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APIP Gene(Protein Coding)

APAF1 Interacting Protein

GCID:
GC11M034854
GIFtS:
45
Genes Participants
UDN Logo

Aliases for APIP Gene

Aliases for APIP Gene

  • APAF1 Interacting Protein 2 3 5
  • Methylthioribulose-1-Phosphate Dehydratase 2 3
  • MTRu-1-P Dehydratase 3 4
  • HAPIP 3 4
  • Probable Methylthioribulose-1-Phosphate Dehydratase 3
  • APAF1-Interacting Protein 4
  • EC 4.2.1.109 4
  • CGI-29 3
  • MMRP19 3
  • APIP2 3
  • CGI29 3

External Ids for APIP Gene

Previous GeneCards Identifiers for APIP Gene

  • GC11M034861
  • GC11M034602

Summaries for APIP Gene

Entrez Gene Summary for APIP Gene

  • APIP is an APAF1 (MIM 602233)-interacting protein that acts as a negative regulator of ischemic/hypoxic injury (Cho et al., 2004 [PubMed 15262985]).[supplied by OMIM, Dec 2008]

GeneCards Summary for APIP Gene

APIP (APAF1 Interacting Protein) is a Protein Coding gene. Diseases associated with APIP include Pyruvate Dehydrogenase E3-Binding Protein Deficiency and Chromosome 17Q11.2 Deletion Syndrome, 1.4-Mb. Among its related pathways are Metabolism and S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation. Gene Ontology (GO) annotations related to this gene include identical protein binding and methylthioribulose 1-phosphate dehydratase activity.

UniProtKB/Swiss-Prot for APIP Gene

  • Catalyzes the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). Functions in the methionine salvage pathway, which plays a key role in cancer, apoptosis, microbial proliferation and inflammation. May inhibit the CASP1-related inflammatory response (pyroptosis), the CASP9-dependent apoptotic pathway and the cytochrome c-dependent and APAF1-mediated cell death.

Gene Wiki entry for APIP Gene

Additional gene information for APIP Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APIP Gene

Genomics for APIP Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for APIP Gene

Promoters and enhancers for APIP Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11J034914 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 709.8 -0.3 -346 4.5 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 APIP PDHX ENSG00000271369 CAT MIR1343
GH11J034928 Enhancer 1.1 Ensembl ENCODE 58.9 -13.4 -13417 2.8 FOXA2 MLX ARID4B DMAP1 ZNF48 ETS1 SLC30A9 NFKBIZ RXRA MXD4 APIP PDHX MIR1343
GH11J034908 Enhancer 1 Ensembl ENCODE 59.5 +6.4 6429 3.5 FOXA2 DNMT3B RAD21 YY1 EGR1 SCRT2 FOS RXRA ZBTB25 CEBPB APIP PDHX MIR1343 EHF GC11M034882
GH11J035006 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 28.5 -94.3 -94307 9.8 PKNOX1 STAT5A BMI1 FEZF1 BATF IRF4 RAD21 RFX5 SCRT2 ZNF207 GC11M035009 APIP CD44 PDHX LOC100507144 MIR1343 PAMR1 GC11P034975
GH11J034975 Enhancer 1.1 Ensembl ENCODE dbSUPER 31.4 -60.9 -60934 4.4 FOXA2 JUN YY1 GATA3 POLR2A FOSL2 HOMEZ MAFK TCF7L2 RXRA APIP PDHX MIR1343 GC11P034975 GC11M035009
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around APIP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the APIP gene promoter:
  • ER-alpha
  • Chx10
  • MEF-2A
  • aMEF-2
  • Tal-1beta
  • ITF-2
  • E4BP4
  • Nkx2-5
  • CUTL1
  • RORalpha1

Genomic Locations for APIP Gene

Genomic Locations for APIP Gene
chr11:34,853,094-34,916,499
(GRCh38/hg38)
Size:
63,406 bases
Orientation:
Minus strand
chr11:34,874,641-34,938,046
(GRCh37/hg19)
Size:
63,406 bases
Orientation:
Minus strand

Genomic View for APIP Gene

Genes around APIP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APIP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APIP Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for APIP Gene

Proteins for APIP Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for APIP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96GX9-MTNB_HUMAN
    Recommended name:
    Methylthioribulose-1-phosphate dehydratase
    Protein Accession:
    Q96GX9
    Secondary Accessions:
    • A8K9D3
    • Q6PJX6
    • Q8WVU2
    • Q96HK2
    • Q9Y318

    Protein attributes for APIP Gene

    Size:
    242 amino acids
    Molecular mass:
    27125 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Homotetramer (PubMed:24367089). Interacts with APAF1 (PubMed:15262985). May interact with CASP1 (PubMed:22837397).

