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    POPDC3 popeye domain cAMP effector 3 [ Homo sapiens (human) ]

    Gene ID: 64208, updated on 10-Dec-2024

    Summary

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    Official Symbol
    POPDC3provided by HGNC
    Official Full Name
    popeye domain cAMP effector 3provided by HGNC
    Primary source
    HGNC:HGNC:17649
    See related
    Ensembl:ENSG00000132429 MIM:605824; AllianceGenome:HGNC:17649
    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
    POP3; LGMDR26; bA355M14.1
    Summary
    This gene encodes a member of the POP family of proteins containing three putative transmembrane domains. This gene is expressed in cardiac and skeletal muscle and may play an important role in these tissues during development. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2008]
    Expression
    Biased expression in heart (RPKM 4.3), testis (RPKM 1.6) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See POPDC3 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (105157900..105180014, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (106333653..106355749, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (105605775..105627889, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene lin-28 homolog B Neighboring gene RNA, U6 small nuclear 1106, pseudogene Neighboring gene popeye domain cAMP effector 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17427 Neighboring gene POPDC1 antisense RNA 1 Neighboring gene MPRA-validated peak5993 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105681181-105681682 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105681683-105682182 Neighboring gene ribosomal protein L7a pseudogene 35 Neighboring gene prolyl endopeptidase Neighboring gene ribosomal protein L35 pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Progress on the study of Popeye domain-containing 3 (POPDC3) in malignancies and striated muscle function and homeostasis. Sun CC, et al. Clin Genet, 2023 Jun. PMID 36843357
    2. Homozygous missense variant in POPDC3 causes recessive limb-girdle muscular dystrophy type 26. Ullah A, et al. J Gene Med, 2022 Apr. PMID 35075722
    3. A homozygous loss of function variant in POPDC3: From invalidating exercise intolerance to a limb-girdle muscular dystrophy phenotype. De Ridder W, et al. Neuromuscul Disord, 2023 May. PMID 37104941
    4. Reduced Popdc3 expression correlates with high risk and poor survival in patients with gastric cancer. Luo D, et al. World J Gastroenterol, 2012 May 21. PMID 22654436, Free PMC Article
    5. The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation. Gingold-Belfer R, et al. Int J Mol Sci, 2021 May 19. PMID 34069715, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A homozygous loss of function variant in POPDC3: From invalidating exercise intolerance to a limb-girdle muscular dystrophy phenotype.
      Title: A homozygous loss of function variant in POPDC3: From invalidating exercise intolerance to a limb-girdle muscular dystrophy phenotype.
    2. Progress on the study of Popeye domain-containing 3 (POPDC3) in malignancies and striated muscle function and homeostasis.
      Title: Progress on the study of Popeye domain-containing 3 (POPDC3) in malignancies and striated muscle function and homeostasis.
    3. Homozygous missense variant in POPDC3 causes recessive limb-girdle muscular dystrophy type 26.
      Title: Homozygous missense variant in POPDC3 causes recessive limb-girdle muscular dystrophy type 26.
    4. The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation.
      Title: The Transition from Gastric Intestinal Metaplasia to Gastric Cancer Involves POPDC1 and POPDC3 Downregulation.
    5. Pathogenic variants in POPDC3 are responsible for a novel type of autosomal recessive limb girdle muscular dystrophy.
      Title: POPDC3 Gene Variants Associate with a New Form of Limb Girdle Muscular Dystrophy.
    6. recently a novel family of cAMP effector proteins emerged and was termed the Popeye domain containing (POPDC) family, which consists of three members POPDC1, POPDC2 and POPDC3. POPDC proteins are transmembrane proteins, which are abundantly present in striated and smooth muscle cells. POPDC proteins bind cAMP with high affinity comparable to PKA
      Title: New kids on the block: The Popeye domain containing (POPDC) protein family acting as a novel class of cAMP effector proteins in striated muscle.
    7. Reduced expression of Popdc3 may play a significant role in the carcinogenesis and progression of gastric cancer. Popdc3 may be an independent prognostic factor.
      Title: Reduced Popdc3 expression correlates with high risk and poor survival in patients with gastric cancer.
    8. Frequent silencing of POPDC3 is associated with promoter hypermethylation in gastric cancer.
      Title: Frequent silencing of popeye domain-containing genes, BVES and POPDC3, is associated with promoter hypermethylation in gastric cancer.
    9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
    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

    Associated conditions

    Description Tests
    Muscular dystrophy, limb-girdle, autosomal recessive 26
    MedGen: C5394268 OMIM: 618848 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche.
    EBI GWAS Catalog
    Genome-wide association study of severity in multiple sclerosis.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC22671

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cAMP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cAMP binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of membrane potential IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of membrane potential ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in skeletal muscle tissue development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in striated muscle cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in sarcolemma IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    popeye domain-containing protein 3
    Names
    popeye domain containing 3
    popeye protein 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_022361.5 → NP_071756.2  popeye domain-containing protein 3

      See identical proteins and their annotated locations for NP_071756.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longer transcript and encodes a protein of 291 aa.
      Source sequence(s)
      AK314101, AL356775, AL359709
      Consensus CDS
      CCDS5052.1
      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1
      Related
      ENSP00000254765.3, ENST00000254765.4
      Conserved Domains (1) summary
      pfam04831
      Location:25 → 249
      Popeye; Popeye protein conserved region

    RNA

    1. NR_024539.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal segment, as compared to variant 1. It is a nonsense-mediated mRNA decay (NMD) candidate and does not make a functional protein.
      Source sequence(s)
      AK225989, AL356775

    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
      105157900..105180014 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536067.4 → XP_011534369.1  popeye domain-containing protein 3 isoform X1

      See identical proteins and their annotated locations for XP_011534369.1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1
      Conserved Domains (1) summary
      pfam04831
      Location:25 → 249
      Popeye; Popeye protein conserved region

    2. XM_047419252.1 → XP_047275208.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1

    3. XM_047419251.1 → XP_047275207.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      106333653..106355749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356217.1 → XP_054212192.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1

    2. XM_054356221.1 → XP_054212196.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1

    3. XM_054356220.1 → XP_054212195.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1

    4. XM_054356219.1 → XP_054212194.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1

    5. XM_054356218.1 → XP_054212193.1  popeye domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RA98, Q5T3Y8, Q8TBW6, Q9HBV1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HBV1.2 GenPept UniProtKB/Swiss-Prot:Q9HBV1

    Gene LinkOut

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