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    APC APC, WNT signaling pathway regulator [ Homo sapiens (human) ]

    Gene ID: 324, updated on 2-Dec-2016
    Official Symbol
    APCprovided by HGNC
    Official Full Name
    APC, WNT signaling pathway regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:583
    See related
    Ensembl:ENSG00000134982 MIM:611731; Vega:OTTHUMG00000128806
    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
    GS; DP2; DP3; BTPS2; DP2.5; PPP1R46
    Summary
    This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    5q22.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (112707505..112846239)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (112043202..112181936)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102467214 Neighboring gene uncharacterized LOC102467216 Neighboring gene RNA, U6 small nuclear 482, pseudogene Neighboring gene chromobox 3 pseudogene 3 Neighboring gene signal recognition particle 19 Neighboring gene receptor accessory protein 5 Neighboring gene X-box binding protein 1 pseudogene 1 Neighboring gene zinc finger CCCH-type, RNA binding motif and serine/arginine rich 1

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Professional guidelines

    Description
    Professional guideline
    ACMG 2013

    The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in APC that are pathogenic or expected to be pathogenic.

    GuidelinePubMed

    Associated conditions

    Description Tests
    Carcinoma of colon
    MedGen: C0699790 OMIM: 114500 GeneReviews: Not available
    Compare labs
    Desmoid disease, hereditary
    MedGen: C1851124 OMIM: 135290 GeneReviews: Not available
    Compare labs
    Familial adenomatous polyposis 1 Compare labs
    Hepatocellular carcinoma
    MedGen: C2239176 OMIM: 114550 GeneReviews: Not available
    Compare labs
    Neoplasm of stomach
    MedGen: C0038356 OMIM: 613659 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-07-06)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-06)

    ClinGen Genome Curation PagePubMed
    • AMER1 mutants destabilize the destruction complex, organism-specific biosystem (from REACTOME)
      AMER1 mutants destabilize the destruction complex, organism-specific biosystemAMER1/WTX is a component of the destruction complex that interacts directly with beta-catenin through its C-terminal half. Depletion of AMER1 through siRNA stabilizes cellular beta-catenin levels an...
    • APC truncation mutants are not K63 polyubiquitinated, organism-specific biosystem (from REACTOME)
      APC truncation mutants are not K63 polyubiquitinated, organism-specific biosystemAPC has been shown to be reversibly modified with K63-linked polyubiquitin chains. This modification is required for the association is required for the assembly of the destruction complex and subse...
    • APC truncation mutants have impaired AXIN binding, organism-specific biosystem (from REACTOME)
      APC truncation mutants have impaired AXIN binding, organism-specific biosystemMutations in the APC tumor suppressor gene are common in colorectal and other cancers and cluster in the central mutation cluster region (MCR) of the gene (Miyoshi et al, 1992; Nagase and Nakamura, ...
    • AXIN missense mutants destabilize the destruction complex, organism-specific biosystem (from REACTOME)
      AXIN missense mutants destabilize the destruction complex, organism-specific biosystemAlterations in AXIN1 have been detected in a number of different cancers including liver and colorectal cancer and medullablastoma, among others (reviewed in Salahshor and Woodgett, 2005). Missense ...
    • AXIN mutants destabilize the destruction complex, activating WNT signaling, organism-specific biosystem (from REACTOME)
      AXIN mutants destabilize the destruction complex, activating WNT signaling, organism-specific biosystemAXIN1 and AXIN2 are critical scaffolding proteins of the beta-catenin destruction complex and make protein-protein interactions with several of the other complex components including APC, GSK3, CK1 a...
    • Apoptosis, organism-specific biosystem (from REACTOME)
      Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
    • Apoptotic cleavage of cellular proteins, organism-specific biosystem (from REACTOME)
      Apoptotic cleavage of cellular proteins, organism-specific biosystemApoptotic cell death is achieved by the caspase-mediatedcleavage of various vital proteins. Among caspase targets are proteins such as E-cadherin, Beta-catenin, alpha fodrin, GAS2, FADK, alpha adduc...
    • Apoptotic execution phase, organism-specific biosystem (from REACTOME)
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    • Association Between Physico-Chemical Features and Toxicity Associated Pathways, organism-specific biosystem (from WikiPathways)
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    • Beta-catenin phosphorylation cascade, organism-specific biosystem (from REACTOME)
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    • Brain-Derived Neurotrophic Factor (BDNF) signaling pathway, organism-specific biosystem (from WikiPathways)
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    • Breast cancer, conserved biosystem (from KEGG)
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    • CDC42 signaling events, organism-specific biosystem (from Pathway Interaction Database)
      CDC42 signaling events, organism-specific biosystem
      CDC42 signaling events
    • Canonical Wnt signaling pathway, organism-specific biosystem (from Pathway Interaction Database)
      Canonical Wnt signaling pathway, organism-specific biosystem
      Canonical Wnt signaling pathway
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    • Colorectal cancer, organism-specific biosystem (from KEGG)
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      Direct p53 effectors, organism-specific biosystem
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    • Truncations of AMER1 destabilize the destruction complex, organism-specific biosystem (from REACTOME)
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    • phosphorylation site mutants of CTNNB1 are not targeted to the proteasome by the destruction complex, organism-specific biosystem (from REACTOME)
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    • truncated APC mutants destabilize the destruction complex, organism-specific biosystem (from REACTOME)
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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Potential readthrough

