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CALCOCO2 calcium binding and coiled-coil domain 2 [ Homo sapiens (human) ]

Gene ID: 10241, updated on 7-Apr-2024

Summary

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Official Symbol
CALCOCO2provided by HGNC
Official Full Name
calcium binding and coiled-coil domain 2provided by HGNC
Primary source
HGNC:HGNC:29912
See related
Ensembl:ENSG00000136436 MIM:604587; AllianceGenome:HGNC:29912
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
NDP52
Summary
This gene encodes a coiled-coil domain-containing protein. The encoded protein functions as a receptor for ubiquitin-coated bacteria and plays an important role in innate immunity by mediating macroautophagy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
Expression
Ubiquitous expression in fat (RPKM 39.0), testis (RPKM 32.6) and 25 other tissues See more
Orthologs
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Genomic context

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See CALCOCO2 in Genome Data Viewer
Location:
17q21.32
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48831035..48865245)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (49694621..49728978)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46908397..46942607)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 125, pseudogene Neighboring gene tubulin tyrosine ligase like 6 Neighboring gene uncharacterized LOC105371813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46908401-46909282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12340 Neighboring gene uncharacterized LOC105371814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12341 Neighboring gene small nucleolar RNA SNORA68 Neighboring gene SUMO2 pseudogene 17

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. NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy. Kataura T, et al. EMBO J, 2023 Mar 1. PMID 36514953, Free PMC Article
  2. Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52. Fu T, et al. Sci Adv, 2021 Aug. PMID 34389544, Free PMC Article
  3. Novel Insights into NDP52 Autophagy Receptor Functioning. Viret C, et al. Trends Cell Biol, 2018 Apr. PMID 29395717
  4. Influenza virus protein PB1-F2 interacts with CALCOCO2 (NDP52) to modulate innate immune response. Leymarie O, et al. J Gen Virol, 2017 Jun. PMID 28613140
  5. A variant in the nuclear dot protein 52kDa gene increases the risk for spontaneous bacterial peritonitis in patients with alcoholic liver cirrhosis. Lutz P, et al. Dig Liver Dis, 2016 Jan. PMID 26493630

See all (121) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2 signalling.
    Title: NDP52 SUMOylation contributes to low-dose X-rays-induced cardiac hypertrophy through PINK1/Parkin-mediated mitophagy via MUL1/SUMO2 signalling.
  2. Crotonylated BEX2 interacts with NDP52 and enhances mitophagy to modulate chemotherapeutic agent-induced apoptosis in non-small-cell lung cancer cells.
    Title: Crotonylated BEX2 interacts with NDP52 and enhances mitophagy to modulate chemotherapeutic agent-induced apoptosis in non-small-cell lung cancer cells.
  3. NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.
    Title: NDP52 acts as a redox sensor in PINK1/Parkin-mediated mitophagy.
  4. Baicalein Activates Parkin-Dependent Mitophagy through NDP52 and OPTN.
    Title: Baicalein Activates Parkin-Dependent Mitophagy through NDP52 and OPTN.
  5. Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy.
    Title: Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy.
  6. Crosstalk Between NDP52 and LUBAC in Innate Immune Responses, Cell Death, and Xenophagy.
    Title: Crosstalk Between NDP52 and LUBAC in Innate Immune Responses, Cell Death, and Xenophagy.
  7. The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment.
    Title: The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment.
  8. The CALCOCO2, but not SQSTM1, suppresses the antiviral type I interferon signaling by promoting autophagy-mediated degradation of the mitochondrial antiviral signaling (MAVS) protein.
    Title: CALCOCO2/NDP52 and SQSTM1/p62 differentially regulate coxsackievirus B3 propagation.
  9. The altered expression of NRBP2 and CALCOCO2 is associated with left ventricular dysfunction parameters in human dilated cardiomyopathy.
    Title: The altered expression of autophagy-related genes participates in heart failure: NRBP2 and CALCOCO2 are associated with left ventricular dysfunction parameters in human dilated cardiomyopathy.
  10. The capability of NDP52 to induce mitophagy is dependent on its interaction with the FIP200/ULK1 complex, which is facilitated by TBK1. Ectopically tethering ULK1 to cargo bypasses the requirement for autophagy receptors and TBK1.
    Title: Spatiotemporal Control of ULK1 Activation by NDP52 and TBK1 during Selective Autophagy.
Submit: New GeneRIF Correction See all GeneRIFs (38)

