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BNIP1 BCL2 interacting protein 1 [ Homo sapiens (human) ]

Gene ID: 662, updated on 3-Nov-2024

Summary

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Official Symbol
BNIP1provided by HGNC
Official Full Name
BCL2 interacting protein 1provided by HGNC
Primary source
HGNC:HGNC:1082
See related
Ensembl:ENSG00000113734 MIM:603291; AllianceGenome:HGNC:1082
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
NIP1; SEC20; TRG-8
Summary
This gene is a member of the BCL2/adenovirus E1B 19 kd-interacting protein (BNIP) family. It interacts with the E1B 19 kDa protein, which protects cells from virally-induced cell death. The encoded protein also interacts with E1B 19 kDa-like sequences of BCL2, another apoptotic protector. In addition, this protein is involved in vesicle transport into the endoplasmic reticulum. Alternative splicing of this gene results in four protein products with identical N- and C-termini. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in bone marrow (RPKM 8.6), testis (RPKM 6.9) and 25 other tissues See more
Orthologs
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Genomic context

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See BNIP1 in Genome Data Viewer
Location:
5q35.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (173144531..173164387)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (173684638..173704487)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (172571534..172591390)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATPase H+ transporting V0 subunit e1 Neighboring gene small nucleolar RNA, H/ACA box 74B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16635 Neighboring gene CREB3 regulatory factor Neighboring gene ReSE screen-validated silencer GRCh37_chr5:172508379-172508618 Neighboring gene CDC42 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172555784-172556284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:172571727-172572255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16636 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:172633891-172634070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:172656189-172656855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:172659129-172660008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:172660009-172660888 Neighboring gene ribosomal protein L7a pseudogene 33 Neighboring gene NK2 homeobox 5

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. A homozygous hypomorphic BNIP1 variant causes an increase in autophagosomes and reduced autophagic flux and results in a spondylo-epiphyseal dysplasia. Holling T, et al. Hum Mutat, 2022 May. PMID 35266227
  2. MTD-like motif of a BH3-only protein, BNIP1, induces necrosis accompanied by an intracellular calcium spike. Park J, et al. Biochem Biophys Res Commun, 2018 Jan 8. PMID 29222049
  3. NIP1, a gene required for nuclear transport in yeast. Gu Z, et al. Proc Natl Acad Sci U S A, 1992 Nov 1. PMID 1332047, Free PMC Article
  4. Novel BNIP1 variants and their interaction with BCL2 family members. Zhang H, et al. FEBS Lett, 1999 Apr 1. PMID 10217402
  5. Endoplasmic reticulum-specific BH3-only protein BNIP1 induces mitochondrial fragmentation in a Bcl-2- and Drp1-dependent manner. Ryu SW, et al. J Cell Physiol, 2012 Aug. PMID 22020994

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A homozygous hypomorphic BNIP1 variant causes an increase in autophagosomes and reduced autophagic flux and results in a spondylo-epiphyseal dysplasia.
    Title: A homozygous hypomorphic BNIP1 variant causes an increase in autophagosomes and reduced autophagic flux and results in a spondylo-epiphyseal dysplasia.
  2. The mitochondrial targeting domain (MTD) of Noxa has necrosis-inducing activity when conjugated with cell-penetrating peptide (CPP). In this study, we report another MTD-like motif, B1MLM, found in BNIP1, a pro-apoptotic BH3-only protein found in the endoplasmic reticulum membrane. The B1MLM peptide, conjugated with CPP, induced necrosis in a way similar to that of R8:MTD.
    Title: MTD-like motif of a BH3-only protein, BNIP1, induces necrosis accompanied by an intracellular calcium spike.
  3. BNip1 functions as a downstream modulator of RNF186 to direct endoplasmic reticulum stress-associated apoptotic signaling.
    Title: A novel RING finger E3 ligase RNF186 regulate ER stress-mediated apoptosis through interaction with BNip1.
  4. three members of the BNIP family, BNIP1, BNIP3 and BNIP3L, are expressed in the developing brain with distinct brain region specificity
    Title: Differential expression of BNIP family members of BH3-only proteins during the development and after axotomy in the rat.
  5. ER-specific BNIP1 plays an important role in mitochondrial dynamics by modulating the mitochondrial fission protein Drp1
    Title: Endoplasmic reticulum-specific BH3-only protein BNIP1 induces mitochondrial fragmentation in a Bcl-2- and Drp1-dependent manner.
  6. Human BNIP1 colocalizes with RNF185 at mitochondria and is polyubiquitinated by RNF185 through K63-based ubiquitin linkage in vivo.
    Title: RNF185, a novel mitochondrial ubiquitin E3 ligase, regulates autophagy through interaction with BNIP1.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Polymorphisms in mitochondrial genes and prostate cancer risk.
  8. soluble N-ethylmaleimide-sensitive factor attachment protein may suppress apoptosis by competing with antiapoptotic proteins for the BH3 domain of BNIP1
    Title: Involvement of BNIP1 in apoptosis and endoplasmic reticulum membrane fusion.
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

