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    CFAP54 cilia and flagella associated protein 54 [ Homo sapiens (human) ]

    Gene ID: 144535, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CFAP54provided by HGNC
    Official Full Name
    cilia and flagella associated protein 54provided by HGNC
    Primary source
    HGNC:HGNC:26456
    See related
    Ensembl:ENSG00000188596 AllianceGenome:HGNC:26456
    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
    C12orf55; C12orf63
    Summary
    Predicted to be involved in cilium assembly; cilium movement involved in cell motility; and spermatogenesis. Predicted to act upstream of or within epithelial cilium movement involved in extracellular fluid movement; establishment of localization in cell; and sperm flagellum assembly. Predicted to be located in axoneme. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 1.4), lung (RPKM 0.4) and 3 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CFAP54 in Genome Data Viewer
    Location:
    12q23.1
    Exon count:
    69
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (96489577..96875555)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (96463738..96849324)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (96883355..97269333)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96709352-96709984 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96709985-96710615 Neighboring gene RNA, U4 small nuclear 24, pseudogene Neighboring gene cyclin dependent kinase 17 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6830 Neighboring gene RN7SK pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6832 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:96878154-96878351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6831 Neighboring gene Sharpr-MPRA regulatory region 2123 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:96894427-96895626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4746 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:96915910-96916410 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:96916411-96916911 Neighboring gene MPRA-validated peak1903 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:97122708-97123302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6837 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 33 Neighboring gene NEDD1 gamma-tubulin ring complex targeting factor

    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. Lack of CFAP54 causes primary ciliary dyskinesia in a mouse model and human patients. Zhao X, et al. Front Med, 2023 Dec. PMID 37725231
    2. Biallelic mutations in CFAP54 cause male infertility with severe MMAF and NOA. Tian S, et al. J Med Genet, 2023 Aug. PMID 36593121
    3. CFAP54 is required for proper ciliary motility and assembly of the central pair apparatus in mice. McKenzie CW, et al. Mol Biol Cell, 2015 Sep 15. PMID 26224312, Free PMC Article
    4. Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women. Croteau-Chonka DC, et al. Obesity (Silver Spring), 2011 May. PMID 20966902, Free PMC Article
    5. The finished DNA sequence of human chromosome 12. Scherer SE, et al. Nature, 2006 Mar 16. PMID 16541075

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lack of CFAP54 causes primary ciliary dyskinesia in a mouse model and human patients.
      Title: Lack of CFAP54 causes primary ciliary dyskinesia in a mouse model and human patients.
    2. Biallelic mutations in CFAP54 cause male infertility with severe MMAF and NOA.
      Title: Biallelic mutations in CFAP54 cause male infertility with severe MMAF and NOA.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ31514, FLJ34470, FLJ44112, MGC183096, MGC184264

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cerebrospinal fluid circulation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cilium movement involved in cell motility ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mucociliary clearance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sperm flagellum assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in axoneme ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cilia- and flagella-associated protein 54
    Names
    cilia and flagella associated 54

    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_001306084.2 → NP_001293013.1  cilia- and flagella-associated protein 54 isoform 1

      See identical proteins and their annotated locations for NP_001293013.1

      Status: VALIDATED

      Source sequence(s)
      AC007564, AC008118, AK056076, AK091789, AK126100, BC041426, BX281772, BX644506, CF887548, CF891050, DB225896, DN831445, DV080224, DV080428, DV080725, EG328110
      Consensus CDS
      CCDS76588.1
      UniProtKB/Swiss-Prot
      E9PJL5, Q6ZTY8, Q96N23
      Related
      ENSP00000431759.5, ENST00000524981.9
      Conserved Domains (1) summary
      pfam14858
      Location:99 → 638
      DUF4486; Domain of unknown function (DUF4486)

    2. NM_001367885.1 → NP_001354814.1  cilia- and flagella-associated protein 54 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC007513, AC007564, AC008118

    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
      96489577..96875555
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      96463738..96849324
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_198520.2: Suppressed sequence

      Description
      NM_198520.2: This RefSeq was permanently suppressed because the CDS was partial and there is insufficient evidence to predict its full-length nature.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96N23.3 GenPept UniProtKB/Swiss-Prot:Q96N23

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials