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APC

APC regulator of WNT signaling pathway, the group of Armadillo repeat containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 5:112707497-112846239

Links

ENSG00000134982NCBI:324OMIM:611731HGNC:583Uniprot:P25054AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • familial adenomatous polyposis 1 (Moderate), mode of inheritance: AD
  • sarcoma (Moderate), mode of inheritance: AD
  • desmoid tumor (Strong), mode of inheritance: AD
  • familial adenomatous polyposis 1 (Strong), mode of inheritance: AD
  • familial adenomatous polyposis 1 (Definitive), mode of inheritance: AD
  • Cenani-Lenz syndactyly syndrome (Supportive), mode of inheritance: AR
  • Turcot syndrome with polyposis (Supportive), mode of inheritance: AD
  • APC-related attenuated familial adenomatous polyposis (Supportive), mode of inheritance: AD
  • gastric adenocarcinoma and proximal polyposis of the stomach (Supportive), mode of inheritance: AD
  • desmoid tumor (Definitive), mode of inheritance: AD
  • familial adenomatous polyposis 1 (Strong), mode of inheritance: AD
  • gastric adenocarcinoma and proximal polyposis of the stomach (Strong), mode of inheritance: AD
  • gastric adenocarcinoma and proximal polyposis of the stomach (Definitive), mode of inheritance: AD
  • classic or attenuated familial adenomatous polyposis (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Familial adenomatous polyposis 1; Desmoid disease, hereditary; Gastric adenocarcinoma and proximal polyposis of the stomachADOncologicDepending on the specific APC-related condition, individuals may be at risk for a variety of neoplasms, and surveillance (including for gastric adenocarcinoma, thyroid disease, duodenal and colonic neoplasms, and hepatoblastoma, the latter with ultrasound and serum AFP measurement, as well as for other types of neoplastic manifestations) may allow early detection and management, which may reduce morbidity and mortality; In FAP, medical management (with NSAIDs) have been reported to result in adenoma regression and decreased polyp number; Colectomy is indicated when a specific numeric/pathologic adenomatous burden has been reached; Prophylactic gastrectomy has been described in Gastric adenocarcinoma and proximal polyposis of the stomachDental; Dermatologic; Musculoskeletal; Oncologic; Ophthalmologic14902760; 14933371; 13707264; 13891268; 13946545; 14136536; 5644968; 5660317; 5660235; 5443116; 4739325; 4853059; 1111674; 856075; 880737; 739523; 758668; 7446647; 7296952; 7067564; 6121129; 7172944; 6887943; 6129922; 6690356; 2435780; 2827474; 3033343; 3821797; 3800608; 2848134; 2848134; 3338026; 2896968; 3354603; 2156161; 1658283; 1651174; 1651563; 1324223; 1317264; 1329510; 1314729; 1544113; 1316610; 1316858; 8281160; 8276387; 8244107; 8105087; 8385741; 8037405; 8064829; 7661930; 8826936; 8940264; 8940262; 8968744; 9215849; 9585611; 10504375; 10077730; 10782927; 10815155; 10874062; 11932472; 12621137; 17135589; 18395100; 19793053; 20301519; 20400027; 20105204; 21813476; 22305464; 22773231; 22886683; 27087319; 27343414; 31409086; 33242120
Gastric adenocarcinoma and proximal polyposis of the stomach results from variants in the APC gene promoter 1B

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APC gene.

