9EKV2, Q6ZWE6, Q8WW68
    UniProtKB/TrEMBL
    C9J119
    Conserved Domains (4) summary
    cd13327
    Location:364 → 451
    PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
    cd14674
    Location:214 → 303
    PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
    pfam00169
    Location:362 → 454
    PH; PH domain
    pfam13901
    Location:529 → 729
    zf-RING_9; Putative zinc-RING and/or ribbon

  4. XM_017004072.3 → XP_016859561.1  pleckstrin homology domain-containing family M member 3 isoform X5

    UniProtKB/TrEMBL
    H7C0J9
    Related
    ENSP00000395354.1, ENST00000447645.5

  5. XM_006712521.5 → XP_006712584.1  pleckstrin homology domain-containing family M member 3 isoform X3

    UniProtKB/TrEMBL
    C9J119
    Conserved Domains (4) summary
    cd13327
    Location:364 → 451
    PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
    cd14674
    Location:214 → 303
    PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
    pfam00169
    Location:362 → 454
    PH; PH domain
    pfam13901
    Location:529 → 650
    zf-RING_9; Putative zinc-RING and/or ribbon

  6. XM_047444266.1 → XP_047300222.1  pleckstrin homology domain-containing family M member 3 isoform X3

  7. XM_011511163.3 → XP_011509465.1  pleckstrin homology domain-containing family M member 3 isoform X2

    UniProtKB/TrEMBL
    C9J119
    Related
    ENSP00000400150.1, ENST00000457206.1
    Conserved Domains (4) summary
    cd13327
    Location:364 → 451
    PH_PLEKHM3_2; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2
    cd14674
    Location:214 → 303
    PH_PLEKHM3_1; Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1
    pfam00169
    Location:362 → 454
    PH; PH domain
    pfam13901
    Location:529 → 652
    zf-RING_9; Putative zinc-RING and/or ribbon

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    208295515..208499792 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341972.1 → XP_054197947.1  pleckstrin homology domain-containing family M member 3 isoform X6

  2. XM_054341970.1 → XP_054197945.1  pleckstrin homology domain-containing family M member 3 isoform X4

  3. XM_054341966.1 → XP_054197941.1  pleckstrin homology domain-containing family M member 3 isoform X1

    UniProtKB/Swiss-Prot
    B9EKV2, Q6ZWE6, Q8WW68

  4. XM_054341971.1 → XP_054197946.1  pleckstrin homology domain-containing family M member 3 isoform X5

  5. XM_054341968.1 → XP_054197943.1  pleckstrin homology domain-containing family M member 3 isoform X3

  6. XM_054341969.1 → XP_054197944.1  pleckstrin homology domain-containing family M member 3 isoform X3

  7. XM_054341967.1 → XP_054197942.1  pleckstrin homology domain-containing family M member 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZWE6.2 GenPept UniProtKB/Swiss-Prot:Q6ZWE6

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