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    NARS2 asparaginyl-tRNA synthetase 2, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 79731, updated on 3-Apr-2024

    Summary

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    Official Symbol
    NARS2provided by HGNC
    Official Full Name
    asparaginyl-tRNA synthetase 2, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:26274
    See related
    Ensembl:ENSG00000137513 MIM:612803; AllianceGenome:HGNC:26274
    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
    SLM5; asnRS; DFNB94
    Summary
    This gene encodes a putative member of the class II family of aminoacyl-tRNA synthetases. These enzymes play a critical role in protein biosynthesis by charging tRNAs with their cognate amino acids. This protein is encoded by the nuclear genome but is likely to be imported to the mitochondrion where it is thought to catalyze the ligation of asparagine to tRNA molecules. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency 24 (COXPD24). [provided by RefSeq, Mar 2015]
    Expression
    Ubiquitous expression in kidney (RPKM 4.7), thyroid (RPKM 3.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    11q14.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (78435968..78574864, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (78369261..78508161, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (78147014..78285909, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene GRB2 associated binding protein 2 Neighboring gene zinc finger protein 75C, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5321 Neighboring gene Sharpr-MPRA regulatory region 74 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:78127852-78128606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5322 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:78137590-78137755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5323 Neighboring gene long intergenic non-protein coding RNA 2728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5325 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:78178372-78178539 Neighboring gene uncharacterized LOC105369403 Neighboring gene Sharpr-MPRA regulatory region 10369 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:78219454-78219651 Neighboring gene uncharacterized LOC101928896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5328 Neighboring gene RNA, U6 small nuclear 311, pseudogene Neighboring gene COP9 signalosome subunit 8 pseudogene 3

    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. Splicing variants in NARS2 are associated with milder phenotypes and intra-familial variability. Ait-El-Mkadem Saadi S, et al. Eur J Med Genet, 2022 Dec. PMID 36252909
    2. The phenotypic variability and natural history of NARS2 associated disease. Sofou K, et al. Eur J Paediatr Neurol, 2021 Mar. PMID 33596490
    3. Inborn errors of metabolism in a cohort of pregnancies with non-immune hydrops fetalis: a single center experience. Bruwer Z, et al. J Perinat Med, 2018 Nov 27. PMID 28822227
    4. Two siblings with homozygous pathogenic splice-site variant in mitochondrial asparaginyl-tRNA synthetase (NARS2). Vanlander AV, et al. Hum Mutat, 2015 Feb. PMID 25385316
    5. Alzheimer's Disease Risk Variant rs2373115 Regulates GAB2 and NARS2 Expression in Human Brain Tissues. Liu G, et al. J Mol Neurosci, 2018 Sep. PMID 30088171

