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    CFAP410 cilia and flagella associated protein 410 [ Homo sapiens (human) ]

    Gene ID: 755, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CFAP410provided by HGNC
    Official Full Name
    cilia and flagella associated protein 410provided by HGNC
    Primary source
    HGNC:HGNC:1260
    See related
    Ensembl:ENSG00000160226 MIM:603191; AllianceGenome:HGNC:1260
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RDMS; SMDAX; LRRC76; YF5/A2; C21orf2
    Summary
    Four alternatively spliced transcript variants encoding four different isoforms have been found for this nuclear gene. All isoforms contain leucine-rich repeats. Three of these isoforms are mitochondrial proteins and one of them lacks the target peptide, so is not located in mitochondrion. This gene is down-regulated in Down syndrome (DS) brain, which may represent mitochondrial dysfunction in DS patients. [provided by RefSeq, Sep 2012]
    Expression
    Ubiquitous expression in kidney (RPKM 7.1), spleen (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CFAP410 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44328944..44339390, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42683001..42693484, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45748827..45759273, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18568 Neighboring gene autoimmune regulator Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45724667-45725466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45725506-45726160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45726161-45726814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45727470-45728123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13381 Neighboring gene phosphofructokinase, liver type Neighboring gene Sharpr-MPRA regulatory region 3786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45751251-45751752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45751753-45752252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13383 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:45761314-45761956 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:45761957-45762600 Neighboring gene NANOG hESC enhancer GRCh37_chr21:45763343-45763898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45765021-45765523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18572 Neighboring gene transient receptor potential cation channel subfamily M member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45790067-45790900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45797213-45797712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45797713-45798214 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45798708-45798913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45821987-45822910 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:45825427-45826626 Neighboring gene TRPM2 antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45846369-45847280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45847281-45848192 Neighboring gene Z6 small nucleolar RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45857057-45857556

    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. The C-terminus of CFAP410 forms a tetrameric helical bundle that is essential for its localization to the basal body. Stadler A, et al. Open Biol, 2024 Sep. PMID 39255848, Free PMC Article
    2. Characterization of a novel gene, C21orf2, on human chromosome 21q22.3 and its exclusion as the APECED gene by mutation analysis. Scott HS, et al. Genomics, 1998 Jan 1. PMID 9465297
    3. Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain: challenging the gene dosage effect hypothesis (Part III). Cheon MS, et al. Amino Acids, 2003. PMID 12624744
    4. A homozygous in-frame duplication within the LRRCT consensus sequence of CFAP410 causes cone-rod dystrophy, macular staphyloma and short stature. Chiu N, et al. Ophthalmic Genet, 2022 Jun. PMID 34915818, Free PMC Article
    5. Homozygous variant in C21orf2 in a case of Jeune syndrome with severe thoracic involvement: Extending the phenotypic spectrum. McInerney-Leo AM, et al. Am J Med Genet A, 2017 Jun. PMID 28422394

