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    CDAN1 codanin 1 [ Homo sapiens (human) ]

    Gene ID: 146059, updated on 5-Mar-2024

    Summary

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    Official Symbol
    CDAN1provided by HGNC
    Official Full Name
    codanin 1provided by HGNC
    Primary source
    HGNC:HGNC:1713
    See related
    Ensembl:ENSG00000140326 MIM:607465; AllianceGenome:HGNC:1713
    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
    DLT; CDA1; CDAI; CDAN1A; PRO1295
    Summary
    This gene encodes a protein that appears to play a role in nuclear envelope integrity, possibly related to microtubule attachments. Mutations in this gene cause congenital dyserythropoietic anemia type I, a disease resulting in morphological and functional abnormalities of erythropoiesis. [provided by RefSeq, Jul 2009]
    Expression
    Ubiquitous expression in ovary (RPKM 7.8), testis (RPKM 5.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q15.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (42723544..42737128, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (40530676..40544263, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (43015742..43029326, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9306 Neighboring gene eukaryotic translation initiation factor 4E binding protein 2 pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:42892996-42893612 Neighboring gene StAR related lipid transfer domain containing 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9307 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42911331-42912096 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42912097-42912861 Neighboring gene NANOG hESC enhancer GRCh37_chr15:42957961-42958533 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43022854-43023381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6378 Neighboring gene TTBK2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:43051195-43051957 Neighboring gene tau tubulin kinase 2 Neighboring gene Sharpr-MPRA regulatory region 5629 Neighboring gene keratin 8 pseudogene 50

    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. [Whole exome sequencing analysis of compound heterozygous variants of CDAN1 gene in a Chinese family with non-immune hydrops fetalis]. Wang Y, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2021 Dec 20. PMID 35012925, Free PMC Article
    2. Codanin-1 mutations engineered in human erythroid cells demonstrate role of CDAN1 in terminal erythroid maturation. Murphy ZC, et al. Exp Hematol, 2020 Nov. PMID 33075436, Free PMC Article
    3. Fetal-onset congenital dyserythropoietic anemia type 1 due to CDAN1 mutations presenting as hydrops fetalis. Liu S, et al. Pediatr Hematol Oncol, 2018 Oct-Nov. PMID 30786798
    4. Codanin-1, the protein encoded by the gene mutated in congenital dyserythropoietic anemia type I (CDAN1), is cell cycle-regulated. Noy-Lotan S, et al. Haematologica, 2009 May. PMID 19336738, Free PMC Article
    5. Congenital dyserythropoietic anemia in a Chinese family with a mutation of the CDAN1-gene. Ru YX, et al. Ann Hematol, 2008 Sep. PMID 18575862

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Discovering a novel pathogenic CDAN1 variant using exome sequencing and bioinformatics analysis.
      Title: Discovering a novel pathogenic CDAN1 variant using exome sequencing and bioinformatics analysis.
    2. [Whole exome sequencing analysis of compound heterozygous variants of CDAN1 gene in a Chinese family with non-immune hydrops fetalis].
      Title: [Whole exome sequencing analysis of compound heterozygous variants of CDAN1 gene in a Chinese family with non-immune hydrops fetalis].
    3. Genetic and functional insights into CDA-I prevalence and pathogenesis.
      Title: Genetic and functional insights into CDA-I prevalence and pathogenesis.
    4. Codanin-1 mutations engineered in human erythroid cells demonstrate role of CDAN1 in terminal erythroid maturation.
      Title: Codanin-1 mutations engineered in human erythroid cells demonstrate role of CDAN1 in terminal erythroid maturation.
    5. Characterization of the interactions between Codanin-1 and C15Orf41, two proteins implicated in congenital dyserythropoietic anemia type I disease.
      Title: Characterization of the interactions between Codanin-1 and C15Orf41, two proteins implicated in congenital dyserythropoietic anemia type I disease.
    6. Fetal-onset congenital dyserythropoietic anemia type 1 due to CDAN1 mutations presenting as hydrops fetalis.
      Title: Fetal-onset congenital dyserythropoietic anemia type 1 due to CDAN1 mutations presenting as hydrops fetalis.
    7. Mutation in CDAN1 gene is associated with congenital dyserythropoietic anemia.
      Title: Identification of CDAN1, C15ORF41 and SEC23B mutations in Chinese patients affected by congenital dyserythropoietic anemia.
    8. The missense substitution in CDAN1, C15ORF41, encodes a novel restriction endonuclease in congenital dyserythropoietic anemia type I.
      Title: Homozygous mutations in a predicted endonuclease are a novel cause of congenital dyserythropoietic anemia type I.
    9. The proband with congenital dyserythropoietic anemia Iota in the first family was a compound heterozygote of CDAN1 with mutation IVS-12+2T>C and c. 3389C>T.
      Title: Congenital dyserythropoietic anemia in China: a case report from two families and a review.
    10. The authors propose that Codanin-1 acts as a negative regulator of Asf1 function in chromatin assembly.
      Title: Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within chromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_positive_effect chromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in import into nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endomembrane system IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    codanin-1
    Names
    congenital dyserythropoietic anemia, type I
    discs lost homolog

