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

Summary

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: mouse all
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Genomic context

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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Telomere Length and Male Fertility.
Title: Telomere Length and Male Fertility.
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.
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.
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.
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.
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.
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.
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.

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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
Pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 7 MedGen: C5830485 OMIM: 620365 GeneReviews: Pulmonary Fibrosis Predisposition Overview, Dyskeratosis Congenita and Related Telomere Biology Disorders	not available

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 EBI GWAS CatalogPubMed
Common variants in the trichohyalin gene are associated with straight hair in Europeans. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-8541 (e-PCR)
- UniSTS:24579

GDB:434012 (e-PCR)
- UniSTS:157204

SHGC-24075 (e-PCR)
- UniSTS:17714

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-80676 (e-PCR)
- UniSTS:102228

SHGC-59340 (e-PCR)
- UniSTS:46261

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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 more info	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)

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
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

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

163103929..163166890 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047416407.1 → XP_047272363.1 H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2
XM_047416408.1 → XP_047272364.1 H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2

RNA

XR_938799.4 RNA Sequence
XR_938798.4 RNA Sequence
XR_001741350.3 RNA Sequence
XR_001741349.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

166457003..166514759 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

D3DP28, E9PAZ2, Q96HR8
XM_054351244.1 → XP_054207219.1 H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2
XM_054351245.1 → XP_054207220.1 H/ACA ribonucleoprotein complex non-core subunit NAF1 isoform X2