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PDCD2 programmed cell death 2 [ Homo sapiens (human) ]

Gene ID: 5134, updated on 14-Nov-2024

Summary

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Official Symbol
PDCD2provided by HGNC
Official Full Name
programmed cell death 2provided by HGNC
Primary source
HGNC:HGNC:8762
See related
Ensembl:ENSG00000071994 MIM:600866; AllianceGenome:HGNC:8762
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
RP8; ZMYND7
Summary
This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]
Expression
Ubiquitous expression in lymph node (RPKM 7.8), thyroid (RPKM 7.5) and 25 other tissues See more
Orthologs
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Genomic context

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See PDCD2 in Genome Data Viewer
Location:
6q27
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (170575295..170584637, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (171948844..171958191, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (170884383..170893725, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25467 Neighboring gene proteasome 20S subunit beta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25468 Neighboring gene TATA-box binding protein repeat instability region Neighboring gene TATA-box binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17802 Neighboring gene uncharacterized LOC101929692 Neighboring gene olfactory receptor family 4 subfamily F member 7 pseudogene Neighboring gene WBP1L pseudogene 8

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. Isolation and mapping of a human gene (PDCD2) that is highly homologous to Rp8, a rat gene associated with programmed cell death. Kawakami T, et al. Cytogenet Cell Genet, 1995. PMID 7606924
  2. PDCD2 functions in cancer cell proliferation and predicts relapsed leukemia. Barboza N, et al. Cancer Biol Ther, 2013 Jun. PMID 23760497, Free PMC Article
  3. Programmed cell death 2 protein induces gastric cancer cell growth arrest at the early S phase of the cell cycle and apoptosis in a p53-dependent manner. Zhang J, et al. Oncol Rep, 2015 Jan. PMID 25334010
  4. Programmed cell death 2 functions as a tumor suppressor in osteosarcoma. Yang Y, et al. Int J Clin Exp Pathol, 2015. PMID 26617804, Free PMC Article
  5. Microbial infections in eight genomic subtypes of chronic fatigue syndrome/myalgic encephalomyelitis. Zhang L, et al. J Clin Pathol, 2010 Feb. PMID 19955554, Free PMC Article

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5 (RPS2).
    Title: PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5 (RPS2).
  2. the present study elucidated for the first time, to the best of our knowledge, that PDCD2 sensitizes sorafenibresistant HepG2 cells to sorafenib by the downregulation of EMT. PDCD2 may serve as a potential therapeutic target in the treatment of sorafenibresistant liver cancer.
    Title: PDCD2 sensitizes HepG2 cells to sorafenib by suppressing epithelial‑mesenchymal transition.
  3. PDCD2 and NCoR1 may act as tumor suppressors in Gastrointestinal stromal tumors cells through the Smad signaling pathway.
    Title: PDCD2 and NCoR1 as putative tumor suppressors in gastric gastrointestinal stromal tumors.
  4. PDCD2 may play an important role in tumor suppression in osteosarcoma. These mechanisms might be related to immune response induced by CD4(+) and CD8(+) T cells.
    Title: Programmed cell death 2 functions as a tumor suppressor in osteosarcoma.
  5. Low PDCD2 expression is associated with gastric cancer.
    Title: miR-129-1-3p promote BGC-823 cell proliferation by targeting PDCD2.
  6. Loss of PDCD2 expression could contribute to gastric cancer development and progression.
    Title: Programmed cell death 2 protein induces gastric cancer cell growth arrest at the early S phase of the cell cycle and apoptosis in a p53-dependent manner.
  7. Expression of human PDCD2 fully rescues the Drosophila Zfrp8 phenotype, underlining the functional conservation of Zfrp8/PDCD2.
    Title: Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery.
  8. PDCD2 RNA expression in acute leukemia patients correlates with disease status and is a significant predictor of clinical relapse.
    Title: PDCD2 functions in cancer cell proliferation and predicts relapsed leukemia.
  9. PDCD2 has a novel regulatory role in human hematopoiesis and is essential for erythroid development.
    Title: PDCD2 knockdown inhibits erythroid but not megakaryocytic lineage differentiation of human hematopoietic stem/progenitor cells.
  10. Transfection of a construct expressing PDCD2 induces apoptosis in human cell lines through activation of the caspase cascade.
    Title: PDCD2, a protein whose expression is repressed by BCL6, induces apoptosis in human cells by activation of the caspase cascade.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC12347

