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NIPSNAP2 nipsnap homolog 2 [ Homo sapiens (human) ]

Gene ID: 2631, updated on 3-Nov-2024

Summary

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Official Symbol
NIPSNAP2provided by HGNC
Official Full Name
nipsnap homolog 2provided by HGNC
Primary source
HGNC:HGNC:4179
See related
Ensembl:ENSG00000146729 MIM:603004; AllianceGenome:HGNC:4179
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
GBAS
Summary
This gene encodes a member of the NipSnap family of proteins that may be involved in vesicular transport. The encoded protein is localized to mitochondria and plays a role in oxidative phosphorylation. A pseudogene of this gene is located on the long arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in heart (RPKM 42.1), thyroid (RPKM 22.8) and 24 other tissues See more
Orthologs
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Genomic context

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See NIPSNAP2 in Genome Data Viewer
Location:
7p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (55964585..56000179)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (56124373..56159980)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (56032278..56067872)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18191 Neighboring gene zinc finger protein 713 Neighboring gene fragile site, folic acid type, rare, fra(7)(p11.2) Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:55979512-55980711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26043 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:56032587-56033320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26044 Neighboring gene mitochondrial ribosomal protein S17 Neighboring gene MPRA-validated peak6528 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26045 Neighboring gene phosphoserine phosphatase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26049 Neighboring gene small nucleolar RNA, H/ACA box 22B Neighboring gene chaperonin containing TCP1 subunit 6A

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. GBAS, a novel gene encoding a protein with tyrosine phosphorylation sites and a transmembrane domain, is co-amplified with EGFR. Wang XY, et al. Genomics, 1998 May 1. PMID 9615231
  2. Knockdown of GBAS regulates esophageal cancer cell viability and apoptosis. Peng J, et al. Mol Med Rep, 2021 Jul. PMID 34036378, Free PMC Article
  3. Mitochondrial proteins NIP-SNAP-1 and -2 are a target for the immunomodulatory activity of clarithromycin, which involves NF-κB-mediated cytokine production. Yamamoto S, et al. Biochem Biophys Res Commun, 2017 Feb 12. PMID 27998764
  4. Intronic variant of EGFR is associated with GBAS expression and survival outcome of early-stage non-small cell lung cancer. Hong MJ, et al. Thorac Cancer, 2018 Aug. PMID 29806744, Free PMC Article
  5. NIP-SNAP-1 and -2 mitochondrial proteins are maintained by heat shock protein 60. Yamamoto S, et al. Biochem Biophys Res Commun, 2017 Feb 12. PMID 28011268

See all (86) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Knockdown of GBAS regulates esophageal cancer cell viability and apoptosis.
    Title: Knockdown of GBAS regulates esophageal cancer cell viability and apoptosis.
  2. NIPSNAP1 and NIPSNAP2 have a redundant function in mitophagy and are predominantly expressed in different tissues.
    Title: NIPSNAP1 and NIPSNAP2 Act as "Eat Me" Signals for Mitophagy.
  3. Results show that the rs9642391C>G variant, which is located in the intron region of EGFR, is associated with GBAS expression and survival outcomes in surgically resected early-stage non-small cell lung cancer patients.
    Title: Intronic variant of EGFR is associated with GBAS expression and survival outcome of early-stage non-small cell lung cancer.
  4. identified mitochondrial proteins 4-nitrophenylphosphatase domain and non-neuronal synaptosomal associated protein 25-like protein homolog (NIP-SNAP)-1 and -2 as clarithromycin-binding proteins. Production of proinflammatory cytokines induced by lipopolysaccharides and Pam3-CSK4 in epithelial cell lines BEAS-2B and T24 were suppressed by knockdown of NIP-SNAP-1 or -2
    Title: Mitochondrial proteins NIP-SNAP-1 and -2 are a target for the immunomodulatory activity of clarithromycin, which involves NF-κB-mediated cytokine production.
  5. NIP-SNAP-1 and -2 localized in the mitochondrial inner membrane space, whereas HSP60 localized in the matrix. Expression levels of NIP-SNAP-1 and -2 in cells were decreased by knockdown of HSP60, but not HSP10. The findings indicate that HSP60 promotes folding and maintains the stability of NIP-SNAP-1 and -2.
    Title: NIP-SNAP-1 and -2 mitochondrial proteins are maintained by heat shock protein 60.
  6. GBAS mutations could not explain phenotype of patients with combined oxidative phosphorylation system deficiencies.
    Title: Sequence variants in four candidate genes (NIPSNAP1, GBAS, CHCHD1 and METT11D1) in patients with combined oxidative phosphorylation system deficiencies.
  7. CHCHD10 and GBAS are involved in oxidative phosphorylation.
    Title: Functional annotation of heart enriched mitochondrial genes GBAS and CHCHD10 through guilt by association.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of glioblastoma amplified sequence (GBAS) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in oxidative phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of high voltage-gated calcium channel activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in mitochondrial matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial outer membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion HDA PubMed 
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
protein NipSnap homolog 2
Names
4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 2
glioblastoma amplified sequence

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)

  1. NM_001202469.2 → NP_001189398.1  protein NipSnap homolog 2 isoform 2

    See identical proteins and their annotated locations for NP_001189398.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two exons in the coding region, which result in a frameshift and then resumption of the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK097049, BC030821, BU753659, CX166452
    Consensus CDS
    CCDS56488.1
    UniProtKB/Swiss-Prot
    O75323
    Related
    ENSP00000406855.1, ENST00000446778.5
    Conserved Domains (1) summary
    pfam07978
    Location:148 → 245
    NIPSNAP; NIPSNAP

  2. NM_001483.3 → NP_001474.1  protein NipSnap homolog 2 isoform 1

    See identical proteins and their annotated locations for NP_001474.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC030821, BU753659, CX166452
    Consensus CDS
    CCDS5521.1
    UniProtKB/Swiss-Prot
    C9IYJ3, O43801, O75323, Q53X96
    Related
    ENSP00000313050.3, ENST00000322090.8
    Conserved Domains (1) summary
    pfam07978
    Location:187 → 284
    NIPSNAP

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    55964585..56000179
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    56124373..56159980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75323.1 GenPept UniProtKB/Swiss-Prot:O75323

Gene LinkOut

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