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

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)

Genotypes

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

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