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The C-terminus of CFAP410 forms a tetrameric helical bundle that is essential for its localization to the basal body.
      Title: The C-terminus of CFAP410 forms a tetrameric helical bundle that is essential for its localization to the basal body.
    2. ALS-associated C21ORF2 variant disrupts DNA damage repair, mitochondrial metabolism, neuronal excitability and NEK1 levels in human motor neurons.
      Title: ALS-associated C21ORF2 variant disrupts DNA damage repair, mitochondrial metabolism, neuronal excitability and NEK1 levels in human motor neurons.
    3. Functional characterization of C21ORF2 association with the NEK1 kinase mutated in human in diseases.
      Title: Functional characterization of C21ORF2 association with the NEK1 kinase mutated in human in diseases.
    4. Identification of a homozygous C21orf2 mutation in this case emphasizes the value of exome sequencing for simultaneously screening known genes and identifying novel genes.the severity of thoracic restriction in this case adds to the phenotypic spectrum attributable to C21orf2 mutations.
      Title: Homozygous variant in C21orf2 in a case of Jeune syndrome with severe thoracic involvement: Extending the phenotypic spectrum.
    5. Mutation in C21ORF2 gene is associated with amyotrophic lateral sclerosis.
      Title: Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis.
    6. reduced levels of functional C21orf2 induced photoreceptor degradation through abnormal cilia formation, leading to arRP or arCRD in the retina.
      Title: Identification of Novel Mutations in the LRR-Cap Domain of C21orf2 in Japanese Patients With Retinitis Pigmentosa and Cone-Rod Dystrophy.
    7. Analysis of patients without C21orf2 mutation indicated genetic heterogeneity of axial SMD. Functional data in chondrocyte suggest C21orf2 is implicated in cartilage differentiation
      Title: Axial Spondylometaphyseal Dysplasia Is Caused by C21orf2 Mutations.
    8. C21ORF2 functions in the same pathway as NEK1 in DNA damage repair.
      Title: The NEK1 interactor, C21ORF2, is required for efficient DNA damage repair.
    9. This retinal dystrophy phenotype is caused by recessive mutations in C21orf2 and can be considered a retinal ciliopathy as C21orf2 encodes a protein that localises to photoreceptor ciliary structures.
      Title: C21orf2 is mutated in recessive early-onset retinal dystrophy with macular staphyloma and encodes a protein that localises to the photoreceptor primary cilium.
    10. Downregulated protein level of C21orf2 in adult brain of patients with Down syndrome (DS) in contrast to Alzheimer's disease indicates that it can be considered specific for changes in DS.
      Title: Reduction of chromatin assembly factor 1 p60 and C21orf2 protein, encoded on chromosome 21, in Down syndrome brain.
    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
    Axial spondylometaphyseal dysplasia
    MedGen: C1865695 OMIM: 602271 GeneReviews: Not available
    		Compare labs
    Retinal dystrophy with or without macular staphyloma
    MedGen: C4479651 OMIM: 617547 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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • AP001062.8

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell shape IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in photoreceptor connecting cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in photoreceptor outer segment IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cilia- and flagella-associated protein 410; nuclear encoded mitochondrial protein C21orf2
    Names
    C21orf-HUMF09G8.5
    leucine rich repeat containing 76
    leucine-rich repeat-containing protein 76
    protein C21orf2

    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_032952.1 RefSeqGene

      Range
      5013..15459
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271440.2 → NP_001258369.1  nuclear encoded mitochondrial protein C21orf2 isoform 2

      See identical proteins and their annotated locations for NP_001258369.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2, also known as YF5) lacks an internal aa, compared to isoform 1.
      Source sequence(s)
      BM761336, U84569, Y11392
      Consensus CDS
      CCDS59445.1
      Related
      ENSP00000317302.7, ENST00000325223.7
      Conserved Domains (4) summary
      smart00446
      Location:104 → 122
      LRRcap; occurring C-terminal to leucine-rich repeats
      sd00035
      Location:42 → 63
      LRR_NTF; leucine-rich repeat [structural motif]
      pfam12799
      Location:40 → 80
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:19 → 74
      LRR_8; Leucine rich repeat

    2. NM_001271441.2 → NP_001258370.1  nuclear encoded mitochondrial protein C21orf2 isoform 3

      See identical proteins and their annotated locations for NP_001258370.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (3) has an additional segment in the C-terminal region, compared to isoform 1.
      Source sequence(s)
      BC031300, Y11392
      Consensus CDS
      CCDS59444.1
      UniProtKB/Swiss-Prot
      O43822
      Related
      ENSP00000381047.3, ENST00000397956.7
      Conserved Domains (4) summary
      smart00446
      Location:104 → 122
      LRRcap; occurring C-terminal to leucine-rich repeats
      sd00035
      Location:42 → 63
      LRR_NTF; leucine-rich repeat [structural motif]
      pfam12799
      Location:40 → 80
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:19 → 74
      LRR_8; Leucine rich repeat

