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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
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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

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