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    NBAS NBAS subunit of NRZ tethering complex [ Homo sapiens (human) ]

    Gene ID: 51594, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NBASprovided by HGNC
    Official Full Name
    NBAS subunit of NRZ tethering complexprovided by HGNC
    Primary source
    HGNC:HGNC:15625
    See related
    Ensembl:ENSG00000151779 MIM:608025; AllianceGenome:HGNC:15625
    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
    NAG; SOPH; ILFS2
    Summary
    This gene encodes a protein with two leucine zipper domains, a ribosomal protein S14 signature domain and a Sec39 like domain. The protein is thought to be involved in Golgi-to-ER transport. Mutations in this gene are associated with short stature, optic nerve atrophy, and Pelger-Huet anomaly. [provided by RefSeq, Oct 2012]
    Expression
    Ubiquitous expression in testis (RPKM 10.3), thyroid (RPKM 7.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NBAS in Genome Data Viewer
    Location:
    2p24.3
    Exon count:
    58
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (14778909..15561334, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (14809697..15592931, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (15307040..15701458, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 276 Neighboring gene RNA, U6 small nuclear 1288, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:14472914-14473113 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14541927-14542484 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:14654042-14654593 Neighboring gene LRAT domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:14988479-14989049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11184 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:15100270-15101469 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr2:15182798-15183298 and GRCh37_chr2:15183299-15183799 Neighboring gene Sharpr-MPRA regulatory region 966 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15213063-15213219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:15224708-15225393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:15225394-15226078 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:15281925-15283124 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15315340-15315550 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:15399317-15400143 Neighboring gene NANOG hESC enhancer GRCh37_chr2:15589330-15589831 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15606309-15606502 Neighboring gene ribosomal protein S26 pseudogene 18 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15672530-15672745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15346 Neighboring gene uncharacterized LOC105373440 Neighboring gene uncharacterized LOC124905975

    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. [Population frequency and age of mutation G5741→A in gene NBAS which is a cause of SOPH syndrome in Sakha (Yakutia) Republic]. Maksimova NR, et al. Genetika, 2016 Oct. PMID 29369590
    2. NBAS pathogenic variants: Defining the associated clinical and facial phenotype and genotype-phenotype correlations. Carli D, et al. Hum Mutat, 2019 Jun. PMID 30825388
    3. Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. Haack TB, et al. Am J Hum Genet, 2015 Jul 2. PMID 26073778, Free PMC Article
    4. NBAS mutations cause a multisystem disorder involving bone, connective tissue, liver, immune system, and retina. Segarra NG, et al. Am J Med Genet A, 2015 Dec. PMID 26286438
    5. Compound heterozygous variants in NBAS as a cause of atypical osteogenesis imperfecta. Balasubramanian M, et al. Bone, 2017 Jan. PMID 27789416, Free PMC Article

    See all (75) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Modulation of NBAS-Related Functions in the Early Response to SARS-CoV-2 Infection.
      Title: Modulation of NBAS-Related Functions in the Early Response to SARS-CoV-2 Infection.
    2. NBAS, a gene involved in cytotoxic degranulation, is recurrently mutated in pediatric hemophagocytic lymphohistiocytosis.
      Title: NBAS, a gene involved in cytotoxic degranulation, is recurrently mutated in pediatric hemophagocytic lymphohistiocytosis.
    3. NBAS Variants Are Associated with Quantitative and Qualitative NK and B Cell Deficiency.
      Title: NBAS Variants Are Associated with Quantitative and Qualitative NK and B Cell Deficiency.
    4. Characterization of a complex phenotype (fever-dependent recurrent acute liver failure and osteogenesis imperfecta) due to NBAS and P4HB variants.
      Title: Characterization of a complex phenotype (fever-dependent recurrent acute liver failure and osteogenesis imperfecta) due to NBAS and P4HB variants.
    5. Severe SOPH syndrome due to a novel NBAS mutation in a 27-year-old woman-Review of this pleiotropic, autosomal recessive disorder: Mystery solved after two decades.
      Title: Severe SOPH syndrome due to a novel NBAS mutation in a 27-year-old woman-Review of this pleiotropic, autosomal recessive disorder: Mystery solved after two decades.
    6. Novel compound heterozygous variants in the NBAS gene in a child with osteogenesis imperfecta and recurrent acute liver failure.
      Title: Novel compound heterozygous variants in the NBAS gene in a child with osteogenesis imperfecta and recurrent acute liver failure.
    7. Mutations in NBAS and SCYL1, genetic causes of recurrent liver failure in children: Three case reports and a literature review.
      Title: Mutations in NBAS and SCYL1, genetic causes of recurrent liver failure in children: Three case reports and a literature review.
    8. Data report two unrelated subjects with a trait associated with defective NBAS function sharing a previously unreported pathogenic "synonymous" change demonstrated to affect proper NBAS transcript processing. Assessing the clinical features and signs of affected subjects with biallelic NBAS variants documents the occurrence of a recognizable facial profile for these patients.
      Title: NBAS pathogenic variants: Defining the associated clinical and facial phenotype and genotype-phenotype correlations.
    9. A novel homozygous truncating mutation in the NBAS gene was identified in a family with Acrofrontofacionasal Dysostosis type 1.
      Title: Mutations in the Neuroblastoma Amplified Sequence gene in a family affected by Acrofrontofacionasal Dysostosis type 1.
    10. NBAS was the only candidate gene mutated in more than one patient. All NBAS mutations were novel and predictedly pathogenic. Of these mutations, 3 lay in distal (C-terminal) regions of NBAS, a novel distribution. Unlike the 2 patients without NBAS mutations, the 3 patients with confirmed NBAS mutations all suffered from a febrile illness before each episode of liver crisis (fever-related recurrent acute liver failure)
      Title: Novel NBAS mutations and fever-related recurrent acute liver failure in Chinese children: a retrospective study.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Infantile liver failure syndrome 2
    MedGen: C3809651 OMIM: 616483 GeneReviews: Not available
    		not available
    Short stature-optic atrophy-Pelger-HuC+t anomaly syndrome
    MedGen: C3541319 OMIM: 614800 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association study of conduct disorder symptomatology.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations
    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)