    3. NM_001271442.1 → NP_001258371.1  cilia- and flagella-associated protein 410 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate 5' exon and an additional exon in the 5' region, which cause translation initiation at a downstream AUG, compared to variant 1. The resulting isoform (4, also known as A2) is shorter and lacks a mitochondrial targeting peptide, compared to isoform 1.
      Source sequence(s)
      AP001062, BC031300, U84570, Y11392
      Conserved Domains (3) summary
      smart00446
      Location:63 → 81
      LRRcap; occurring C-terminal to leucine-rich repeats
      sd00035
      Location:23 → 46
      LRR_NTF; leucine-rich repeat [structural motif]
      pfam12799
      Location:2 → 39
      LRR_4; Leucine Rich repeats (2 copies)

    4. NM_004928.3 → NP_004919.1  nuclear encoded mitochondrial protein C21orf2 isoform 1

      See identical proteins and their annotated locations for NP_004919.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes a mitochondrial protein (isoform 1).
      Source sequence(s)
      BC072012, BM761336, Y11392
      Consensus CDS
      CCDS13709.1
      UniProtKB/Swiss-Prot
      A8MPS9, O14993, O43822, Q8N5X6, Q99837, Q99838
      Related
      ENSP00000344566.4, ENST00000339818.9
      Conserved Domains (4) summary
      smart00446
      Location:104 → 122
      LRRcap; occurring C-terminal to leucine-rich repeats
      sd00035
      Location:42 → 63
      LRR_NTF; leucine-rich repeat [structural motif]
      pfam12799
      Location:40 → 80
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:19 → 74
      LRR_8; Leucine rich repeat

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      44328944..44339390 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440986.1 → XP_047296942.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

    2. XM_047440982.1 → XP_047296938.1  nuclear encoded mitochondrial protein C21orf2 isoform X3

    3. XM_047440981.1 → XP_047296937.1  nuclear encoded mitochondrial protein C21orf2 isoform X2

    4. XM_047440980.1 → XP_047296936.1  nuclear encoded mitochondrial protein C21orf2 isoform X1

    5. XM_047440983.1 → XP_047296939.1  nuclear encoded mitochondrial protein C21orf2 isoform X5

    6. XM_006724051.4 → XP_006724114.1  nuclear encoded mitochondrial protein C21orf2 isoform X4

      Conserved Domains (3) summary
      smart00446
      Location:129 → 147
      LRRcap; occurring C-terminal to leucine-rich repeats
      sd00035
      Location:89 → 112
      LRR_NTF; leucine-rich repeat [structural motif]
      pfam12799
      Location:87 → 123
      LRR_4; Leucine Rich repeats (2 copies)

    7. XM_047440987.1 → XP_047296943.1  nuclear encoded mitochondrial protein C21orf2 isoform X7

    8. XM_047440984.1 → XP_047296940.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

    9. XM_047440985.1 → XP_047296941.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      42683001..42693484 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324849.1 → XP_054180824.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

    2. XM_054324844.1 → XP_054180819.1  nuclear encoded mitochondrial protein C21orf2 isoform X3

    3. XM_054324843.1 → XP_054180818.1  nuclear encoded mitochondrial protein C21orf2 isoform X2

    4. XM_054324842.1 → XP_054180817.1  nuclear encoded mitochondrial protein C21orf2 isoform X1

    5. XM_054324846.1 → XP_054180821.1  nuclear encoded mitochondrial protein C21orf2 isoform X5

    6. XM_054324845.1 → XP_054180820.1  nuclear encoded mitochondrial protein C21orf2 isoform X4

    7. XM_054324850.1 → XP_054180825.1  nuclear encoded mitochondrial protein C21orf2 isoform X7

    8. XM_054324847.1 → XP_054180822.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

    9. XM_054324848.1 → XP_054180823.1  nuclear encoded mitochondrial protein C21orf2 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43822.1 GenPept UniProtKB/Swiss-Prot:O43822

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