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    NAF1 nuclear assembly factor 1 ribonucleoprotein [ Homo sapiens (human) ]

    Gene ID: 92345, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NAF1provided by HGNC
    Official Full Name
    nuclear assembly factor 1 ribonucleoproteinprovided by HGNC
    Primary source
    HGNC:HGNC:25126
    See related
    Ensembl:ENSG00000145414 MIM:617868; AllianceGenome:HGNC:25126
    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
    PFBMFT7
    Summary
    Enables identical protein binding activity and telomerase RNA binding activity. Involved in ribosome biogenesis; telomerase RNA stabilization; and telomerase holoenzyme complex assembly. Acts upstream of or within telomerase RNA localization to Cajal body. Located in cytoplasm and nucleoplasm. Part of sno(s)RNA-containing ribonucleoprotein complex. Implicated in melanoma. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 1.9), endometrium (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NAF1 in Genome Data Viewer
    Location:
    4q32.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (163103929..163166890, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (166457003..166514759, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (164047860..164088042, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377516 Neighboring gene NANOG hESC enhancer GRCh37_chr4:163636456-163637075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22096 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75656 Neighboring gene uncharacterized LOC101928081 Neighboring gene microRNA 4454 Neighboring gene Sharpr-MPRA regulatory region 7208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:164087187-164088054 Neighboring gene uncharacterized LOC105377517 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75696 Neighboring gene mitochondrial ribosomal protein S5 pseudogene

    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. First clinical description of a pedigree with complete NAF1 deletion. Galtier J, et al. Leuk Lymphoma, 2023 Feb. PMID 36416722
    2. Association between genetic variants and esophageal cancer risk. Yue C, et al. Oncotarget, 2017 Jul 18. PMID 28454086, Free PMC Article
    3. Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters. Darash-Yahana M, et al. Proc Natl Acad Sci U S A, 2016 Sep 27. PMID 27621439, Free PMC Article
    4. Colorectal cancer-associated SNP rs17042479 is involved in the regulation of NAF1 promoter activity. Olsson JB, et al. PLoS One, 2022. PMID 36067202, Free PMC Article
    5. NAF1 rs4691896 Is Significantly Associated with Coal Workers' Pneumoconiosis in a Chinese Han Population: A Case-Control Study. Yuan B, et al. Med Sci Monit, 2020 Apr 25. PMID 32333749, Free PMC Article

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Relationship between common telomere length-related genetic variations, telomere length, and risk of antituberculosis drug-induced hepatotoxicity in Chinese Han population: As assessed for causality using the updated Roussel Uclaf Causality Assessment Method.
      Title: Relationship between common telomere length-related genetic variations, telomere length, and risk of antituberculosis drug-induced hepatotoxicity in Chinese Han population: As assessed for causality using the updated Roussel Uclaf Causality Assessment Method.
    2. Colorectal cancer-associated SNP rs17042479 is involved in the regulation of NAF1 promoter activity.
      Title: Colorectal cancer-associated SNP rs17042479 is involved in the regulation of NAF1 promoter activity.
    3. Telomere Length and Male Fertility.
      Title: Telomere Length and Male Fertility.
    4. NAF1 rs4691896 Is Significantly Associated with Coal Workers' Pneumoconiosis in a Chinese Han Population: A Case-Control Study.
      Title: NAF1 rs4691896 Is Significantly Associated with Coal Workers' Pneumoconiosis in a Chinese Han Population: A Case-Control Study.
    5. Study presents a novel genome-wide candidate for ductal adenocarcinoma (PDAC) - TERT-rs2736100 and a completely new signal for PDAC in NAF1-rs7675998 that approaches the genome-wide threshold. In addition, study found a strong association between the teloscore and risk of pancreatic cancer, suggesting that telomeres are a potential risk factor for pancreatic cancer.
      Title: Genetic determinants of telomere length and risk of pancreatic cancer: A PANDoRA study.
    6. the current study has identified that rs2320615 in the NAF1 was associated with the risk of esophageal cancer in the Han Chinese population.
      Title: Association between genetic variants and esophageal cancer risk.
    7. These findings point to a key role for the unique 3Cys-1His cluster of NAF-1 in promoting rapid tumor growth through cellular resistance to oxidative stress.
      Title: Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters.
    8. Data indicate that disease in NAF1 mutation carriers is telomere-mediated; they show that NAF1 haploinsufficiency selectively disturbs telomere length homeostasis by decreasing the levels of telomerase RNA while sparing rRNA pseudouridylation.
      Title: Loss-of-function mutations in the RNA biogenesis factor NAF1 predispose to pulmonary fibrosis-emphysema.
    9. Telomere length is associated with Esophageal squamous cell carcinoma risk in a U-shaped pattern and demonstrates that TL-SNPs may not be important in carcinogenesis in Chinese population.
      Title: U-shaped association between telomere length and esophageal squamous cell carcinoma risk: a case-control study in Chinese population.
    10. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Analysis of copy number variation in 8,842 Korean individuals reveals 39 genes associated with hepatic biomarkers AST and ALT.
    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2024-08-20)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2024-08-20)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A novel colorectal cancer risk locus at 4q32.2 identified from an international genome-wide association study.
    EBI GWAS Catalog
    Common variants in the trichohyalin gene are associated with straight hair in Europeans.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables telomerase RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in box H/ACA snoRNP assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in box H/ACA snoRNP assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in box H/ACA snoRNP assembly TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of positive regulation of telomere maintenance via telomerase IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of telomere maintenance via telomerase TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of positive regulation of telomere maintenance via telomere lengthening IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosome biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosome biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in snoRNA guided rRNA pseudouridine synthesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within telomerase RNA localization to Cajal body HMP PubMed 
    involved_in telomerase RNA stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in telomerase holoenzyme complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of sno(s)RNA-containing ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of sno(s)RNA-containing ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    H/ACA ribonucleoprotein complex non-core subunit NAF1
    Names
    nuclear assembly factor 1 homolog