EBI GWAS Catalog

Description
Common variants near MBNL1 and NKX2-5 are associated with infantile hypertrophic pyloric stenosis.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNAP receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables calcium-induced calcium release activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within apoptotic process IPI
Inferred from Physical Interaction
more info
 PubMed 
involved_in apoptotic process in response to mitochondrial fragmentation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in calcium-mediated signaling IEA
Inferred from Electronic Annotation
more info
  
involved_in endoplasmic reticulum membrane fusion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in execution phase of apoptosis IC
Inferred by Curator
more info
 PubMed 
involved_in negative regulation of apoptotic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of SNARE complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SNARE complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrial outer membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
vesicle transport protein SEC20
Names
BCL2/adenovirus E1B 19 kDa protein-interacting protein 1
BCL2/adenovirus E1B 19kDa interacting protein 1
transformation-related gene 8 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.

mRNA and Protein(s)

  1. NM_001205.3 → NP_001196.2  vesicle transport protein SEC20 isoform BNIP1

    See identical proteins and their annotated locations for NP_001196.2

    Status: REVIEWED

    Description
    Transcript Variant: Transcript variant BNIP1 contains the entire coding region of the gene. This variant contains a fully conserved BH3 domain, which has been associated with pro-apoptotic function.
    Source sequence(s)
    BC010959, BP384034
    Consensus CDS
    CCDS4384.1
    UniProtKB/Swiss-Prot
    D3DQM3, D3DQM4, D3DQM5, D3DQM6, O75622, O75623, O75624, Q12981, Q6K044, Q96FG4
    Related
    ENSP00000239215.7, ENST00000351486.10
    Conserved Domains (1) summary
    cd15865
    Location:132 → 224
    SNARE_SEC20; SNARE motif of SEC20

  2. NM_013978.3 → NP_053581.2  vesicle transport protein SEC20 isoform BNIP1-a

    See identical proteins and their annotated locations for NP_053581.2

    Status: REVIEWED

    Description
    Transcript Variant: Transcript variant BNIP1-a contains a 102-nucleotide in-frame deletion as compared to the full-length BNIP1 variant. This variant lacks the BH3 domain which is associated with pro-apoptotic function, and therefore, may function similarly to anti-apoptotic members of the BCL2 family.
    Source sequence(s)
    AF083956, AU311051, BC010959, BP384034
    Consensus CDS
    CCDS43400.1
    UniProtKB/Swiss-Prot
    Q12981
    Related
    ENSP00000377365.4, ENST00000393770.4
    Conserved Domains (2) summary
    TIGR02302
    Location:44 → 124
    aProt_lowcomp; TIGR02302 family protein
    cd15865
    Location:98 → 190
    SNARE_SEC20; SNARE motif of SEC20

  3. NM_013979.3 → NP_053582.2  vesicle transport protein SEC20 isoform BNIP1-b

    See identical proteins and their annotated locations for NP_053582.2

    Status: REVIEWED

    Description
    Transcript Variant: Transcript variant BNIP1-b contains a 129-nucleotide in-frame insertion relative to the full-length BNIP1 variant. This variant contains a fully conserved BH3 domain which has been associated with pro-apoptotic function.
    Source sequence(s)
    AF083957, AU311051, BC010959, BP384034
    Consensus CDS
    CCDS4385.1
    UniProtKB/Swiss-Prot
    Q12981
    Related
    ENSP00000231668.9, ENST00000231668.13
    Conserved Domains (1) summary
    cd15865
    Location:175 → 267
    SNARE_SEC20; SNARE motif of SEC20

  4. NM_013980.3 → NP_053583.2  vesicle transport protein SEC20 isoform BNIP1-c

    See identical proteins and their annotated locations for NP_053583.2

    Status: REVIEWED

    Description
    Transcript Variant: Transcript variant BNIP1-c contains the same 129-nucleotide insertion as BNIP1-b, but also the same 102-nucleotide deletion as BNIP1-a. This variant lacks a BH3 domain which is associated with pro-apoptotic function, and therefore, may function similarly to anti-apoptotic members of the BCL2 family.
    Source sequence(s)
    AF083958, AU311051, BC010959, BP384034
    Consensus CDS
    CCDS4386.1
    UniProtKB/Swiss-Prot
    Q12981
    Related
    ENSP00000239214.8, ENST00000352523.10
    Conserved Domains (1) summary
    cd15865
    Location:141 → 233
    SNARE_SEC20; SNARE motif of SEC20

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    173144531..173164387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534638.2 → XP_011532940.1  vesicle transport protein SEC20 isoform X1

    Conserved Domains (1) summary
    cl22856
    Location:175 → 206
    SNARE; SNARE motif

  2. XM_047417623.1 → XP_047273579.1  vesicle transport protein SEC20 isoform X3

  3. XM_047417624.1 → XP_047273580.1  vesicle transport protein SEC20 isoform X4

  4. XM_011534639.2 → XP_011532941.1  vesicle transport protein SEC20 isoform X2

    Conserved Domains (1) summary
    cl22856
    Location:175 → 206
    SNARE; SNARE motif

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    173684638..173704487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353302.1 → XP_054209277.1  vesicle transport protein SEC20 isoform X1

  2. XM_054353304.1 → XP_054209279.1  vesicle transport protein SEC20 isoform X3

  3. XM_054353305.1 → XP_054209280.1  vesicle transport protein SEC20 isoform X4

  4. XM_054353303.1 → XP_054209278.1  vesicle transport protein SEC20 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q12981.3 GenPept UniProtKB/Swiss-Prot:Q12981

Gene LinkOut

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