  • Familial adenomatous polyposis 1 (9650 variants)
  • Hereditary cancer-predisposing syndrome (7008 variants)
  • not provided (2004 variants)
  • not specified (968 variants)
  • APC-Associated Polyposis Disorders (199 variants)
  • Familial multiple polyposis syndrome (151 variants)
  • Carcinoma of colon (144 variants)
  • APC-related condition (64 variants)
  • 6 conditions (58 variants)
  • Familial colorectal cancer (47 variants)
  • Ovarian cancer (21 variants)
  • Colorectal cancer (21 variants)
  • Colorectal cancer, susceptibility to (17 variants)
  • Hereditary cancer (16 variants)
  • Colorectal adenoma (13 variants)
  • Gardner syndrome (10 variants)
  • Gastric cancer (10 variants)
  • Neoplasm of the large intestine (9 variants)
  • Neoplasm of the liver (9 variants)
  • Desmoid disease, hereditary (8 variants)
  • Inborn genetic diseases (8 variants)
  • Malignant tumor of breast (6 variants)
  • Desmoid disease, hereditary;Familial adenomatous polyposis 1;Neoplasm of stomach;Carcinoma of colon;Hepatocellular carcinoma (6 variants)
  • Carcinoma of colon;Hepatocellular carcinoma;Familial adenomatous polyposis 1;Neoplasm of stomach;Desmoid disease, hereditary (5 variants)
  • Neoplasm of stomach (4 variants)
  • Colon cancer (4 variants)
  • Intrahepatic cholangiocarcinoma (3 variants)
  • Carcinoma of colon;Hepatocellular carcinoma;Desmoid disease, hereditary;Familial adenomatous polyposis 1;Neoplasm of stomach (3 variants)
  • Gastric adenocarcinoma and proximal polyposis of the stomach (3 variants)
  • Colon adenocarcinoma (3 variants)
  • Neoplasm of stomach;Carcinoma of colon;Hepatocellular carcinoma;Desmoid disease, hereditary;Familial adenomatous polyposis 1 (3 variants)
  • Rectum adenocarcinoma (3 variants)
  • Carcinoma of colon;Familial adenomatous polyposis 1;Neoplasm of stomach;Desmoid disease, hereditary;Hepatocellular carcinoma (3 variants)
  • Periampullary adenoma (2 variants)
  • Lung adenocarcinoma (2 variants)
  • Endometrial carcinoma (2 variants)
  • Breast carcinoma (2 variants)
  • Desmoid disease, hereditary;Neoplasm of stomach;Carcinoma of colon;Familial adenomatous polyposis 1;Hepatocellular carcinoma (2 variants)
  • Diffuse midline glioma, H3 K27-altered (2 variants)
  • Brain tumor-polyposis syndrome 2 (2 variants)
  • Desmoid disease, hereditary;Carcinoma of colon;Hepatocellular carcinoma;Familial adenomatous polyposis 1;Neoplasm of stomach (2 variants)
  • Hepatocellular carcinoma (2 variants)
  • Hepatocellular carcinoma;Neoplasm of stomach;Familial adenomatous polyposis 1;Desmoid disease, hereditary;Carcinoma of colon (2 variants)
  • Carcinoma of colon;Familial adenomatous polyposis 1;Hepatocellular carcinoma;Desmoid disease, hereditary;Neoplasm of stomach (1 variants)
  • Adenomatous colonic polyposis (1 variants)
  • Familial cancer of breast (1 variants)
  • Intestinal polyp;Duodenal polyposis;Adenomatous colonic polyposis;Gastric polyposis;Hyperplastic colonic polyposis (1 variants)
  • Craniopharyngioma (1 variants)
  • Atypical endometrial hyperplasia (1 variants)
  • Adenomatous polyposis coli, susceptibility to (1 variants)
  • Squamous cell carcinoma (1 variants)
  • Colonic neoplasm (1 variants)
  • Desmoid tumor (1 variants)
  • Neoplasm of stomach;Hepatocellular carcinoma;Desmoid disease, hereditary;Familial adenomatous polyposis 1;Carcinoma of colon (1 variants)
  • Familial adenomatous polyposis 1;Attenuated familial adenomatous polyposis (1 variants)
  • Gastrointestinal stromal tumor of small intestine (1 variants)
  • Familial adenomatous polyposis 1;Neoplasm of stomach (1 variants)
  • Klatskin tumor (1 variants)
  • Malignant tumor of ascending colon (1 variants)
  • Hepatocellular carcinoma;Desmoid disease, hereditary;Familial adenomatous polyposis 1;Neoplasm of stomach;Carcinoma of colon (1 variants)
  • Carcinoma of colon;Desmoid disease, hereditary;Familial adenomatous polyposis 1;Neoplasm of stomach;Hepatocellular carcinoma (1 variants)
  • Breast cancer, susceptibility to (1 variants)
  • Gastrointestinal stromal tumor (1 variants)
  • Familial adenomatous polyposis 1;Gastric adenocarcinoma and proximal polyposis of the stomach;APC-related attenuated familial adenomatous polyposis (1 variants)
  • Familial adenomatous polyposis 1;Desmoid disease, hereditary (1 variants)
  • Hepatoblastoma (1 variants)
  • APC-related attenuated familial adenomatous polyposis;Gastric adenocarcinoma and proximal polyposis of the stomach;Familial adenomatous polyposis 1 (1 variants)
  • Monoclonal B-Cell Lymphocytosis (1 variants)
  • Duodenal adenocarcinoma (1 variants)
  • Colorectal cancer;Familial adenomatous polyposis 1 (1 variants)
  • Adenomatous polyposis coli with congenital cholesteatoma (1 variants)
  • Sigmoid colon cancer (1 variants)
  • Familial adenomatous polyposis 1;APC-related attenuated familial adenomatous polyposis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
25
clinvar
2135
clinvar
16
clinvar
2176
missense
6
clinvar
11
clinvar
5789
clinvar
43
clinvar
14
clinvar
5863
nonsense
511
clinvar
55
clinvar
5
clinvar
571
start loss
2
clinvar
2
frameshift
1249
clinvar
141
clinvar
11
clinvar
1401
inframe indel
157
clinvar
1
clinvar
1
clinvar
159
splice donor/acceptor (+/-2bp)
29
clinvar
81
clinvar
5
clinvar
1
clinvar
116
splice region
17
28
69
64
3
181
non coding
2
clinvar
13
clinvar
63
clinvar
295
clinvar
57
clinvar
430
Total 1797 301 6057 2475 88