    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_001128931.2 → NP_001122403.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate exon in the 3' terminus, compared to variant 1, which results in a protein (isoform B) with a shorter and distinct C-terminus, compared to isoform A.
      Source sequence(s)
      AK308601
      Consensus CDS
      CCDS47159.1
      UniProtKB/Swiss-Prot
      Q96HR8
      Related
      ENSP00000408963.2, ENST00000422287.6
      Conserved Domains (1) summary
      pfam04410
      Location:180 → 328
      Gar1; Gar1/Naf1 RNA binding region

    2. NM_138386.3 → NP_612395.2  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform a

      See identical proteins and their annotated locations for NP_612395.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (A).
      Source sequence(s)
      AK308601, BC008207
      Consensus CDS
      CCDS3803.1
      UniProtKB/Swiss-Prot
      D3DP28, E9PAZ2, Q96HR8
      Related
      ENSP00000274054.2, ENST00000274054.3
      Conserved Domains (1) summary
      pfam04410
      Location:180 → 328
      Gar1; Gar1/Naf1 RNA binding region

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      163103929..163166890 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011532410.4 → XP_011530712.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X1

      See identical proteins and their annotated locations for XP_011530712.1

      UniProtKB/Swiss-Prot
      D3DP28, E9PAZ2, Q96HR8
      Conserved Domains (1) summary
      pfam04410
      Location:180 → 328
      Gar1; Gar1/Naf1 RNA binding region

    2. XM_047416407.1 → XP_047272363.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2

    3. XM_047416408.1 → XP_047272364.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2

    RNA

    1. XR_938799.4 RNA Sequence

    2. XR_938798.4 RNA Sequence

    3. XR_001741350.3 RNA Sequence

    4. XR_001741349.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      166457003..166514759 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351243.1 → XP_054207218.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X1

      UniProtKB/Swiss-Prot
      D3DP28, E9PAZ2, Q96HR8

    2. XM_054351244.1 → XP_054207219.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2

    3. XM_054351245.1 → XP_054207220.1  H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2

    RNA

    1. XR_008487060.1 RNA Sequence

    2. XR_008487056.1 RNA Sequence

    3. XR_008487054.1 RNA Sequence

    4. XR_008487055.1 RNA Sequence

    5. XR_008487059.1 RNA Sequence

    6. XR_008487057.1 RNA Sequence

    7. XR_008487058.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HR8.2 GenPept UniProtKB/Swiss-Prot:Q96HR8

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
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