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POPDC1 popeye domain cAMP effector 1 [ Homo sapiens (human) ]

Gene ID: 11149, updated on 27-Nov-2024

Summary

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Official Symbol
POPDC1provided by HGNC
Official Full Name
popeye domain cAMP effector 1provided by HGNC
Primary source
HGNC:HGNC:1152
See related
Ensembl:ENSG00000112276 MIM:604577; AllianceGenome:HGNC:1152
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
BVES; POP1; HBVES; CARICK; LGMD2X; LGMDR25
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 development of these tissues. The mouse ortholog may be involved in the regeneration of adult skeletal muscle and may act as a cell adhesion molecule in coronary vasculogenesis. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2010]
Expression
Broad expression in heart (RPKM 3.6), testis (RPKM 1.9) and 16 other tissues See more
Orthologs
mouse all
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Genomic context

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See POPDC1 in Genome Data Viewer
Location:
6q21
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (105096822..105137157, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (106272906..106312920, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (105544697..105585032, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105384704-105385204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105385205-105385705 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105388624-105389458 Neighboring gene LIN28B antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:105403995-105404932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:105404933-105405870 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 POPDC1 antisense RNA 1 Neighboring gene popeye domain cAMP effector 3 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

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 novel biallelic variant in the Popeye domain-containing protein 1 (POPDC1) underlies limb girdle muscle dystrophy type 25. Mahmood A, et al. Clin Genet, 2023 Feb. PMID 36155908
  2. Proteomic and morphological insights and clinical presentation of two young patients with novel mutations of BVES (POPDC1). Gangfuß A, et al. Mol Genet Metab, 2022 Jul. PMID 35660068
  3. Popeye domain-containing 1 is down-regulated in failing human hearts. Gingold-Belfer R, et al. Int J Mol Med, 2011 Jan. PMID 21069264
  4. Bves modulates tight junction associated signaling. Russ PK, et al. PLoS One, 2011 Jan 20. PMID 21283798, Free PMC Article
  5. BVES regulates EMT in human corneal and colon cancer cells and is silenced via promoter methylation in human colorectal carcinoma. Williams CS, et al. J Clin Invest, 2011 Oct. PMID 21911938, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel biallelic variant in the Popeye domain-containing protein 1 (POPDC1) underlies limb girdle muscle dystrophy type 25.
    Title: A novel biallelic variant in the Popeye domain-containing protein 1 (POPDC1) underlies limb girdle muscle dystrophy type 25.
  2. Differential effects of mutations of POPDC proteins on heteromeric interaction and membrane trafficking.
    Title: Differential effects of mutations of POPDC proteins on heteromeric interaction and membrane trafficking.
  3. Proteomic and morphological insights and clinical presentation of two young patients with novel mutations of BVES (POPDC1).
    Title: Proteomic and morphological insights and clinical presentation of two young patients with novel mutations of BVES (POPDC1).
  4. An interaction of heart disease-associated proteins POPDC1/2 with XIRP1 in transverse tubules and intercalated discs.
    Title: An interaction of heart disease-associated proteins POPDC1/2 with XIRP1 in transverse tubules and intercalated discs.
  5. 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.
  6. BVES downregulation in non-syndromic tetralogy of fallot is associated with ventricular outflow tract stenosis.
    Title: BVES downregulation in non-syndromic tetralogy of fallot is associated with ventricular outflow tract stenosis.
  7. c.385C>T (p.R129W) is a functional SNP of the BVES gene that reduces the transcriptional activity of BVES in vitro and in vivo in TOF tissues. This subsequently affects the transcriptional activities of GATA4 and NKX2.5 related to TOF. These findings suggest that c.385C>T may be associated with the risk of TOF in the Han Chinese population.
    Title: The Functional Polymorphism R129W in the BVES Gene Is Associated with Sporadic Tetralogy of Fallot in the Han Chinese Population.
  8. BVES plays a protective role both in ulcerative and infectious colitis.
    Title: BVES is required for maintenance of colonic epithelial integrity in experimental colitis by modifying intestinal permeability.
  9. Functional suppression of POPDC1 promoted breast cancer cell migration and proliferation, cAMP interacts with POPDC1 and up-regulates its expression in breast cancer cells.
    Title: Dysregulation of POPDC1 promotes breast cancer cell migration and proliferation.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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
Autosomal recessive limb-girdle muscular dystrophy type 2X
MedGen: C5568138 OMIM: 616812 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche.
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

  • MGC42413

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cAMP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables structural molecule activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell migration involved in heart development IEA
Inferred from Electronic Annotation
more info
  
involved_in epithelial cell-cell adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in heart development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heart development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in hematopoietic progenitor cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in muscle organ development NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of locomotion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of receptor recycling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of cell shape ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of endocytic recycling IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of heart rate IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to ischemia ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in sinoatrial node cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in skeletal muscle tissue development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal muscle tissue development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in striated muscle cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in substrate adhesion-dependent cell spreading ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in vesicle docking IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in bicellular tight junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in caveola ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cell junction IDA
Inferred from Direct Assay
more info
  
located_in cell projection membrane IEA
Inferred from Electronic Annotation
more info
  
located_in lateral plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in sarcolemma IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in sarcolemma IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
blood vessel epicardial substance
Names
popeye domain-containing protein 1

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.

Genomic

  1. NG_046732.1 RefSeqGene

    Range
    5018..45353
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001199563.2 → NP_001186492.1  blood vessel epicardial substance

    See identical proteins and their annotated locations for NP_001186492.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (C) has an alternate 5' UTR exon and encodes the same protein, as compared to variant A.
    Source sequence(s)
    AK289979, AL356775, BC040502, Z95329
    Consensus CDS
    CCDS5051.1
    UniProtKB/Swiss-Prot
    A8K1R4, E1P5D8, Q5T550, Q5T551, Q8IWC6, Q8NE79, Q9HBV0, Q9UNG6
    Related
    ENSP00000313172.5, ENST00000314641.10
    Conserved Domains (1) summary
    pfam04831
    Location:40 → 267
    Popeye; Popeye protein conserved region

  2. NM_007073.4 → NP_009004.2  blood vessel epicardial substance

    See identical proteins and their annotated locations for NP_009004.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) and variants B and C encode the same protein.
    Source sequence(s)
    AF204172, BC034425, BC040502, Z95329
    Consensus CDS
    CCDS5051.1
    UniProtKB/Swiss-Prot
    A8K1R4, E1P5D8, Q5T550, Q5T551, Q8IWC6, Q8NE79, Q9HBV0, Q9UNG6
    Related
    ENSP00000337259.5, ENST00000336775.9
    Conserved Domains (1) summary
    pfam04831
    Location:40 → 267
    Popeye; Popeye protein conserved region

  3. NM_147147.4 → NP_671488.1  blood vessel epicardial substance

    See identical proteins and their annotated locations for NP_671488.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (B) has an alternate 5' UTR exon and encodes the same protein, as compared to variant A.
    Source sequence(s)
    AL356775, BC034425, BC040502, Z95329
    Consensus CDS
    CCDS5051.1
    UniProtKB/Swiss-Prot
    A8K1R4, E1P5D8, Q5T550, Q5T551, Q8IWC6, Q8NE79, Q9HBV0, Q9UNG6
    Related
    ENSP00000397310.2, ENST00000446408.2
    Conserved Domains (1) summary
    pfam04831
    Location:40 → 267
    Popeye; Popeye protein conserved region

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
    105096822..105137157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    106272906..106312920 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NE79.1 GenPept UniProtKB/Swiss-Prot:Q8NE79

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