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cysteine-type endopeptidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of hematopoietic stem cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of hematopoietic progenitor cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
programmed cell death protein 2
Names
zinc finger MYND domain-containing protein 7
zinc finger protein Rp-8

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_001199461.2 → NP_001186390.1  programmed cell death protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AL031259, AW966881
    Consensus CDS
    CCDS75557.1
    UniProtKB/TrEMBL
    A0A087WYJ3
    Related
    ENSP00000481860.1, ENST00000614056.4
    Conserved Domains (1) summary
    pfam01753
    Location:135 → 172
    zf-MYND; MYND finger

  2. NM_001199462.2 → NP_001186391.1  programmed cell death protein 2 isoform 4

    See identical proteins and their annotated locations for NP_001186391.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting protein (isoform 4) is shorter, compared to isoform 1.
    Source sequence(s)
    AK055180, AL031259, AY948416, DC351104
    Consensus CDS
    CCDS56461.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000375940.2, ENST00000392090.6
    Conserved Domains (2) summary
    pfam01753
    Location:102 → 139
    zf-MYND; MYND finger
    pfam04194
    Location:193 → 306
    PDCD2_C; Programmed cell death protein 2, C-terminal putative domain

  3. NM_001199463.2 → NP_001186392.1  programmed cell death protein 2 isoform 5

    See identical proteins and their annotated locations for NP_001186392.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region and differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 5) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AK297343, AL031259
    Consensus CDS
    CCDS56460.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000397272.2, ENST00000443345.2
    Conserved Domains (1) summary
    pfam01753
    Location:102 → 139
    zf-MYND; MYND finger

  4. NM_001199464.2 → NP_001186393.1  programmed cell death protein 2 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 5' coding region and differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 6) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AK297343, AL031259, BX385363
    Consensus CDS
    CCDS56462.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000440572.1, ENST00000537445.5
    Conserved Domains (1) summary
    pfam01753
    Location:102 → 139
    zf-MYND; MYND finger

  5. NM_001363655.2 → NP_001350584.1  programmed cell death protein 2 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (7) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL031259
    Consensus CDS
    CCDS87471.1
    UniProtKB/TrEMBL
    F5H4V9
    Related
    ENSP00000439914.1, ENST00000542896.5
    Conserved Domains (2) summary
    pfam01753
    Location:135 → 172
    zf-MYND; MYND finger
    pfam04194
    Location:226 → 292
    PDCD2_C; Programmed cell death protein 2, C-terminal putative domain

  6. NM_002598.4 → NP_002589.2  programmed cell death protein 2 isoform 1

    See identical proteins and their annotated locations for NP_002589.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK055180, AL031259, BC008378
    Consensus CDS
    CCDS5316.1
    UniProtKB/Swiss-Prot
    E9PCU7, F5GYS7, Q16342, Q58HM9, Q58HN0, Q9UH12
    Related
    ENSP00000439467.1, ENST00000541970.6
    Conserved Domains (2) summary
    pfam01753
    Location:135 → 172
    zf-MYND; MYND finger
    pfam04194
    Location:226 → 339
    PDCD2_C; Programmed cell death protein 2, C-terminal putative domain

  7. NM_144781.3 → NP_659005.1  programmed cell death protein 2 isoform 2

    See identical proteins and their annotated locations for NP_659005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and UTR, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AJ420535, AL031259
    Consensus CDS
    CCDS47521.1
    UniProtKB/Swiss-Prot
    Q16342
    Related
    ENSP00000402524.2, ENST00000453163.6
    Conserved Domains (1) summary
    pfam01753
    Location:135 → 172
    zf-MYND; MYND finger

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    170575295..170584637 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418861.1 → XP_047274817.1  programmed cell death protein 2 isoform X1

    UniProtKB/TrEMBL
    J3QK82
    Related
    ENSP00000167218.5, ENST00000167218.9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    171948844..171958191 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355579.1 → XP_054211554.1  programmed cell death protein 2 isoform X1

    UniProtKB/TrEMBL
    J3QK82
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16342.2 GenPept UniProtKB/Swiss-Prot:Q16342

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