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PHLDB2 pleckstrin homology like domain family B member 2 [ Homo sapiens (human) ]

Gene ID: 90102, updated on 3-Nov-2024

Summary

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Official Symbol
PHLDB2provided by HGNC
Official Full Name
pleckstrin homology like domain family B member 2provided by HGNC
Primary source
HGNC:HGNC:29573
See related
Ensembl:ENSG00000144824 MIM:610298; AllianceGenome:HGNC:29573
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
LL5b; LL5beta
Summary
Enables cadherin binding activity. Involved in several processes, including negative regulation of focal adhesion assembly; regulation of cytoskeleton organization; and regulation of embryonic development. Located in several cellular components, including basal cortex; cytoskeleton; and focal adhesion. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in placenta (RPKM 18.1), kidney (RPKM 15.7) and 24 other tissues See more
Orthologs
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Genomic context

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See PHLDB2 in Genome Data Viewer
Location:
3q13.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (111732496..111976517)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (114453343..114697610)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (111451343..111695364)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CD96 molecule Neighboring gene NT5C3A pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20225 Neighboring gene PLCXD2 antisense RNA 1 Neighboring gene phosphatidylinositol specific phospholipase C X domain containing 2 Neighboring gene Sharpr-MPRA regulatory region 10775 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:111453476-111454675 Neighboring gene uncharacterized LOC107984087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111511689-111512190 Neighboring gene uncharacterized LOC105374040 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111577934-111578520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111578521-111579105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20226 Neighboring gene uncharacterized LOC124906336 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:111637713-111638912 Neighboring gene Sharpr-MPRA regulatory region 1117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111697515-111698074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:111704853-111705354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:111705355-111705854 Neighboring gene NANOG hESC enhancer GRCh37_chr3:111719684-111720311 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:111720792-111721991 Neighboring gene abhydrolase domain containing 10, depalmitoylase Neighboring gene transgelin 3

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 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. Depletion of PHLDB2 Suppresses Epithelial-Mesenchymal Transition and Enhances Anti-Tumor Immunity in Head and Neck Squamous Cell Carcinoma. Li H, et al. Biomolecules, 2024 Feb 17. PMID 38397469, Free PMC Article
  2. Functions of intronic nucleotide variants in the gene encoding pleckstrin homology like domain beta 2 (PHLDB2) on susceptibility to vascular dementia. Eom S, et al. World J Biol Psychiatry, 2013 Apr. PMID 22111664
  3. Oncometabolite L-2-hydroxyglurate directly induces vasculogenic mimicry through PHLDB2 in renal cell carcinoma. Wang H, et al. Int J Cancer, 2021 Apr 1. PMID 33320958, Free PMC Article
  4. RNA-seq-Based Screening in Coal Dust-Treated Cells Identified PHLDB2 as a Novel Lung Cancer-Related Molecular Marker. Ge D, et al. Biomed Res Int, 2021. PMID 34337001, Free PMC Article
  5. PHLDB2 Mediates Cetuximab Resistance via Interacting With EGFR in Latent Metastasis of Colorectal Cancer. Luo M, et al. Cell Mol Gastroenterol Hepatol, 2022. PMID 34952201, Free PMC Article

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Depletion of PHLDB2 Suppresses Epithelial-Mesenchymal Transition and Enhances Anti-Tumor Immunity in Head and Neck Squamous Cell Carcinoma.
    Title: Depletion of PHLDB2 Suppresses Epithelial-Mesenchymal Transition and Enhances Anti-Tumor Immunity in Head and Neck Squamous Cell Carcinoma.
  2. Interfering with the ERC1-LL5beta interaction disrupts plasma membrane-Associated platforms and affects tumor cell motility.
    Title: Interfering with the ERC1-LL5β interaction disrupts plasma membrane-Associated platforms and affects tumor cell motility.
  3. PHLDB2 Mediates Cetuximab Resistance via Interacting With EGFR in Latent Metastasis of Colorectal Cancer.
    Title: PHLDB2 Mediates Cetuximab Resistance via Interacting With EGFR in Latent Metastasis of Colorectal Cancer.
  4. RNA-seq-Based Screening in Coal Dust-Treated Cells Identified PHLDB2 as a Novel Lung Cancer-Related Molecular Marker.
    Title: RNA-seq-Based Screening in Coal Dust-Treated Cells Identified PHLDB2 as a Novel Lung Cancer-Related Molecular Marker.
  5. Oncometabolite L-2-hydroxyglurate directly induces vasculogenic mimicry through PHLDB2 in renal cell carcinoma.
    Title: Oncometabolite L-2-hydroxyglurate directly induces vasculogenic mimicry through PHLDB2 in renal cell carcinoma.
  6. NOTCH3, a crucial target of miR-491-5p/miR-875-5p, promotes gastric carcinogenesis by upregulating PHLDB2 expression and activating Akt pathway.
    Title: NOTCH3, a crucial target of miR-491-5p/miR-875-5p, promotes gastric carcinogenesis by upregulating PHLDB2 expression and activating Akt pathway.
  7. Prickle1 localized to the membrane through its farnesyl moiety, and the membrane localization was necessary for Prickle1 to regulate migration, to bind to CLASPs and LL5beta, and to promote microtubule targeting of focal adhesions.
    Title: Prickle1 promotes focal adhesion disassembly in cooperation with the CLASP-LL5β complex in migrating cells.
  8. Collectively, our findings present the first to elucidate that miR-29c is a direct p53 target gene, and also identify PHLDB2 as an important miR-29c target gene involved in colon cancer metastasis.
    Title: p53 target miR-29c-3p suppresses colon cancer cell invasion and migration through inhibition of PHLDB2.
  9. Liprin-alpha1, ERC1a and LL5 also define new highly polarized and dynamic cytoplasmic structures uniquely localized near the protruding cell edge
    Title: Liprin-α1, ERC1 and LL5 define polarized and dynamic structures that are implicated in cell migration.
  10. These and other LL5beta-interacting proteins are associated with conventional podosomes in macrophages and podosome-like invadopodia in fibroblasts, strengthening the close relationship between synaptic and non-synaptic podosomes.
    Title: Amotl2 interacts with LL5β, localizes to podosomes and regulates postsynaptic differentiation in muscle.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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

