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POPDC3 popeye domain containing 3 [ Homo sapiens (human) ]

Gene ID: 64208, updated on 5-Mar-2024

Summary

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Official Symbol
POPDC3provided by HGNC
Official Full Name
popeye domain containing 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
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Genomic context

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Location:
6q21
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (105157900..105180014, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (106333653..106355749, complement)
105.20220307 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 ATAC-STARR-seq lymphoblastoid silent region 17426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17427 Neighboring gene blood vessel epicardial substance Neighboring gene BVES 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: 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. 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
  2. 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
  3. Homozygous missense variant in POPDC3 causes recessive limb-girdle muscular dystrophy type 26. Ullah A, et al. J Gene Med, 2022 Apr. PMID 35075722
  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
not available

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)

Genotypes

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 molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
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 protein 3

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_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_2023_10

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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