    Included gene: SRP19

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    beta-catenin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT cadherin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    gamma-catenin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    microtubule binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    microtubule plus-end binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase regulator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ubiquitin protein ligase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    Wnt signaling pathway TAS
    Traceable Author Statement
    more info
     
    beta-catenin destruction complex assembly TAS
    Traceable Author Statement
    more info
     
    beta-catenin destruction complex disassembly TAS
    Traceable Author Statement
    more info
     
    bicellular tight junction assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    canonical Wnt signaling pathway IC
    Inferred by Curator
    more info
    PubMed 
    canonical Wnt signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell cycle arrest IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell fate specification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular component disassembly involved in execution phase of apoptosis TAS
    Traceable Author Statement
    more info
     
    cellular response to DNA damage stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitotic cytokinesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mitotic spindle assembly checkpoint IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of canonical Wnt signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of canonical Wnt signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    negative regulation of cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of cyclin-dependent protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of microtubule depolymerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of microtubule depolymerization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    pattern specification process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    positive regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of protein catabolic process IC
    Inferred by Curator
    more info
    PubMed 
    positive regulation of protein catabolic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of pseudopodium assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    proteasome-mediated ubiquitin-dependent protein catabolic process TAS
    Traceable Author Statement
    more info
     
    protein complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of attachment of spindle microtubules to kinetochore IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of attachment of spindle microtubules to kinetochore NAS
    Non-traceable Author Statement
    more info
    PubMed 
    regulation of cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    regulation of microtubule-based process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    Wnt signalosome NAS
    Non-traceable Author Statement
    more info
    PubMed 
    beta-catenin destruction complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    bicellular tight junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    catenin complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with cell-cell adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with cytoplasmic microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    kinetochore IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lamellipodium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ruffle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    adenomatous polyposis coli protein
    Names
    WNT signaling pathway regulator
    adenomatosis polyposis coli tumor suppressor
    deleted in polyposis 2.5
    protein phosphatase 1, regulatory subunit 46
    truncated adenomatosis polyposis coli

    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_008481.4 RefSeqGene

      Range
      19985..158719
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_130

    mRNA and Protein(s)