    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

    • FLJ40407, FLJ45050, DKFZp586G1219

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNARE binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Dsl1/NZR complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Dsl1/NZR complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Dsl1/NZR complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    NBAS subunit of NRZ tethering complex
    Names
    NAG/BC035112 fusion
    NAG/FAM49A fusion
    neuroblastoma amplified sequence
    neuroblastoma-amplified gene protein

    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_032964.2 RefSeqGene

      Range
      5000..399418
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015909.4 → NP_056993.2  NBAS subunit of NRZ tethering complex

      See identical proteins and their annotated locations for NP_056993.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and is protein-coding.
      Source sequence(s)
      AB621813, AF388385, AL832774, BC108693, BC131735
      Consensus CDS
      CCDS1685.1
      UniProtKB/Swiss-Prot
      A2RRP1, O95790, Q2VPJ7, Q53TK6, Q86V39, Q8NFY8, Q9Y3W5
      Related
      ENSP00000281513.5, ENST00000281513.10
      Conserved Domains (2) summary
      pfam08314
      Location:726 → 1370
      Sec39; Secretory pathway protein Sec39
      pfam15492
      Location:90 → 371
      Nbas_N; Neuroblastoma-amplified sequence, N terminal

    RNA

    1. NR_052013.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB621813, AL832774, BC131735, BQ878688

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      14778909..15561334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004317.2 → XP_016859806.1  NBAS subunit of NRZ tethering complex isoform X3

    2. XM_047444733.1 → XP_047300689.1  NBAS subunit of NRZ tethering complex isoform X3

    3. XM_047444734.1 → XP_047300690.1  NBAS subunit of NRZ tethering complex isoform X4

    4. XM_011510357.3 → XP_011508659.1  NBAS subunit of NRZ tethering complex isoform X1

      Conserved Domains (2) summary
      pfam08314
      Location:683 → 1327
      Sec39; Secretory pathway protein Sec39
      pfam15492
      Location:90 → 328
      Nbas_N; Neuroblastoma-amplified sequence, N terminal

    5. XM_011510358.3 → XP_011508660.1  NBAS subunit of NRZ tethering complex isoform X2

      Conserved Domains (2) summary
      pfam08314
      Location:726 → 1370
      Sec39; Secretory pathway protein Sec39
      pfam15492
      Location:90 → 371
      Nbas_N; Neuroblastoma-amplified sequence, N terminal

    6. XM_047444735.1 → XP_047300691.1  NBAS subunit of NRZ tethering complex isoform X5

    7. XM_011510361.3 → XP_011508663.1  NBAS subunit of NRZ tethering complex isoform X7

      UniProtKB/TrEMBL
      A0A8V8TPS6
      Related
      ENSP00000398411.1, ENST00000442506.5
      Conserved Domains (1) summary
      pfam08314
      Location:162 → 634
      Sec39; Secretory pathway protein Sec39

    8. XM_011510360.3 → XP_011508662.1  NBAS subunit of NRZ tethering complex isoform X6

      UniProtKB/TrEMBL
      A0A8V8TPS6
      Conserved Domains (1) summary
      pfam08314
      Location:165 → 637
      Sec39; Secretory pathway protein Sec39

    RNA

    1. XR_007076390.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      14809697..15592931 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342528.1 → XP_054198503.1  NBAS subunit of NRZ tethering complex isoform X3

    2. XM_054342527.1 → XP_054198502.1  NBAS subunit of NRZ tethering complex isoform X3

    3. XM_054342529.1 → XP_054198504.1  NBAS subunit of NRZ tethering complex isoform X4

    4. XM_054342525.1 → XP_054198500.1  NBAS subunit of NRZ tethering complex isoform X1

    5. XM_054342526.1 → XP_054198501.1  NBAS subunit of NRZ tethering complex isoform X2

    6. XM_054342530.1 → XP_054198505.1  NBAS subunit of NRZ tethering complex isoform X5

    7. XM_054342532.1 → XP_054198507.1  NBAS subunit of NRZ tethering complex isoform X7

    8. XM_054342531.1 → XP_054198506.1  NBAS subunit of NRZ tethering complex isoform X6

    RNA

    1. XR_008486394.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2RRP1.2 GenPept UniProtKB/Swiss-Prot:A2RRP1

    Gene LinkOut

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

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