    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.

    Genomic

    1. NG_012491.1 RefSeqGene

      Range
      5092..18676
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1164

    mRNA and Protein(s)

    1. NM_138477.4 → NP_612486.2  codanin-1

      See identical proteins and their annotated locations for NP_612486.2

      Status: REVIEWED

      Source sequence(s)
      AC090510, AF525398, BC001092, BC052568, BE884119, HY112237
      Consensus CDS
      CCDS32209.1
      UniProtKB/Swiss-Prot
      Q6NYD0, Q7Z7L5, Q8IWY9, Q969N3
      Related
      ENSP00000348564.3, ENST00000356231.4
      Conserved Domains (1) summary
      pfam15296
      Location:784 → 899
      Codanin-1_C; Codanin-1 C-terminus

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      42723544..42737128 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005254176.6 → XP_005254233.1  codanin-1 isoform X3

      Conserved Domains (1) summary
      pfam15296
      Location:785 → 900
      Codanin-1_C; Codanin-1 C-terminus

    2. XM_011521271.3 → XP_011519573.1  codanin-1 isoform X2

      Conserved Domains (1) summary
      pfam15296
      Location:792 → 907
      Codanin-1_C; Codanin-1 C-terminus

    3. XM_011521270.3 → XP_011519572.1  codanin-1 isoform X1

      Conserved Domains (1) summary
      pfam15296
      Location:793 → 908
      Codanin-1_C; Codanin-1 C-terminus

    4. XM_047432195.1 → XP_047288151.1  codanin-1 isoform X6

    5. XM_011521274.3 → XP_011519576.1  codanin-1 isoform X6

      See identical proteins and their annotated locations for XP_011519576.1

      Conserved Domains (1) summary
      pfam15296
      Location:448 → 563
      Codanin-1_C; Codanin-1 C-terminus

    6. XM_047432193.1 → XP_047288149.1  codanin-1 isoform X4

    7. XM_047432194.1 → XP_047288150.1  codanin-1 isoform X5

    RNA

    1. XR_931757.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      40530676..40544263 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377364.1 → XP_054233339.1  codanin-1 isoform X2

    2. XM_054377363.1 → XP_054233338.1  codanin-1 isoform X1

    3. XM_054377365.1 → XP_054233340.1  codanin-1 isoform X3

    4. XM_054377368.1 → XP_054233343.1  codanin-1 isoform X6

    5. XM_054377369.1 → XP_054233344.1  codanin-1 isoform X6

    6. XM_054377366.1 → XP_054233341.1  codanin-1 isoform X4

    7. XM_054377367.1 → XP_054233342.1  codanin-1 isoform X5

    RNA

    1. XR_008488925.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWY9.4 GenPept UniProtKB/Swiss-Prot:Q8IWY9

    Gene LinkOut

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

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