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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
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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
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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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