    1. NM_000038.5NP_000029.2  adenomatous polyposis coli protein isoform b

      See identical proteins and their annotated locations for NP_000029.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also contains an alternate in-frame exon compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is longer than isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AB210001, CA313732, DA795663, M73548
      Consensus CDS
      CCDS4107.1
      UniProtKB/Swiss-Prot
      P25054
      UniProtKB/TrEMBL
      Q4LE70
      Related
      ENSP00000257430, OTTHUMP00000159019, ENST00000257430, OTTHUMT00000250738
      Conserved Domains (14) summary
      cd00020
      Location:611731
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
      pfam05923
      Location:16371661
      APC_crr; APC cysteine-rich region
      pfam05924
      Location:20342053
      SAMP; SAMP Motif
      pfam05937
      Location:26702843
      EB1_binding; EB-1 Binding Domain
      pfam05956
      Location:22232568
      APC_basic; APC basic domain
      pfam11414
      Location:127207
      Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein
      pfam16629
      Location:7321019
      Arm_APC_u3; Armadillo-associated region on APC
      pfam16630
      Location:10361135
      APC_u5; Unstructured region on APC between 1st and 2nd catenin-bdg motifs
      pfam16633
      Location:12831368
      APC_u9; Unstructured region on APC between 1st two creatine-rich regions
      pfam16634
      Location:16621718
      APC_u13; Unstructured region on APC between APC_crr and SAMP
      pfam16635
      Location:17391839
      APC_u14; Unstructured region on APC between SAMP and APC_crr
      pfam16636
      Location:18761947
      APC_u15; Unstructured region on APC between APC_crr regions 5 and 6
      pfam16689
      Location:455
      APC_N_CC; Coiled-coil N-terminus of APC, dimerization domain
      sd00043
      Location:465508
      ARM; armadillo repeat [structural motif]
    2. NM_001127510.2NP_001120982.1  adenomatous polyposis coli protein isoform b

      See identical proteins and their annotated locations for NP_001120982.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also contains an alternate in-frame exon compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is longer than isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AB210001, CA313732, DA795663
      Consensus CDS
      CCDS4107.1
      UniProtKB/Swiss-Prot
      P25054
      UniProtKB/TrEMBL
      Q4LE70
      Related
      ENSP00000427089, OTTHUMP00000222841, ENST00000508376, OTTHUMT00000370794
      Conserved Domains (14) summary
      cd00020
      Location:611731
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
      pfam05923
      Location:16371661
      APC_crr; APC cysteine-rich region
      pfam05924
      Location:20342053
      SAMP; SAMP Motif
      pfam05937
      Location:26702843
      EB1_binding; EB-1 Binding Domain
      pfam05956
      Location:22232568
      APC_basic; APC basic domain
      pfam11414
      Location:127207
      Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein
      pfam16629
      Location:7321019
      Arm_APC_u3; Armadillo-associated region on APC
      pfam16630
      Location:10361135
      APC_u5; Unstructured region on APC between 1st and 2nd catenin-bdg motifs
      pfam16633
      Location:12831368
      APC_u9; Unstructured region on APC between 1st two creatine-rich regions
      pfam16634
      Location:16621718
      APC_u13; Unstructured region on APC between APC_crr and SAMP
      pfam16635
      Location:17391839
      APC_u14; Unstructured region on APC between SAMP and APC_crr
      pfam16636
      Location:18761947
      APC_u15; Unstructured region on APC between APC_crr regions 5 and 6
      pfam16689
      Location:455
      APC_N_CC; Coiled-coil N-terminus of APC, dimerization domain
      sd00043
      Location:465508
      ARM; armadillo repeat [structural motif]
    3. NM_001127511.2NP_001120983.2  adenomatous polyposis coli protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the shorter isoform (a).
      Source sequence(s)
      AB210001, AK294544, BP230350, CA313732
      UniProtKB/TrEMBL
      B7Z2B6, Q4LE70
      Conserved Domains (13) summary
      cd00020
      Location:593713
      ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
      pfam05923
      Location:16191643
      APC_crr; APC cysteine-rich region
      pfam05924
      Location:20162035
      SAMP; SAMP Motif
      pfam05937
      Location:26522825
      EB1_binding; EB-1 Binding Domain
      pfam05956
      Location:22052550
      APC_basic; APC basic domain
      pfam11414
      Location:137217
      Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein
      pfam16629
      Location:7141001
      Arm_APC_u3; Armadillo-associated region on APC
      pfam16630
      Location:10181117
      APC_u5; Unstructured region on APC between 1st and 2nd catenin-bdg motifs
      pfam16633
      Location:12651350
      APC_u9; Unstructured region on APC between 1st two creatine-rich regions
      pfam16634
      Location:16441700
      APC_u13; Unstructured region on APC between APC_crr and SAMP
      pfam16635
      Location:17211821
      APC_u14; Unstructured region on APC between SAMP and APC_crr
      pfam16636
      Location:18581929
      APC_u15; Unstructured region on APC between APC_crr regions 5 and 6
      sd00043
      Location:447490
      ARM; armadillo repeat [structural motif]

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p7 Primary Assembly

      Range
      112707505..112846239
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018916.2 Alternate CHM1_1.1

      Range
      111476576..111615241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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