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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
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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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