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    CFAP47 cilia and flagella associated protein 47 [ Homo sapiens (human) ]

    Gene ID: 286464, updated on 5-Mar-2024

    Summary

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    Official Symbol
    CFAP47provided by HGNC
    Official Full Name
    cilia and flagella associated protein 47provided by HGNC
    Primary source
    HGNC:HGNC:26708
    See related
    Ensembl:ENSG00000165164 MIM:301057; AllianceGenome:HGNC:26708
    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
    CHDC2; SPGF52; SPGFX3; CXorf22; CXorf30; CXorf59
    Summary
    While this gene is well-supported by transcript data, no functional information on its protein product is currently available. [provided by RefSeq, Dec 2009]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    Xp21.1
    Exon count:
    65
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (35919734..36385317)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (35515293..35981097)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (35937851..36403432)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chrX:35841387-35842135 Neighboring gene NFYC pseudogene 1 Neighboring gene MAGE family member B16 Neighboring gene RNA, U6 small nuclear 641, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:36216564-36217118 Neighboring gene NANOG hESC enhancer GRCh37_chrX:36233110-36233611 Neighboring gene high mobility group box 1 pseudogene 16 Neighboring gene uncharacterized LOC101928627 Neighboring gene ribosomal protein S15a pseudogene 40 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:36449855-36451054 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:36451102-36451307 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:36489007-36489587 Neighboring gene uncharacterized LOC105373155 Neighboring gene H2A.L variant histone 1Q

    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. A novel mutation in CFAP47 causes male infertility due to multiple morphological abnormalities of the sperm flagella. Liu M, et al. Front Endocrinol (Lausanne), 2023. PMID 37424856, Free PMC Article
    2. WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly. Liao HQ, et al. Mol Hum Reprod, 2022 Dec 28. PMID 36571501
    3. Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Clark MB, et al. Nat Methods, 2015 Apr. PMID 25751143
    4. Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility. Liu C, et al. Am J Hum Genet, 2021 Feb 4. PMID 33472045, Free PMC Article
    5. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Tarpey PS, et al. Nat Genet, 2009 May. PMID 19377476, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mutations in CFAP47, a previously reported MMAF causative gene, also contribute to the respiratory defects in patients with PCD.
      Title: Mutations in CFAP47, a previously reported MMAF causative gene, also contribute to the respiratory defects in patients with PCD.
    2. A novel mutation in CFAP47 causes male infertility due to multiple morphological abnormalities of the sperm flagella.
      Title: A novel mutation in CFAP47 causes male infertility due to multiple morphological abnormalities of the sperm flagella.
    3. WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly.
      Title: WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly.
    4. Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility.
      Title: Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility.
    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
    Spermatogenic failure, X-linked, 3
    MedGen: C5542347 OMIM: 301059 GeneReviews: Not available
    		Compare labs

    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

    • FLJ36601, FLJ44315, MGC34831, MGC126747, MGC126749

    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 cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sperm axoneme assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sperm axoneme assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sperm connecting piece IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cilia- and flagella-associated protein 47
    Names
    calponin homology domain-containing protein 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.

    Genomic

    1. NG_016381.2 RefSeqGene

      Range
      5001..470584
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001304548.2 → NP_001291477.1  cilia- and flagella-associated protein 47 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC233304, AK093920, AK126295, AL590065, AL606467, BC027936, BC101698, BG186336, BG190566, BG197183, BG200277, CD106515, CD686506, DV080105, DV080141, DV080142, DV080305, DV080519, DV080613, DV080632, DV080683, DV080684, DY655297
      Consensus CDS
      CCDS83464.1
      UniProtKB/Swiss-Prot
      A0A140T8X2, A6PW82, B1ARL5, Q5JRM8, Q6ZTR5, Q8N6X8, Q8N9S7
      Related
      ENSP00000367922.5, ENST00000378653.8
      Conserved Domains (1) summary
      pfam00307
      Location:1748 → 1870
      CH; Calponin homology (CH) domain

    2. NM_152632.4 → NP_689845.2  cilia- and flagella-associated protein 47 isoform 2

      See identical proteins and their annotated locations for NP_689845.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple exons in the central and 3' coding regions, and its 3' terminal exon extends beyond a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is significantly shorter, and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK126295, AL590065, BC027936, CD686506
      Consensus CDS
      CCDS14237.2
      UniProtKB/Swiss-Prot
      Q6ZTR5
      Related
      ENSP00000297866.5, ENST00000297866.9

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      35919734..36385317
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029452.2 → XP_016884941.1  cilia- and flagella-associated protein 47 isoform X1

      Conserved Domains (1) summary
      pfam00307
      Location:1748 → 1870
      CH; Calponin homology (CH) domain

    2. XM_017029453.2 → XP_016884942.1  cilia- and flagella-associated protein 47 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      35515293..35981097
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326900.1 → XP_054182875.1  cilia- and flagella-associated protein 47 isoform X1

    2. XM_054326901.1 → XP_054182876.1  cilia- and flagella-associated protein 47 isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_021289.1: Suppressed sequence

      Description
      NG_021289.1: This RefSeq was permanently suppressed because gene CXorf22 was merged into gene CFAP47.

    2. NM_173695.2: Suppressed sequence

      Description
      NM_173695.2: This RefSeq was permanently suppressed because both the transcript and CDS are partial and do not represent the full length of the gene.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZTR5.5 GenPept UniProtKB/Swiss-Prot:Q6ZTR5

    Gene LinkOut

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

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