This gene is located in a cluster of imprinted genes on chromosome 11p15.5, which is considered to be an important tumor suppressor gene region. Alterations in this region may be associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. This gene has been shown to be imprinted, with preferenti... See more...

Aliases for PHLDA2 Gene

Aliases for PHLDA2 Gene

  • Pleckstrin Homology Like Domain Family A Member 2 2 3 5
  • BWR1C 2 3 4
  • HLDA2 2 3 4
  • IPL 2 3 4
  • Tumor-Suppressing Subchromosomal Transferable Fragment Candidate Gene 3 Protein 3 4
  • Beckwith-Wiedemann Syndrome Chromosomal Region 1 Candidate Gene C Protein 3 4
  • Pleckstrin Homology-Like Domain Family A Member 2 3 4
  • Tumor Suppressing Subtransferable Candidate 3 2 3
  • Imprinted In Placenta And Liver Protein 3 4
  • P17-Beckwith-Wiedemann Region 1 C 3 4
  • P17-BWR1C 3 4
  • TSSC3 3 4
  • Tumor Suppressing Subchromosomal Transferable Fragment CDNA 3 3
  • Pleckstrin Homology-Like Domain, Family A, Member 2 2
  • Tumor-Suppressing STF CDNA 3 Protein 4
  • P17-Beckwith-Wiedemann Region 1C 3
  • Tumor-Supressing STF CDNA 3 3
  • PHLDA2 5
  • BRW1C 3

External Ids for PHLDA2 Gene

Previous HGNC Symbols for PHLDA2 Gene

  • TSSC3

Previous GeneCards Identifiers for PHLDA2 Gene

  • GC11M002908
  • GC11M002913
  • GC11M002906
  • GC11M002737
  • GC11M002949

Summaries for PHLDA2 Gene

Entrez Gene Summary for PHLDA2 Gene

  • This gene is located in a cluster of imprinted genes on chromosome 11p15.5, which is considered to be an important tumor suppressor gene region. Alterations in this region may be associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. This gene has been shown to be imprinted, with preferential expression from the maternal allele in placenta and liver. [provided by RefSeq, Oct 2010]

GeneCards Summary for PHLDA2 Gene

PHLDA2 (Pleckstrin Homology Like Domain Family A Member 2) is a Protein Coding gene. Diseases associated with PHLDA2 include Beckwith-Wiedemann Syndrome and Esophageal Adenoid Cystic Carcinoma. An important paralog of this gene is PHLDA3.

UniProtKB/Swiss-Prot Summary for PHLDA2 Gene

  • Plays a role in regulating placenta growth. May act via its PH domain that competes with other PH domain-containing proteins, thereby preventing their binding to membrane lipids (By similarity).

Gene Wiki entry for PHLDA2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHLDA2 Gene

Genomics for PHLDA2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PHLDA2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHLDA2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHLDA2

Top Transcription factor binding sites by QIAGEN in the PHLDA2 gene promoter:
  • CUTL1
  • FOXC1
  • FOXL1
  • GR
  • GR-alpha
  • GR-beta
  • Ik-2
  • Nkx2-5
  • Pax-4a
  • Zic1

Genomic Locations for PHLDA2 Gene

Genomic Locations for PHLDA2 Gene
chr11:2,928,273-2,929,420
(GRCh38/hg38)
Size:
1,148 bases
Orientation:
Minus strand
chr11:2,949,503-2,950,685
(GRCh37/hg19)
Size:
1,183 bases
Orientation:
Minus strand

Genomic View for PHLDA2 Gene

Genes around PHLDA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHLDA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHLDA2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHLDA2 Gene

Proteins for PHLDA2 Gene

  • Protein details for PHLDA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q53GA4-PHLA2_HUMAN
    Recommended name:
    Pleckstrin homology-like domain family A member 2
    Protein Accession:
    Q53GA4
    Secondary Accessions:
    • O00496

