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CCDC92 coiled-coil domain containing 92 [ Homo sapiens (human) ]

Gene ID: 80212, updated on 2-Nov-2024

Summary

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Official Symbol
CCDC92provided by HGNC
Official Full Name
coiled-coil domain containing 92provided by HGNC
Primary source
HGNC:HGNC:29563
See related
Ensembl:ENSG00000119242 AllianceGenome:HGNC:29563
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables identical protein binding activity. Predicted to be involved in innate immune response and regulation of defense response to virus. Located in centriole; centrosome; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in brain (RPKM 20.8), testis (RPKM 19.4) and 25 other tissues See more
Orthologs
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Genomic context

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See CCDC92 in Genome Data Viewer
Location:
12q24.31
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123935626..123972831, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123937063..123974347, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (124420173..124457378, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 10 Neighboring gene uncharacterized LOC124903043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124422596-124423096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124423097-124423597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124438925-124439426 Neighboring gene dynein axonemal heavy chain 10 opposite strand Neighboring gene NANOG hESC enhancer GRCh37_chr12:124453330-124453831 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124456863-124457600 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124456125-124456862 Neighboring gene ZNF664-RFLNA readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7279 Neighboring gene zinc finger protein 664 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:124556312-124557118 Neighboring gene NANOG hESC enhancer GRCh37_chr12:124594949-124595450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124600014-124600560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124601106-124601651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124601652-124602196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:124608857-124609358 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:124624781-124625523 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124625524-124626265 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:124630091-124630857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124666563-124667068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124672143-124672663 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124672664-124673183 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124673184-124673704 Neighboring gene Sharpr-MPRA regulatory region 13038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124725860-124726762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124786919-124787420 Neighboring gene refilin A

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 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. Identification of interferon-stimulated genes that attenuate Ebola virus infection. Kuroda M, et al. Nat Commun, 2020 Jun 11. PMID 32528005, Free PMC Article
  2. Association between single nucleotide polymorphism rs11057401 of CCDC92 gene and the risk of coronary heart disease (CHD). Xiao L, et al. Lipids Health Dis, 2018 Feb 13. PMID 29439709, Free PMC Article
  3. Genetic ablation of diabetes-associated gene Ccdc92 reduces obesity and insulin resistance in mice. Ren L, et al. iScience, 2023 Jan 20. PMID 36594018, Free PMC Article
  4. Genetic analysis in UK Biobank links insulin resistance and transendothelial migration pathways to coronary artery disease. Klarin D, et al. Nat Genet, 2017 Sep. PMID 28714974, Free PMC Article
  5. Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance. Lotta LA, et al. Nat Genet, 2017 Jan. PMID 27841877, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel genetic variants of CCDC92 were associated with both Diabetes and Coronary Artery Disease .
    Title: The Genetic Link Between Diabetes and Atherosclerosis.
  2. The genotypic and allelic frequencies of the rs11057401 SNP of CCDC92 gene were significantly different between the patients with coronary heart disease and controls.
    Title: Association between single nucleotide polymorphism rs11057401 of CCDC92 gene and the risk of coronary heart disease (CHD).
  3. Phenome-wide association scanning showed that CCDC92 likely affects coronary artery disease through insulin resistance pathways, whereas experimental analysis suggests that ARHGEF26 influences the transendothelial migration of leukocytes.
    Title: Genetic analysis in UK Biobank links insulin resistance and transendothelial migration pathways to coronary artery disease.
  4. Mutation in CCDC92 gene is associated with insulin-resistant cardiometabolic disease.
    Title: Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance.
  5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
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

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
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

  • FLJ22471

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of defense response to virus IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in centriole IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centriole IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
coiled-coil domain-containing protein 92
Names
limkain beta 2

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_001304957.2 → NP_001291886.1  coiled-coil domain-containing protein 92 isoform 1

    See identical proteins and their annotated locations for NP_001291886.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1-5 encode the same protein (isoform 1).
    Source sequence(s)
    AC079315, AK222661, BC017186, HY035895
    Consensus CDS
    CCDS9256.1
    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  2. NM_001304958.2 → NP_001291887.1  coiled-coil domain-containing protein 92 isoform 1

    See identical proteins and their annotated locations for NP_001291887.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate exon in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1-5 encode the same protein (isoform 1).
    Source sequence(s)
    AC079315, BC017186, DA370549, HY035895
    Consensus CDS
    CCDS9256.1
    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  3. NM_001304959.2 → NP_001291888.1  coiled-coil domain-containing protein 92 isoform 1

    See identical proteins and their annotated locations for NP_001291888.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate exon in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1-5 encode the same protein (isoform 1).
    Source sequence(s)
    AC079315, BC017186, DA263704
    Consensus CDS
    CCDS9256.1
    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  4. NM_001304960.2 → NP_001291889.1  coiled-coil domain-containing protein 92 isoform 1

    See identical proteins and their annotated locations for NP_001291889.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has multiple differences in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1-5 encode the same protein (isoform 1).
    Source sequence(s)
    AC079315, AW953473, BC017186, DA263704
    Consensus CDS
    CCDS9256.1
    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  5. NM_001304961.2 → NP_001291890.1  coiled-coil domain-containing protein 92 isoform 2

    See identical proteins and their annotated locations for NP_001291890.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks a 5' exon which results in the use of an in-frame, downstream start codon, compared to variant 1. This variant encodes an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC079315, BC017186, BX394686, HY035895
    Consensus CDS
    CCDS76619.1
    UniProtKB/Swiss-Prot
    Q53HC0
    Related
    ENSP00000440024.1, ENST00000545891.5
    Conserved Domains (1) summary
    pfam14916
    Location:7 → 62
    CCDC92; Coiled-coil domain of unknown function

  6. NM_025140.3 → NP_079416.1  coiled-coil domain-containing protein 92 isoform 1

    See identical proteins and their annotated locations for NP_079416.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1. Variants 1-5 encode the same protein (isoform 1).
    Source sequence(s)
    AC079315, BC017186, HY035895
    Consensus CDS
    CCDS9256.1
    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Related
    ENSP00000238156.3, ENST00000238156.8
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    123935626..123972831 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429566.1 → XP_047285522.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  2. XM_024449197.2 → XP_024304965.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  3. XM_024449194.2 → XP_024304962.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  4. XM_024449193.2 → XP_024304961.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  5. XM_024449196.2 → XP_024304964.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  6. XM_024449199.2 → XP_024304967.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  7. XM_005253624.3 → XP_005253681.1  coiled-coil domain-containing protein 92 isoform X1

    See identical proteins and their annotated locations for XP_005253681.1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  8. XM_047429567.1 → XP_047285523.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  9. XM_024449192.2 → XP_024304960.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
    Conserved Domains (2) summary
    pfam04111
    Location:45 → 167
    APG6; Autophagy protein Apg6
    pfam14916
    Location:24 → 79
    CCDC92; Coiled-coil domain of unknown function

  10. XM_047429565.1 → XP_047285521.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187590.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    109170..119347 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    123937063..123974347 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373288.1 → XP_054229263.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  2. XM_054373285.1 → XP_054229260.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  3. XM_054373284.1 → XP_054229259.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  4. XM_054373283.1 → XP_054229258.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  5. XM_054373286.1 → XP_054229261.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697

  6. XM_054373287.1 → XP_054229262.1  coiled-coil domain-containing protein 92 isoform X1

    UniProtKB/Swiss-Prot
    B3KNQ0, Q53HC0, Q9H697
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q53HC0.2 GenPept UniProtKB/Swiss-Prot:Q53HC0

Gene LinkOut

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