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel NARS2 variants in a patient with early-onset status epilepticus: case study and literature review.
      Title: Novel NARS2 variants in a patient with early-onset status epilepticus: case study and literature review.
    2. Splicing variants in NARS2 are associated with milder phenotypes and intra-familial variability.
      Title: Splicing variants in NARS2 are associated with milder phenotypes and intra-familial variability.
    3. The phenotypic variability and natural history of NARS2 associated disease.
      Title: The phenotypic variability and natural history of NARS2 associated disease.
    4. The AARS2 variant accounts for a significant number of cases with Non-immune Hydrops Fetalis in the cohort of pregnancies Omani patients.
      Title: Inborn errors of metabolism in a cohort of pregnancies with non-immune hydrops fetalis: a single center experience.
    5. NARS2 expression is reduced in AD brain tissue compared with controls. NARS2 expression in brain is associated with GAB2 AD risk variant rs2373115.
      Title: Alzheimer's Disease Risk Variant rs2373115 Regulates GAB2 and NARS2 Expression in Human Brain Tissues.
    6. The individuals with PARS2 and NARS2 mutations demonstrate similar neurological features as those previously reported, with diversity in clinical presentation such as hearing loss and seizure type.
      Title: PARS2 and NARS2 mutations in infantile-onset neurodegenerative disorder.
    7. Genome-wide SNP analysis identified multiple suggestive novel loci and two of them were also significant in gene-based analysis (CCDC85C and NARS2) that survived after controlling for false-discovery rate at 0.05.
      Title: Genetic Determinants of Survival in Patientswith Alzheimer’s Disease.
    8. In these cells we show that a decrease in oxygen consumption rates (OCR) and electron transport chain (ETC) activity can be rescued by overexpression of wild type NARS2
      Title: Mutations of human NARS2, encoding the mitochondrial asparaginyl-tRNA synthetase, cause nonsyndromic deafness and Leigh syndrome.
    9. A variant in NARS2 results in a combined OXPHOS complex deficiency involving complex I and IV, making NARS2 a new member of disease-associated aminoacyl-tRNA synthetases.
      Title: Two siblings with homozygous pathogenic splice-site variant in mitochondrial asparaginyl-tRNA synthetase (NARS2).
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    Combined oxidative phosphorylation defect type 24
    MedGen: C4015643 OMIM: 616239 GeneReviews: Not available
    		Compare labs
    Hearing loss, autosomal recessive 94
    MedGen: C5193096 OMIM: 618434 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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    matrix gag HIV-1 MA is identified to have a physical interaction with asparaginyl-tRNA synthetase 2, mitochondrial (NARS2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ23441

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables asparagine-tRNA ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables asparagine-tRNA ligase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in asparaginyl-tRNA aminoacylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in asparaginyl-tRNA aminoacylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrial matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    asparaginyl-tRNA synthetase; probable asparagine--tRNA ligase, mitochondrial
    Names
    asparagine tRNA ligase 2, mitochondrial (putative)
    asparagine--tRNA ligase, mitochondrial
    asparaginyl-tRNA synthetase 2, mitochondrial (putative)
    deafness, autosomal recessive 94
    probable asparaginyl-tRNA synthetase, mitochondrial
    NP_001230180.1
    NP_078954.4
    XP_011543555.1
    XP_016873791.1
    XP_047283547.1
    XP_047283548.1
    XP_047283549.1
    XP_047283550.1
    XP_047283551.1
    XP_054225925.1
    XP_054225926.1
    XP_054225927.1
    XP_054225928.1
    XP_054225929.1
    XP_054225930.1

    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_042046.1 RefSeqGene

      Range
      5001..143897
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243251.2 → NP_001230180.1  asparaginyl-tRNA synthetase isoform 2

      See identical proteins and their annotated locations for NP_001230180.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream, in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK027094, AK056980, AP003110, AW968557, BP196275, DB565980
      Consensus CDS
      CCDS58164.1
      UniProtKB/TrEMBL
      B2RD66, Q9H5H1
      Related
      ENSP00000511817.1, ENST00000695342.1
      Conserved Domains (1) summary
      cl00268
      Location:1 → 246
      class_II_aaRS-like_core; Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches ...

    2. NM_001425299.1 → NP_001412228.1  asparaginyl-tRNA synthetase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    3. NM_001425300.1 → NP_001412229.1  asparaginyl-tRNA synthetase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    4. NM_001425301.1 → NP_001412230.1  asparaginyl-tRNA synthetase isoform 5

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    5. NM_001425302.1 → NP_001412231.1  asparaginyl-tRNA synthetase isoform 6

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    6. NM_001425303.1 → NP_001412232.1  asparaginyl-tRNA synthetase isoform 7

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110
      UniProtKB/TrEMBL
      A0A8Q3SHL5

    7. NM_001425304.1 → NP_001412233.1  asparaginyl-tRNA synthetase isoform 8

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    8. NM_001425305.1 → NP_001412234.1  asparaginyl-tRNA synthetase isoform 9

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110
      UniProtKB/TrEMBL
      A0A8Q3WKF4