    Protein attributes for PHLDA2 Gene

    Size:
    152 amino acids
    Molecular mass:
    17092 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • The PHLDA2 locus is imprinted. Loss of imprinting results in overexpression. Imprinting is dependent on RNAi machinery.

neXtProt entry for PHLDA2 Gene

Post-translational modifications for PHLDA2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PHLDA2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PHLDA2 Gene

Domains & Families for PHLDA2 Gene

Gene Families for PHLDA2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PHLDA2 Gene

Suggested Antigen Peptide Sequences for PHLDA2 Gene

GenScript: Design optimal peptide antigens:
  • p17-Beckwith-Wiedemann region 1 C (PHLA2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q53GA4

UniProtKB/Swiss-Prot:

PHLA2_HUMAN :
  • The PH domain binds phosphoinositides with a broad specificity. It may compete with the PH domain of some other proteins, thereby interfering with their binding to phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3) (By similarity).
  • Belongs to the PHLDA2 family.
Domain:
  • The PH domain binds phosphoinositides with a broad specificity. It may compete with the PH domain of some other proteins, thereby interfering with their binding to phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-trisphosphate (PIP3) (By similarity).
Family:
  • Belongs to the PHLDA2 family.
genes like me logo Genes that share domains with PHLDA2: view

Function for PHLDA2 Gene

Molecular function for PHLDA2 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in regulating placenta growth. May act via its PH domain that competes with other PH domain-containing proteins, thereby preventing their binding to membrane lipids (By similarity).
UniProtKB/Swiss-Prot Induction:
Maternal PHLDA2 allele is activated, while paternal Phlda2 is repressed due to genomic imprinting. Down-regulated by hypoxia. Although highly similar to PHLDA3 protein, it is not regulated by p53/TP53.

Phenotypes From GWAS Catalog for PHLDA2 Gene

Gene Ontology (GO) - Molecular Function for PHLDA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:1901981 phosphatidylinositol phosphate binding IEA --
genes like me logo Genes that share ontologies with PHLDA2: view
genes like me logo Genes that share phenotypes with PHLDA2: view

Animal Models for PHLDA2 Gene

MGI Knock Outs for PHLDA2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHLDA2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PHLDA2 Gene

Localization for PHLDA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHLDA2 Gene

Cytoplasm. Membrane. Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHLDA2 gene
Compartment Confidence
nucleus 4
cytoskeleton 2
cytosol 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHLDA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PHLDA2: view

Pathways & Interactions for PHLDA2 Gene

PathCards logo

SuperPathways for PHLDA2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHLDA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001890 placenta development IBA 21873635
GO:0006915 apoptotic process TAS 9328465
GO:0009887 animal organ morphogenesis IEA --
GO:0010468 regulation of gene expression IEA --
GO:0030334 regulation of cell migration IEA --
genes like me logo Genes that share ontologies with PHLDA2: view

No data available for Pathways by source and SIGNOR curated interactions for PHLDA2 Gene

Drugs & Compounds for PHLDA2 Gene

No Compound Related Data Available

Transcripts for PHLDA2 Gene

mRNA/cDNA for PHLDA2 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHLDA2

Alternative Splicing Database (ASD) splice patterns (SP) for PHLDA2 Gene

No ASD Table

Relevant External Links for PHLDA2 Gene

GeneLoc Exon Structure for
PHLDA2

Expression for PHLDA2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHLDA2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PHLDA2 Gene

This gene is overexpressed in Esophagus - Mucosa (x5.6) and Minor Salivary Gland (x5.3).

Protein differential expression in normal tissues from HIPED for PHLDA2 Gene

This gene is overexpressed in Lung (36.3), Breast (13.8), Placenta (9.4), and Bone (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHLDA2 Gene



Protein tissue co-expression partners for PHLDA2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHLDA2

SOURCE GeneReport for Unigene cluster for PHLDA2 Gene:

Hs.154036

mRNA Expression by UniProt/SwissProt for PHLDA2 Gene:

Q53GA4-PHLA2_HUMAN
Tissue specificity: Expressed in placenta and adult prostate gland. In placenta, it is present in all cells of the villous cytotrophoblast. The protein is absent in cells from hydatidiform moles. Hydatidiform mole is a gestation characterized by abnormal development of both fetus and trophoblast. The majority of hydatidiform moles are associated with an excess of paternal to maternal genomes and are likely to result from the abnormal expression of imprinted genes (at protein level). Expressed at low levels in adult liver and lung, and fetal liver. Expressed in adult brain and neuroblastoma, medullablastoma and glioblastoma cell lines.