Highest pathogenic variant AF is 0.0000131

Variants in APC

This is a list of pathogenic ClinVar variants found in the APC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
5-112707498-G-A Familial adenomatous polyposis 1 Uncertain significance (Nov 18, 2023)650293
5-112707499-C-A Familial adenomatous polyposis 1 Uncertain significance (Sep 17, 2022)2417404
5-112707499-C-T Familial adenomatous polyposis 1 Likely benign (Jan 19, 2024)469861
5-112707500-A-G Familial adenomatous polyposis 1 Uncertain significance (Nov 10, 2022)537606
5-112707501-T-C Familial adenomatous polyposis 1 Uncertain significance (Jul 08, 2023)1037649
5-112707503-G-A Familial adenomatous polyposis 1 Uncertain significance (Oct 03, 2023)1041870
5-112707504-T-C Familial adenomatous polyposis 1 Uncertain significance (Dec 18, 2023)663026
5-112707505-A-C Familial adenomatous polyposis 1 Uncertain significance (Jan 16, 2024)2739242
5-112707505-A-G Familial adenomatous polyposis 1 Uncertain significance (Nov 02, 2023)537657
5-112707505-A-T Familial adenomatous polyposis 1 Uncertain significance (Oct 07, 2018)641700
5-112707506-G-A Familial adenomatous polyposis 1 • APC-related disorder Conflicting classifications of pathogenicity (Oct 16, 2023)469860
5-112707508-C-T Familial adenomatous polyposis 1 Uncertain significance (Nov 21, 2023)1053776
5-112707510-T-C Familial adenomatous polyposis 1 Uncertain significance (Aug 04, 2023)1009705
5-112707511-C-T not specified • Familial adenomatous polyposis 1 Uncertain significance (Aug 15, 2023)2575447
5-112707512-C-T Familial adenomatous polyposis 1 Uncertain significance (Sep 01, 2021)1062527
5-112707513-C-G Familial adenomatous polyposis 1 Uncertain significance (Sep 01, 2021)1037374
5-112707513-C-T Familial adenomatous polyposis 1 Uncertain significance (Jul 11, 2022)1016911
5-112707514-A-G Familial adenomatous polyposis 1;Desmoid disease, hereditary;Carcinoma of colon;Neoplasm of stomach;Hepatocellular carcinoma • Familial adenomatous polyposis 1 • APC-related disorder Conflicting classifications of pathogenicity (Jan 24, 2024)469859
5-112707515-C-A Familial adenomatous polyposis 1 Uncertain significance (Jan 31, 2024)1059105
5-112707515-C-T Familial adenomatous polyposis 1 Uncertain significance (Dec 23, 2023)1051274
5-112707517-T-C Familial adenomatous polyposis 1 Uncertain significance (Dec 06, 2018)660746
5-112707518-C-A Familial adenomatous polyposis 1 Uncertain significance (Apr 04, 2019)1023330
5-112707518-C-T Familial adenomatous polyposis 1 Uncertain significance (Dec 25, 2023)1062677
5-112707519-C-G Familial adenomatous polyposis 1 Uncertain significance (Sep 01, 2022)1052999
5-112707519-C-T Familial adenomatous polyposis 1 Likely benign (Jan 09, 2024)1111220