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)

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

  • MGC17318

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in positive regulation of autophagosome maturation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to type II interferon IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in viral process TAS
Traceable Author Statement
more info
 PubMed 
involved_in xenophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in xenophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in PML body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in PML body IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in autophagosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in autophagosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in autophagosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in membrane HDA PubMed 
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
calcium-binding and coiled-coil domain-containing protein 2
Names
antigen nuclear dot 52 kDa protein
nuclear domain 10 protein 52
nuclear domain 10 protein NDP52
nuclear dot protein 52

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_001261390.2 → NP_001248319.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001248319.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC068531, AK298177, AL042638
    Consensus CDS
    CCDS58559.1
    UniProtKB/Swiss-Prot
    Q13137
    Related
    ENSP00000398523.2, ENST00000448105.6
    Conserved Domains (3) summary
    pfam06273
    Location:150 → 211
    eIF-4B; Plant specific eukaryotic initiation factor 4B
    cl19219
    Location:189 → 269
    DUF342; Protein of unknown function (DUF342)
    cl24005
    Location:253 → 334
    DUF2570; Protein of unknown function (DUF2570)

  2. NM_001261391.2 → NP_001248320.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon and includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC068531, AK293329
    Consensus CDS
    CCDS58558.1
    UniProtKB/Swiss-Prot
    Q13137
    Related
    ENSP00000424352.1, ENST00000509507.5
    Conserved Domains (3) summary
    pfam06273
    Location:147 → 208
    eIF-4B; Plant specific eukaryotic initiation factor 4B
    cl23720
    Location:164 → 259
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    cl24005
    Location:250 → 331
    DUF2570; Protein of unknown function (DUF2570)

  3. NM_001261393.2 → NP_001248322.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC068531, AK303313
    Consensus CDS
    CCDS58560.1
    UniProtKB/Swiss-Prot
    Q13137
    Related
    ENSP00000406974.2, ENST00000416445.6
    Conserved Domains (3) summary
    pfam04871
    Location:139 → 211
    Uso1_p115_C; Uso1 / p115 like vesicle tethering protein, C terminal region
    pfam07888
    Location:22 → 301
    CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
    cl24005
    Location:187 → 268
    DUF2570; Protein of unknown function (DUF2570)

  4. NM_001261395.2 → NP_001248324.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two consecutive internal exons and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (5) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC068531, AK293137, BE315542
    Consensus CDS
    CCDS58561.1
    UniProtKB/Swiss-Prot
    Q13137
    Related
    ENSP00000423437.1, ENST00000508679.5
    Conserved Domains (3) summary
    pfam06273
    Location:54 → 115
    eIF-4B; Plant specific eukaryotic initiation factor 4B
    cl19219
    Location:93 → 173
    DUF342; Protein of unknown function (DUF342)
    cl24005
    Location:157 → 238
    DUF2570; Protein of unknown function (DUF2570)

  5. NM_005831.5 → NP_005822.1  calcium-binding and coiled-coil domain-containing protein 2 isoform 3

    See identical proteins and their annotated locations for NP_005822.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC068531, U22897
    Consensus CDS
    CCDS11538.1
    UniProtKB/Swiss-Prot
    B2RBT0, B4DDC4, B4DDT4, B4DP36, B4E0C0, E7ENK0, E7ETP5, E9PBE5, Q13137, Q53FQ5, Q53HB5, Q6IBN9, Q9BTF7
    Related
    ENSP00000258947.3, ENST00000258947.8
    Conserved Domains (1) summary
    cl25732
    Location:22 → 316
    SMC_N; RecF/RecN/SMC N terminal domain

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    48831035..48865245
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435100.1 → XP_047291056.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

  2. XM_047435099.1 → XP_047291055.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    49694621..49728978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314673.1 → XP_054170648.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

  2. XM_054314672.1 → XP_054170647.1  calcium-binding and coiled-coil domain-containing protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13137.1 GenPept UniProtKB/Swiss-Prot:Q13137

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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