    9. NM_001425306.1 → NP_001412235.1  asparaginyl-tRNA synthetase isoform 10

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    10. NM_001425307.1 → NP_001412236.1  asparaginyl-tRNA synthetase isoform 11

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    11. NM_001425308.1 → NP_001412237.1  asparaginyl-tRNA synthetase isoform 12

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    12. NM_001425309.1 → NP_001412238.1  asparaginyl-tRNA synthetase isoform 13

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    13. NM_001425310.1 → NP_001412239.1  asparaginyl-tRNA synthetase isoform 14

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    14. NM_001425311.1 → NP_001412240.1  asparaginyl-tRNA synthetase isoform 15

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    15. NM_001425312.1 → NP_001412241.1  asparaginyl-tRNA synthetase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    16. NM_001425313.1 → NP_001412242.1  asparaginyl-tRNA synthetase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    17. NM_001425314.1 → NP_001412243.1  asparaginyl-tRNA synthetase isoform 16

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110
      UniProtKB/TrEMBL
      H0YE96

    18. NM_024678.6 → NP_078954.4  asparaginyl-tRNA synthetase isoform 1 precursor

      See identical proteins and their annotated locations for NP_078954.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AW968557, BC007800, BP199309, DB565980
      Consensus CDS
      CCDS8261.1
      UniProtKB/Swiss-Prot
      G3V178, Q96I59
      UniProtKB/TrEMBL
      B3KPX5
      Related
      ENSP00000281038.5, ENST00000281038.10
      Conserved Domains (1) summary
      PRK03932
      Location:27 → 474
      asnC; asparaginyl-tRNA synthetase; Validated

    RNA

    1. NR_189154.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    2. NR_189155.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    3. NR_189156.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    4. NR_189157.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003086, AP003110

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      78435968..78574864 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011545253.3 → XP_011543555.1  probable asparagine--tRNA ligase, mitochondrial isoform X1

      Related
      ENSP00000511819.1, ENST00000695344.1
      Conserved Domains (3) summary
      PRK03932
      Location:27 → 465
      asnC; asparaginyl-tRNA synthetase; Validated
      cd00776
      Location:133 → 464
      AsxRS_core; Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as ...
      cd04318
      Location:44 → 120
      EcAsnRS_like_N; EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB ...

    2. XM_047427593.1 → XP_047283549.1  probable asparagine--tRNA ligase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      A0A8Q3SHT7

    3. XM_047427592.1 → XP_047283548.1  probable asparagine--tRNA ligase, mitochondrial isoform X2

      Related
      ENSP00000511829.1, ENST00000695354.1

    4. XM_047427591.1 → XP_047283547.1  probable asparagine--tRNA ligase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      A0A8Q3SHT7

    5. XM_047427594.1 → XP_047283550.1  probable asparagine--tRNA ligase, mitochondrial isoform X3

    6. XM_047427595.1 → XP_047283551.1  probable asparagine--tRNA ligase, mitochondrial isoform X4

    7. XM_017018302.3 → XP_016873791.1  probable asparagine--tRNA ligase, mitochondrial isoform X5

      UniProtKB/TrEMBL
      A0A8Q3WLI0
      Related
      ENSP00000511832.1, ENST00000695357.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      78369261..78508161 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369952.1 → XP_054225927.1  probable asparagine--tRNA ligase, mitochondrial isoform X2

    2. XM_054369951.1 → XP_054225926.1  probable asparagine--tRNA ligase, mitochondrial isoform X2

    3. XM_054369950.1 → XP_054225925.1  probable asparagine--tRNA ligase, mitochondrial isoform X2

    4. XM_054369953.1 → XP_054225928.1  probable asparagine--tRNA ligase, mitochondrial isoform X3

    5. XM_054369954.1 → XP_054225929.1  probable asparagine--tRNA ligase, mitochondrial isoform X4

    6. XM_054369955.1 → XP_054225930.1  probable asparagine--tRNA ligase, mitochondrial isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96I59.3 GenPept UniProtKB/Swiss-Prot:Q96I59

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