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

Summary

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

Location:: 2p24.3

Exon count:: 58

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (14778909..15561334, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (14809697..15592931, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (15307040..15701458, complement)

Chromosome 2 - NC_000002.12 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?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations 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

HSC08G032 (e-PCR)
- UniSTS:81155

D2S2118 (e-PCR)
- UniSTS:154121

RH66856 (e-PCR)
- UniSTS:74541

D2S1968 (e-PCR)
- UniSTS:18759

D15S954 (e-PCR)
- UniSTS:90712

SHGC-79906 (e-PCR)
- UniSTS:101475

SHGC-84097 (e-PCR)
- UniSTS:104561

D15S1477 (e-PCR)
- UniSTS:474482

D1S1425 (e-PCR)
- UniSTS:149621

B313ZH5 (e-PCR)
- UniSTS:54651

D3S3825 (e-PCR)
- UniSTS:28849

RH12241 (e-PCR)
- UniSTS:78285

fj17b01.x1 (e-PCR)
- UniSTS:198652

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 more info	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

NG_032964.2 RefSeqGene

Range

5000..399418

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

14778909..15561334 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017004317.2 → XP_016859806.1 NBAS subunit of NRZ tethering complex isoform X3
XM_047444733.1 → XP_047300689.1 NBAS subunit of NRZ tethering complex isoform X3
XM_047444734.1 → XP_047300690.1 NBAS subunit of NRZ tethering complex isoform X4
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
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
XM_047444735.1 → XP_047300691.1 NBAS subunit of NRZ tethering complex isoform X5
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
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

XR_007076390.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

14809697..15592931 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054342528.1 → XP_054198503.1 NBAS subunit of NRZ tethering complex isoform X3
XM_054342527.1 → XP_054198502.1 NBAS subunit of NRZ tethering complex isoform X3
XM_054342529.1 → XP_054198504.1 NBAS subunit of NRZ tethering complex isoform X4
XM_054342525.1 → XP_054198500.1 NBAS subunit of NRZ tethering complex isoform X1
XM_054342526.1 → XP_054198501.1 NBAS subunit of NRZ tethering complex isoform X2
XM_054342530.1 → XP_054198505.1 NBAS subunit of NRZ tethering complex isoform X5
XM_054342532.1 → XP_054198507.1 NBAS subunit of NRZ tethering complex isoform X7
XM_054342531.1 → XP_054198506.1 NBAS subunit of NRZ tethering complex isoform X6