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    PLEKHA4 pleckstrin homology domain containing A4 [ Homo sapiens (human) ]

    Gene ID: 57664, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PLEKHA4provided by HGNC
    Official Full Name
    pleckstrin homology domain containing A4provided by HGNC
    Primary source
    HGNC:HGNC:14339
    See related
    Ensembl:ENSG00000105559 MIM:607769; AllianceGenome:HGNC:14339
    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
    PEPP1
    Summary
    This gene encodes a pleckstrin homology (PH) domain-containing protein. The PH domain is found near the N-terminus and contains a putative phosphatidylinositol 3, 4, 5-triphosphate-binding motif (PPBM). Elevated expression of this gene has been observed in some melanomas. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2017]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Ubiquitous expression in ovary (RPKM 7.2), endometrium (RPKM 6.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19q13.33
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48837097..48868617, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51831976..51863478, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (49340354..49371874, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene branched chain amino acid transaminase 2 Neighboring gene uncharacterized LOC105372432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14908 Neighboring gene Sharpr-MPRA regulatory region 11839 Neighboring gene CRISPRi-FlowFISH-validated BCAT2 regulatory element Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49316517-49317128 Neighboring gene hydroxysteroid 17-beta dehydrogenase 14 Neighboring gene CRISPRi-FlowFISH-validated FTL regulatory element 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10904 Neighboring gene MPRA-validated peak3541 silencer Neighboring gene Sharpr-MPRA regulatory region 3566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10905 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49374623-49375235 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49375236-49375847 Neighboring gene CRISPRi-FlowFISH-validated BAX, FTL and NUCB1 regulatory elements Neighboring gene CRISPRi-FlowFISH-validated FTL and NUCB1 regulatory element 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14916 Neighboring gene CRISPRi-FlowFISH-validated FTL and NUCB1 regulatory element 2 Neighboring gene protein phosphatase 1 regulatory subunit 15A Neighboring gene CRISPRi-validated cis-regulatory element chr19.5328 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:49382795-49383507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49390815-49391709 Neighboring gene TUB like protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49398133-49398948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10906 Neighboring gene CRISPRi-FlowFISH-validated BAX and NUCB1 regulatory element

    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. PLEKHA4 Is a Prognostic Biomarker and Correlated with Immune Infiltrates in Glioma. Zhang W, et al. Biomed Res Int, 2023. PMID 36714030, Free PMC Article
    2. PLEKHA4 Promotes Wnt/β-Catenin Signaling-Mediated G(1)-S Transition and Proliferation in Melanoma. Shami Shah A, et al. Cancer Res, 2021 Apr 15. PMID 33574086, Free PMC Article
    3. Mapping the human genetic architecture of COVID-19. COVID-19 Host Genetics Initiative. Nature, 2021 Dec. PMID 34237774, Free PMC Article
    4. A first update on mapping the human genetic architecture of COVID-19. COVID-19 Host Genetics Initiative. Nature, 2022 Aug. PMID 35922517, Free PMC Article
    5. Legionella effector AnkX interacts with host nuclear protein PLEKHN1. Yu X, et al. BMC Microbiol, 2018 Jan 5. PMID 29433439, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PLEKHA4 promotes glioblastoma progression through apoptosis inhibition, tumor cell migration, and macrophage infiltration.
      Title: PLEKHA4 promotes glioblastoma progression through apoptosis inhibition, tumor cell migration, and macrophage infiltration.
    2. PLEKHA4 is Associated with Tumour Microenvironment, Stemness, Proliferation and Poor Prognosis of Gliomas.
      Title: PLEKHA4 is Associated with Tumour Microenvironment, Stemness, Proliferation and Poor Prognosis of Gliomas.
    3. PLEKHA4 Is a Prognostic Biomarker and Correlated with Immune Infiltrates in Glioma.
      Title: PLEKHA4 Is a Prognostic Biomarker and Correlated with Immune Infiltrates in Glioma.
    4. PLEKHA4 Promotes Wnt/beta-Catenin Signaling-Mediated G1-S Transition and Proliferation in Melanoma.
      Title: PLEKHA4 Promotes Wnt/β-Catenin Signaling-Mediated G(1)-S Transition and Proliferation in Melanoma.
    5. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling.
      Title: PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-3,4-bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,4-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3,5-bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-4,5-bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of Wnt signaling pathway, planar cell polarity pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of Wnt signaling pathway, planar cell polarity pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extrinsic component of cytoplasmic side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extrinsic component of cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    pleckstrin homology domain-containing family A member 4
    Names
    PH domain-containing family A member 4
    phosphoinositol 3-phosphate-binding PH domain protein 1
    pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4

    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.

