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

Gene ID: 92345, updated on 27-Nov-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, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 1.9), endometrium (RPKM 1.8) and 25 other tissues See more
Orthologs
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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.

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