EBI GWAS Catalog

Description
Common genetic variation and performance on standardized cognitive tests.
EBI GWAS Catalog

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: PLCXD2

Homology

Clone Names

  • FLJ21791, DKFZp434G227, DKFZp313O2433, DKFZp686J05113

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cadherin binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in establishment of cell polarity IEA
Inferred from Electronic Annotation
more info
  
involved_in establishment of protein localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in microtubule cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of focal adhesion assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of wound healing, spreading of epidermal cells IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of basement membrane assembly involved in embryonic body morphogenesis IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in positive regulation of basement membrane assembly involved in embryonic body morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of gastrulation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of microtubule cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of microtubule cytoskeleton organization IGI
Inferred from Genetic Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in basal cortex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in basal cortex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell cortex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell leading edge IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
colocalizes_with focal adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in podosome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
pleckstrin homology-like domain family B member 2
Names
LL5 beta
protein LL5-beta

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_001134437.2 → NP_001127909.1  pleckstrin homology-like domain family B member 2 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has a longer N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC060225, AF506820, AW264132, CA310697, CR749654, DA447763
    Consensus CDS
    CCDS46885.1
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000377500.3, ENST00000393923.7
    Conserved Domains (4) summary
    cd14673
    Location:1126 → 1230
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:1129 → 1225
    PH; PH domain
    cl02488
    Location:610 → 774
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:1020 → 1089
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  2. NM_001134438.2 → NP_001127910.1  pleckstrin homology-like domain family B member 2 isoform a

    See identical proteins and their annotated locations for NP_001127910.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC060225, AK315050, AW264132, DA438817
    Consensus CDS
    CCDS46886.1
    UniProtKB/Swiss-Prot
    A5PKZ3, Q59EA8, Q68CY3, Q6NT98, Q86SQ0, Q8N8U8, Q8NAB1, Q8NCU5
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000405405.2, ENST00000431670.7
    Conserved Domains (5) summary
    cd14673
    Location:1142 → 1246
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:1145 → 1241
    PH; PH domain
    pfam06008
    Location:524 → 779
    Laminin_I; Laminin Domain I
    cl02488
    Location:583 → 790
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:1036 → 1095
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  3. NM_001134439.2 → NP_001127911.1  pleckstrin homology-like domain family B member 2 isoform a

    See identical proteins and their annotated locations for NP_001127911.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AB209903, AC060225, AW264132, DA272187
    Consensus CDS
    CCDS46886.1
    UniProtKB/Swiss-Prot
    A5PKZ3, Q59EA8, Q68CY3, Q6NT98, Q86SQ0, Q8N8U8, Q8NAB1, Q8NCU5
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000377502.3, ENST00000393925.7
    Conserved Domains (5) summary
    cd14673
    Location:1142 → 1246
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:1145 → 1241
    PH; PH domain
    pfam06008
    Location:524 → 779
    Laminin_I; Laminin Domain I
    cl02488
    Location:583 → 790
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:1036 → 1095
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  4. NM_145753.2 → NP_665696.1  pleckstrin homology-like domain family B member 2 isoform c

    See identical proteins and their annotated locations for NP_665696.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC060225, AK315050, AW264132, BC069194, DA438817
    Consensus CDS
    CCDS2962.1
    UniProtKB/TrEMBL
    E9PFQ4
    Related
    ENSP00000405292.1, ENST00000412622.5
    Conserved Domains (4) summary
    cd14673
    Location:1099 → 1203
    PH_PHLDB1_2; Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain
    pfam00169
    Location:1102 → 1198
    PH; PH domain
    cl02488
    Location:583 → 747
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
    cl19107
    Location:993 → 1062
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    111732496..111976517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    114453343..114697610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86SQ0.2 GenPept UniProtKB/Swiss-Prot:Q86SQ0

Gene LinkOut

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Chemical Information
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