    Genomic

    1. NG_054880.1 RefSeqGene

      Range
      5011..36531
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001161354.2 → NP_001154826.1  pleckstrin homology domain-containing family A member 4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 1, one of which results in a frameshift. This results in a shorter isoform (2) with a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC026803, BC024157, BC064601
      Consensus CDS
      CCDS54291.1
      UniProtKB/Swiss-Prot
      Q9H4M7
      Related
      ENSP00000347683.4, ENST00000355496.9
      Conserved Domains (2) summary
      cd13248
      Location:49 → 152
      PH_PEPP1_2_3; Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain
      pfam00169
      Location:55 → 153
      PH; PH domain

    2. NM_020904.3 → NP_065955.2  pleckstrin homology domain-containing family A member 4 isoform 1

      See identical proteins and their annotated locations for NP_065955.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC026803, BC024157
      Consensus CDS
      CCDS12737.1
      UniProtKB/Swiss-Prot
      Q8N4M8, Q8N658, Q9H4M7
      Related
      ENSP00000263265.5, ENST00000263265.11
      Conserved Domains (2) summary
      cd13248
      Location:49 → 152
      PH_PEPP1_2_3; Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain
      pfam00169
      Location:55 → 153
      PH; PH domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      48837097..48868617 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439136.1 → XP_047295092.1  pleckstrin homology domain-containing family A member 4 isoform X6

    2. XM_047439135.1 → XP_047295091.1  pleckstrin homology domain-containing family A member 4 isoform X4

    3. XM_011527158.4 → XP_011525460.1  pleckstrin homology domain-containing family A member 4 isoform X3

      UniProtKB/TrEMBL
      M0R0J1
      Related
      ENSP00000471274.2, ENST00000594100.2
      Conserved Domains (2) summary
      cd13248
      Location:32 → 116
      PH_PEPP1_2_3; Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain
      pfam00169
      Location:36 → 117
      PH; PH domain

    4. XM_005259107.3 → XP_005259164.1  pleckstrin homology domain-containing family A member 4 isoform X2

      Conserved Domains (2) summary
      cd13248
      Location:49 → 152
      PH_PEPP1_2_3; Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain
      pfam00169
      Location:55 → 153
      PH; PH domain

    5. XM_011527157.2 → XP_011525459.1  pleckstrin homology domain-containing family A member 4 isoform X1

      Conserved Domains (2) summary
      cd13248
      Location:49 → 152
      PH_PEPP1_2_3; Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain
      pfam00169
      Location:55 → 153
      PH; PH domain

    6. XM_011527159.2 → XP_011525461.1  pleckstrin homology domain-containing family A member 4 isoform X5

      Conserved Domains (2) summary
      pfam00169
      Location:49 → 113
      PH; PH domain
      cl17171
      Location:47 → 112
      PH-like; Pleckstrin homology-like domain

    7. XM_017027037.2 → XP_016882526.1  pleckstrin homology domain-containing family A member 4 isoform X8

      Conserved Domains (1) summary
      cl17171
      Location:2 → 25
      PH-like; Pleckstrin homology-like domain

    8. XM_011527162.3 → XP_011525464.1  pleckstrin homology domain-containing family A member 4 isoform X9

      Conserved Domains (2) summary
      PHA03247
      Location:155 → 417
      PHA03247; large tegument protein UL36; Provisional
      COG1196
      Location:15 → 123
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    9. XM_047439138.1 → XP_047295094.1  pleckstrin homology domain-containing family A member 4 isoform X10

    10. XM_047439137.1 → XP_047295093.1  pleckstrin homology domain-containing family A member 4 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      51831976..51863478 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321563.1 → XP_054177538.1  pleckstrin homology domain-containing family A member 4 isoform X6

    2. XM_054321561.1 → XP_054177536.1  pleckstrin homology domain-containing family A member 4 isoform X4

    3. XM_054321560.1 → XP_054177535.1  pleckstrin homology domain-containing family A member 4 isoform X3

      UniProtKB/TrEMBL
      M0R0J1

    4. XM_054321559.1 → XP_054177534.1  pleckstrin homology domain-containing family A member 4 isoform X2

    5. XM_054321558.1 → XP_054177533.1  pleckstrin homology domain-containing family A member 4 isoform X1

    6. XM_054321562.1 → XP_054177537.1  pleckstrin homology domain-containing family A member 4 isoform X5

    7. XM_054321565.1 → XP_054177540.1  pleckstrin homology domain-containing family A member 4 isoform X8

    8. XM_054321566.1 → XP_054177541.1  pleckstrin homology domain-containing family A member 4 isoform X9

    9. XM_054321567.1 → XP_054177542.1  pleckstrin homology domain-containing family A member 4 isoform X10

    10. XM_054321564.1 → XP_054177539.1  pleckstrin homology domain-containing family A member 4 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H4M7.2 GenPept UniProtKB/Swiss-Prot:Q9H4M7

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