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
APCprotein_codingprotein_codingENST00000457016 15138742
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.005.56e-111257100381257480.000151
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.16814361.45e+30.9880.000075418618
Missense in Polyphen499573.430.87027508
Synonymous-1.985645071.110.00002535556
Loss of Function8.90111130.09720.000007121436

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004750.000474
Ashkenazi Jewish0.0001090.0000992
East Asian0.00005440.0000544
Finnish0.0002770.000231
European (Non-Finnish)0.0001240.000123
Middle Eastern0.00005440.0000544
South Asian0.00006540.0000653
Other0.0003270.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Tumor suppressor. Promotes rapid degradation of CTNNB1 and participates in Wnt signaling as a negative regulator. APC activity is correlated with its phosphorylation state. Activates the GEF activity of SPATA13 and ARHGEF4. Plays a role in hepatocyte growth factor (HGF)-induced cell migration. Required for MMP9 up-regulation via the JNK signaling pathway in colorectal tumor cells. Acts as a mediator of ERBB2-dependent stabilization of microtubules at the cell cortex. It is required for the localization of MACF1 to the cell membrane and this localization of MACF1 is critical for its function in microtubule stabilization. {ECO:0000269|PubMed:10947987, ECO:0000269|PubMed:17599059, ECO:0000269|PubMed:19151759, ECO:0000269|PubMed:19893577, ECO:0000269|PubMed:20937854}.;
Disease
DISEASE: Familial adenomatous polyposis (FAP) [MIM:175100]: A cancer predisposition syndrome characterized by adenomatous polyps of the colon and rectum, but also of upper gastrointestinal tract (ampullary, duodenal and gastric adenomas). This is a viciously premalignant disease with one or more polyps progressing through dysplasia to malignancy in untreated gene carriers with a median age at diagnosis of 40 years. {ECO:0000269|PubMed:10470088, ECO:0000269|PubMed:1338691, ECO:0000269|PubMed:1338764, ECO:0000269|PubMed:1338904, ECO:0000269|PubMed:1651563, ECO:0000269|PubMed:21643010, ECO:0000269|PubMed:27217144, ECO:0000269|PubMed:7661930, ECO:0000269|PubMed:7833149, ECO:0000269|PubMed:7833931, ECO:0000269|PubMed:8990002}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hereditary desmoid disease (HDD) [MIM:135290]: Autosomal dominant trait with 100% penetrance and possible variable expression among affected relatives. HDD patients show multifocal fibromatosis of the paraspinal muscles, breast, occiput, arms, lower ribs, abdominal wall, and mesentery. Desmoid tumors appears also as a complication of familial adenomatous polyposis. {ECO:0000269|PubMed:10782927, ECO:0000269|PubMed:8940264}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Medulloblastoma (MDB) [MIM:155255]: Malignant, invasive embryonal tumor of the cerebellum with a preferential manifestation in children. {ECO:0000269|PubMed:10666372}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Gastric cancer (GASC) [MIM:613659]: A malignant disease which starts in the stomach, can spread to the esophagus or the small intestine, and can extend through the stomach wall to nearby lymph nodes and organs. It also can metastasize to other parts of the body. The term gastric cancer or gastric carcinoma refers to adenocarcinoma of the stomach that accounts for most of all gastric malignant tumors. Two main histologic types are recognized, diffuse type and intestinal type carcinomas. Diffuse tumors are poorly differentiated infiltrating lesions, resulting in thickening of the stomach. In contrast, intestinal tumors are usually exophytic, often ulcerating, and associated with intestinal metaplasia of the stomach, most often observed in sporadic disease. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Hepatocellular carcinoma (HCC) [MIM:114550]: A primary malignant neoplasm of epithelial liver cells. The major risk factors for HCC are chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, prolonged dietary aflatoxin exposure, alcoholic cirrhosis, and cirrhosis due to other causes. Note=The gene represented in this entry may be involved in disease pathogenesis.;
Pathway
Gastric cancer - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Cell Cycle;Angiogenesis overview;Regulation of Microtubule Cytoskeleton;Gastric Cancer Network 1;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Endoderm Differentiation;Extracellular vesicle-mediated signaling in recipient cells;Copper homeostasis;Wnt Signaling Pathway;Wnt-beta-catenin Signaling Pathway in Leukemia;Regulation of Wnt-B-catenin Signaling by Small Molecule Compounds;Association Between Physico-Chemical Features and Toxicity Associated Pathways;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Endometrial cancer;Chromosomal and microsatellite instability in colorectal cancer;Wnt Signaling Pathway;Regulation of Actin Cytoskeleton;DNA Damage Response (only ATM dependent);Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Apoptotic cleavage of cellular proteins;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Disassembly of the destruction complex and recruitment of AXIN to the membrane;Ovarian tumor domain proteases;Deubiquitination;Beta-catenin phosphorylation cascade;Direct p53 effectors;Wnt;Wnt Canonical;Regulation of nuclear beta catenin signaling and target gene transcription;Degradation of beta catenin;Regulation of CDC42 activity;CDC42 signaling events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);TCF dependent signaling in response to WNT;Canonical Wnt signaling pathway;Wnt Mammals;Presenilin action in Notch and Wnt signaling (Consensus)

