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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH12849 (e-PCR)
- UniSTS:17202

G32743 (e-PCR)
- UniSTS:117324

SHGC-77194 (e-PCR)
- UniSTS:72786

G32762 (e-PCR)
- UniSTS:117343

SHGC-12085 (e-PCR)
- UniSTS:20343

A009Q05 (e-PCR)
- UniSTS:82554

RH45577 (e-PCR)
- UniSTS:72828

RH17931 (e-PCR)
- UniSTS:81024

SHGC-148219 (e-PCR)
- UniSTS:176266

SHGC-77196 (e-PCR)
- UniSTS:24717

SHGC-32892 (e-PCR)
- UniSTS:15510

RH80031 (e-PCR)
- UniSTS:91103

SHGC-58070 (e-PCR)
- UniSTS:52706

Clone Names

FLJ21791, DKFZp434G227, DKFZp313O2433, DKFZp686J05113

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cadherin binding	HDA more info	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)

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
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
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
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