    Three dimensional structures from OCA and Proteopedia for APIP Gene

    Alternative splice isoforms for APIP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for APIP Gene

Protein Expression for APIP Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for APIP Gene

  • Ubiquitination at posLast=3333
  • Modification sites at PhosphoSitePlus

Other Protein References for APIP Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for APIP Gene

Domains & Families for APIP Gene

Gene Families for APIP Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for APIP Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for APIP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96GX9

UniProtKB/Swiss-Prot:

MTNB_HUMAN :
  • Belongs to the aldolase class II family. MtnB subfamily.
Family:
  • Belongs to the aldolase class II family. MtnB subfamily.
genes like me logo Genes that share domains with APIP: view

Function for APIP Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for APIP Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). Functions in the methionine salvage pathway, which plays a key role in cancer, apoptosis, microbial proliferation and inflammation. May inhibit the CASP1-related inflammatory response (pyroptosis), the CASP9-dependent apoptotic pathway and the cytochrome c-dependent and APAF1-mediated cell death.
UniProtKB/Swiss-Prot CatalyticActivity:
S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=9.3 uM for S-methyl-5-thio-D-ribulose 1-phosphate; Vmax=1.39 umol/min/mg enzyme;

Enzyme Numbers (IUBMB) for APIP Gene

Phenotypes From GWAS Catalog for APIP Gene

Gene Ontology (GO) - Molecular Function for APIP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IDA 24367089
GO:0016829 lyase activity IEA --
GO:0042802 identical protein binding IPI 16189514
GO:0046570 methylthioribulose 1-phosphate dehydratase activity IDA,IEA 24367089
genes like me logo Genes that share ontologies with APIP: view
genes like me logo Genes that share phenotypes with APIP: view

Animal Models for APIP Gene

MGI Knock Outs for APIP:
  • Apip Apip<tm1b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APIP

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for APIP Gene

Localization for APIP Gene

Subcellular locations from UniProtKB/Swiss-Prot for APIP Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for APIP gene
Compartment Confidence
cytosol 3
nucleus 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for APIP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 23285211
genes like me logo Genes that share ontologies with APIP: view

Pathways & Interactions for APIP Gene

genes like me logo Genes that share pathways with APIP: view

UniProtKB/Swiss-Prot Q96GX9-MTNB_HUMAN

  • Pathway: Amino-acid biosynthesis; L-methionine biosynthesis via salvage pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate: step 2/6.

SIGNOR curated interactions for APIP Gene

Inactivates:

Gene Ontology (GO) - Biological Process for APIP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006915 apoptotic process IEA --
GO:0008652 cellular amino acid biosynthetic process IEA --
GO:0009086 methionine biosynthetic process IEA --
GO:0019509 L-methionine salvage from methylthioadenosine IMP 22837397
GO:0043066 negative regulation of apoptotic process IEA,IMP 22837397
genes like me logo Genes that share ontologies with APIP: view

Drugs & Compounds for APIP Gene

Products:

  1. Drug

(1) Drugs for APIP Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0

(2) Additional Compounds for APIP Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-(methylthio)-2,3-Dioxopentyl phosphate
  • 1-phospho-2,3-diketo-5-S-Methylthiopentane
  • 2,3-diketo-5-methylthio-1-Phosphopentane
  • 5-(methylthio)-2,3-Dioxopentyl phosphate
  • 5-methylthio-1-(Phosphonooxy)pentane-2,3-dione
  • 2,3-diketo-5-Methylthiopentyl-1-phosphoric acid
5-Methylthioribulose 1-phosphate
  • 5-S-Methyl-1-O-phosphono-5-thio-D-ribulose
  • 5-Methylthioribulose 1-phosphoric acid
  • 1-phospho-5-S-Methylthioribulose
  • 1-Phosphomethylthioribulose
  • 1PMT-Ribulose
 86316-83-8
genes like me logo Genes that share compounds with APIP: view

Transcripts for APIP Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for APIP Gene

(3) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(178) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for APIP Gene

APAF1 interacting protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for APIP

Alternative Splicing Database (ASD) splice patterns (SP) for APIP Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8
SP1: - -
SP2: - - -
SP3:
SP4:

Relevant External Links for APIP Gene

GeneLoc Exon Structure for
APIP
ECgene alternative splicing isoforms for
APIP

Expression for APIP Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APIP Gene

mRNA expression in normal human tissues for APIP Gene
mRNA expression by GTEx for APIP GenemRNA expression by BioGPS for APIP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for APIP Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.3) and Salivary gland (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for APIP Gene



Protein tissue co-expression partners for APIP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of APIP Gene:

APIP

SOURCE GeneReport for Unigene cluster for APIP Gene:

Hs.447794

mRNA Expression by UniProt/SwissProt for APIP Gene:

Q96GX9-MTNB_HUMAN
Tissue specificity: Isoform 1 is ubiquitously expressed. Isoform 2 is expressed at lower levels and detected in heart, brain, pancreas, liver, placenta, skeletal muscle and kidney.