Recessive Scores

pRec
0.571

Intolerance Scores

loftool
0.00386
rvis_EVS
-2.52
rvis_percentile_EVS
0.9

Haploinsufficiency Scores

pHI
0.532
hipred
Y
hipred_score
0.731
ghis
0.625

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.859

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Apc
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; pigmentation phenotype; neoplasm; embryo phenotype;

Zebrafish Information Network

Gene name
apc
Affected structure
hepatocyte
Phenotype tag
abnormal
Phenotype quality
increased amount

Gene ontology

Biological process
mitotic cytokinesis;cell fate specification;cellular response to DNA damage stimulus;negative regulation of microtubule depolymerization;cell cycle arrest;mitotic spindle assembly checkpoint;cell adhesion;pattern specification process;negative regulation of cell population proliferation;insulin receptor signaling pathway;positive regulation of cell death;Wnt signaling pathway;cell migration;protein deubiquitination;positive regulation of cell migration;positive regulation of pseudopodium assembly;regulation of microtubule-based process;positive regulation of apoptotic process;regulation of cell differentiation;positive regulation of protein catabolic process;negative regulation of cyclin-dependent protein serine/threonine kinase activity;protein homooligomerization;regulation of attachment of spindle microtubules to kinetochore;protein-containing complex assembly;bicellular tight junction assembly;negative regulation of canonical Wnt signaling pathway;positive regulation of cold-induced thermogenesis;positive regulation of protein localization to centrosome;beta-catenin destruction complex assembly;beta-catenin destruction complex disassembly
Cellular component
kinetochore;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;microtubule;cytoplasmic microtubule;plasma membrane;cell-cell adherens junction;bicellular tight junction;lateral plasma membrane;catenin complex;lamellipodium;beta-catenin destruction complex;ruffle membrane;perinuclear region of cytoplasm;Wnt signalosome
Molecular function
protein binding;beta-catenin binding;microtubule binding;protein kinase regulator activity;protein kinase binding;ubiquitin protein ligase binding;identical protein binding;gamma-catenin binding;cadherin binding;microtubule plus-end binding;dynein complex binding