Evidence on tissue expression from TISSUES for PHLDA2 Gene

  • Skin(4.4)
  • Nervous system(2.9)
  • Heart(2.4)
  • Muscle(2.3)
  • Stomach(2.2)
  • Kidney(2.2)
  • Intestine(2.2)
  • Liver(2.2)
  • Eye(2.1)
genes like me logo Genes that share expression patterns with PHLDA2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PHLDA2 Gene

Orthologs for PHLDA2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PHLDA2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PHLDA2 30 31
  • 96.71 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PHLDA2 30 31
  • 89.08 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Phlda2 30
  • 83.03 (n)
Mouse
(Mus musculus)
Mammalia Phlda2 30 17 31
  • 82.32 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PHLDA2 31
  • 66 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PHLDA2 30 31
  • 79.13 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 60 (a)
OneToMany
-- 31
  • 54 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia phlda2 30
  • 64.58 (n)
Str.15512 30
Zebrafish
(Danio rerio)
Actinopterygii phlda2 30 31
  • 65.44 (n)
OneToOne
Dr.13050 30
Species where no ortholog for PHLDA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PHLDA2 Gene

ENSEMBL:
Gene Tree for PHLDA2 (if available)
TreeFam:
Gene Tree for PHLDA2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHLDA2: view image

Paralogs for PHLDA2 Gene

Paralogs for PHLDA2 Gene

(1) SIMAP similar genes for PHLDA2 Gene using alignment to 1 proteins:

  • PHLA2_HUMAN
genes like me logo Genes that share paralogs with PHLDA2: view

Variants for PHLDA2 Gene

Additional dbSNP identifiers (rs#s) for PHLDA2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PHLDA2 Gene

Variant ID Type Subtype PubMed ID
esv2759795 CNV gain 17122850
nsv553121 CNV loss 21841781
nsv832050 CNV loss 17160897

Variation tolerance for PHLDA2 Gene

Residual Variation Intolerance Score: 49.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.14; 61.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHLDA2 Gene

Human Gene Mutation Database (HGMD)
PHLDA2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHLDA2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHLDA2 Gene

Disorders for PHLDA2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PHLDA2 Gene - From: DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PHLDA2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PHLDA2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHLDA2 Gene

Publications for PHLDA2 Gene

  1. Hypoxia regulates the expression of PHLDA2 in primary term human trophoblasts. (PMID: 16584773) Kim HS … Sadovsky Y (Placenta 2007) 3 4 23
  2. The product of the imprinted gene IPL marks human villous cytotrophoblast and is lost in complete hydatidiform mole. (PMID: 13129680) Saxena A … Thaker H (Placenta 2003) 3 4 23
  3. Retention of imprinting of the human apoptosis-related gene TSSC3 in human brain tumors. (PMID: 10749982) Müller S … Zumkeller W (Human molecular genetics 2000) 3 4 23
  4. A novel pleckstrin homology-related gene family defined by Ipl/Tssc3, TDAG51, and Tih1: tissue-specific expression, chromosomal location, and parental imprinting. (PMID: 10594239) Frank D … Tycko B (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 3 4 23
  5. Transcriptional map of 170-kb region at chromosome 11p15.5: identification and mutational analysis of the BWR1A gene reveals the presence of mutations in tumor samples. (PMID: 9520460) Schwienbacher C … Negrini M (Proceedings of the National Academy of Sciences of the United States of America 1998) 3 4 23

Products for PHLDA2 Gene

Sources for PHLDA2 Gene