Evidence on tissue expression from TISSUES for APIP Gene

  • Eye(4.2)
  • Intestine(4.2)
  • Bone marrow(4.1)
  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with APIP: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for APIP Gene

Orthologs for APIP Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for APIP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia APIP 34 33
  • 99.45 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia APIP 34 33
  • 92.59 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia APIP 34
  • 89 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia APIP 34 33
  • 88.84 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Apip 16 34 33
  • 87.69 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 84 (a)
 OneToMany
-- 34
  • 67 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves APIP 34 33
  • 80.51 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia APIP 34
  • 81 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia apip 33
  • 72.39 (n)
Str.1776 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.6992 33
zebrafish
(Danio rerio)
 Actinopterygii apip 34 33
  • 70.4 (n)
 OneToOne
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.9020 33
fruit fly
(Drosophila melanogaster)
 Insecta CG11134 34 33
  • 61.82 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta MTNB_ANOGA 33
  • 60.93 (n)
worm
(Caenorhabditis elegans)
 Secernentea ZC373.5 34 33
  • 51.27 (n)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes MDE1 34 33
  • 55.56 (n)
 OneToOne
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ACL126W 33
  • 50.77 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G53850 33
  • 58.17 (n)
soybean
(Glycine max)
 eudicotyledons Gma.4561 33
rice
(Oryza sativa)
 Liliopsida Os11g0484000 33
  • 60.33 (n)
Os.11937 33
wheat
(Triticum aestivum)
 Liliopsida Ta.14582 33
corn
(Zea mays)
 Liliopsida Zm.2643 33
bread mold
(Neurospora crassa)
 Ascomycetes NCU09264 33
  • 55.92 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC20H4.05c 33
  • 52.43 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea Cin.9700 33
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.9700 33
Species where no ortholog for APIP was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for APIP Gene

ENSEMBL:
Gene Tree for APIP (if available)
TreeFam:
Gene Tree for APIP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for APIP: view image

Paralogs for APIP Gene

Pseudogenes.org Pseudogenes for APIP Gene

genes like me logo Genes that share paralogs with APIP: view

No data available for Paralogs for APIP Gene

Variants for APIP Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for APIP Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1049306 benign, not specified, Pyruvate dehydrogenase complex deficiency 34,916,722(-) C/T upstream_transcript_variant
rs1049307 benign, not specified, Pyruvate dehydrogenase complex deficiency 34,916,763(-) T/C/G upstream_transcript_variant
rs112032820 benign, Pyruvate dehydrogenase complex deficiency 34,916,527(-) C/G/T upstream_transcript_variant
rs113073242 benign, Pyruvate dehydrogenase complex deficiency 34,916,454(-) A/G upstream_transcript_variant
rs11539201 benign, likely-benign, not specified, Pyruvate dehydrogenase complex deficiency 34,916,725(-) C/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for APIP Gene

Variant ID Type Subtype PubMed ID
esv2666133 CNV deletion 23128226
esv2673788 CNV deletion 23128226
esv2759817 CNV loss 17122850
esv34511 CNV loss 17911159
esv3625916 CNV loss 21293372
esv3625917 CNV loss 21293372
nsv1144547 CNV deletion 24896259
nsv832118 CNV gain 17160897
nsv832119 CNV gain 17160897
nsv8807 CNV gain 18304495

Variation tolerance for APIP Gene

Residual Variation Intolerance Score: 84% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.36; 97.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for APIP Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
APIP

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APIP Gene

Disorders for APIP Gene

MalaCards: The human disease database

(2) MalaCards diseases for APIP Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pyruvate dehydrogenase e3-binding protein deficiency
  • pdhxd
chromosome 17q11.2 deletion syndrome, 1.4-mb
  • neurofibromatosis 1 microdeletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search APIP in MalaCards View complete list of genes associated with diseases

Additional Disease Information for APIP

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with APIP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for APIP Gene

Publications for APIP Gene

  1. Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme. (PMID: 24367089) Kang W … Yang JK (Proceedings of the National Academy of Sciences of the United States of America 2014) 2 3 4 58
  2. Induced inhibition of ischemic/hypoxic injury by APIP, a novel Apaf-1-interacting protein. (PMID: 15262985) Cho DH … Jung YK (The Journal of biological chemistry 2004) 2 3 4 58
  3. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4 58
  4. Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death. (PMID: 22837397) Ko DC … Miller SI (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4 58
  5. Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway. (PMID: 23285211) Mary C … Lane L (PloS one 2012) 3 4 58

Products for APIP Gene

Sources for APIP Gene

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