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    CLXN calaxin [ Homo sapiens (human) ]

    Gene ID: 79645, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CLXNprovided by HGNC
    Official Full Name
    calaxinprovided by HGNC
    Primary source
    HGNC:HGNC:25678
    See related
    Ensembl:ENSG00000034239 MIM:619564; AllianceGenome:HGNC:25678
    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
    Also known as
    ODAD5; CILD53; EFCAB1
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in cilium movement; outer dynein arm assembly; and regulation of flagellated sperm motility. Predicted to be located in cilium. Implicated in primary ciliary dyskinesia. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 3.0), lung (RPKM 2.5) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLXN in Genome Data Viewer
    Location:
    8q11.21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (48710789..48735311, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (49088639..49113160, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (49623348..49647870, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929268 Neighboring gene uncharacterized LOC124901943 Neighboring gene long intergenic non-protein coding RNA 2847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49536704-49537208 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:49539781-49540980 Neighboring gene long intergenic non-protein coding RNA 3054 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:49549377-49550576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49558419-49558919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49608983-49609482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49647232-49647906 Neighboring gene uncharacterized LOC105375825 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:49700925-49702124 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:49711615-49712177 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49731577-49732548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49770863-49771363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:49777111-49777698 Neighboring gene snail family transcriptional repressor 2

    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. Pathogenic variants in CLXN encoding the outer dynein arm docking-associated calcium-binding protein calaxin cause primary ciliary dyskinesia. Hjeij R, et al. Genet Med, 2023 May. PMID 36727596
    2. Calaxin is required for cilia-driven determination of vertebrate laterality. Sasaki K, et al. Commun Biol, 2019. PMID 31240264, Free PMC Article
    3. Blood pressure and hypertension are associated with 7 loci in the Japanese population. Takeuchi F, et al. Circulation, 2010 Jun 1. PMID 20479155
    4. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. Aouizerat BE, et al. BMC Cardiovasc Disord, 2011 Jun 10. PMID 21658281, Free PMC Article
    5. De novo identification of mammalian ciliary motility proteins using cryo-EM. Gui M, et al. Cell, 2021 Nov 11. PMID 34715025, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pathogenic variants in CLXN encoding the outer dynein arm docking-associated calcium-binding protein calaxin cause primary ciliary dyskinesia.
      Title: Pathogenic variants in CLXN encoding the outer dynein arm docking-associated calcium-binding protein calaxin cause primary ciliary dyskinesia.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Blood pressure and hypertension are associated with 7 loci in the Japanese population.
    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
    Ciliary dyskinesia, primary, 53
    MedGen: C5882728 OMIM: 620642 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.
    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

    • FLJ11767

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cilium movement ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in outer dynein arm assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cilium movement ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of flagellated sperm motility ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    calaxin
    Names
    EF-hand calcium binding domain 1
    EF-hand calcium-binding domain-containing protein 1
    outer dynein arm docking complex subunit 5

    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_001142857.2 → NP_001136329.1  calaxin isoform b

      See identical proteins and their annotated locations for NP_001136329.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AC022915, AK299659, DB204697, DC336596
      Consensus CDS
      CCDS47853.1
      Related
      ENSP00000400873.1, ENST00000433756.1
      Conserved Domains (1) summary
      cl25352
      Location:19 → 118
      EFh_PEF; The penta-EF hand (PEF) family

    2. NM_001363973.3 → NP_001350902.1  calaxin isoform b

      Status: VALIDATED

      Source sequence(s)
      AC022915, BC025676, BP376567, CB250588, DB204697, DC414358
      Consensus CDS
      CCDS47853.1
      Related
      ENSP00000430940.1, ENST00000522254.5
      Conserved Domains (1) summary
      cl25352
      Location:19 → 118
      EFh_PEF; The penta-EF hand (PEF) family

    3. NM_001363974.2 → NP_001350903.1  calaxin isoform b

      Status: VALIDATED

      Source sequence(s)
      AC022915, AK316037, BC025676, CB250588, DB204697, DB536362, DC414358
      Consensus CDS
      CCDS47853.1
      Related
      ENSP00000430765.1, ENST00000523092.5
      Conserved Domains (1) summary
      cl25352
      Location:19 → 118
      EFh_PEF; The penta-EF hand (PEF) family

    4. NM_024593.4 → NP_078869.1  calaxin isoform a

      See identical proteins and their annotated locations for NP_078869.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC022915, BC025676, CB250588, DB204697, DB536362
      Consensus CDS
      CCDS6145.1
      UniProtKB/Swiss-Prot
      B4DSB4, E7EVN7, Q9HAE3
      Related
      ENSP00000262103.3, ENST00000262103.8
      Conserved Domains (1) summary
      cl25352
      Location:48 → 170
      EFh_PEF; The penta-EF hand (PEF) family

    RNA

    1. NR_024605.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' region, uses an alternate splice site in the central region and includes an additional splice junction in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as in variant 1, would result in nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC022915, BC025676, BP375493, CB250588, DA174619, DB204697

    2. NR_157026.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC022915, AK307101, DB204697

    3. NR_157027.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC022915, BC029586, DB204697, DC414358
      Related
      ENST00000521002.5

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      48710789..48735311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517589.2 → XP_011515891.1  calaxin isoform X1

      See identical proteins and their annotated locations for XP_011515891.1

      UniProtKB/Swiss-Prot
      B4DSB4, E7EVN7, Q9HAE3
      Conserved Domains (1) summary
      cl25352
      Location:48 → 170
      EFh_PEF; The penta-EF hand (PEF) family

    2. XM_005251303.2 → XP_005251360.1  calaxin isoform X1

      See identical proteins and their annotated locations for XP_005251360.1

      UniProtKB/Swiss-Prot
      B4DSB4, E7EVN7, Q9HAE3
      Conserved Domains (1) summary
      cl25352
      Location:48 → 170
      EFh_PEF; The penta-EF hand (PEF) family

    3. XM_011517591.3 → XP_011515893.1  calaxin isoform X2

      See identical proteins and their annotated locations for XP_011515893.1

      UniProtKB/TrEMBL
      H0YC53
      Conserved Domains (2) summary
      cd00051
      Location:9 → 68
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:40 → 113
      EF-hand_7; EF-hand domain pair

    4. XM_047422231.1 → XP_047278187.1  calaxin isoform X2

    5. XM_017013827.2 → XP_016869316.1  calaxin isoform X2

      UniProtKB/TrEMBL
      H0YC53
      Conserved Domains (2) summary
      cd00051
      Location:9 → 68
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:40 → 113
      EF-hand_7; EF-hand domain pair

    6. XM_017013828.2 → XP_016869317.1  calaxin isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      49088639..49113160 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361219.1 → XP_054217194.1  calaxin isoform X1

      UniProtKB/Swiss-Prot
      B4DSB4, E7EVN7, Q9HAE3

    2. XM_054361218.1 → XP_054217193.1  calaxin isoform X1

      UniProtKB/Swiss-Prot
      B4DSB4, E7EVN7, Q9HAE3

    3. XM_054361222.1 → XP_054217197.1  calaxin isoform X2

    4. XM_054361221.1 → XP_054217196.1  calaxin isoform X2

    5. XM_054361220.1 → XP_054217195.1  calaxin isoform X2

    6. XM_054361223.1 → XP_054217198.1  calaxin isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAE3.1 GenPept UniProtKB/Swiss-Prot:Q9HAE3

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