APC2 APC regulator of WNT signaling pathway 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: APC2provided by HGNC
Official Full Name: APC regulator of WNT signaling pathway 2provided by HGNC
Primary source: HGNC:HGNC:24036
See related: Ensembl:ENSG00000115266 MIM:612034; AllianceGenome:HGNC:24036
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: APCL; MRT74
Summary: This gene encodes a strongly conserved protein that has an N-terminal coiled-coil domain followed by an armadillo domain, five 20-amino acid repeats, and two SAMP domains. This protein promotes the assembly of a multiprotein complex that recruits and phosphorylates the Wnt effector beta-catenin and targets beta-catenin for ubiquitylation and proteasomal degradation. This protein therefore plays a role in the reduction of cytoplasmic levels of beta-catenin which in turn reduces activation of Wnt target genes that play a pivotal role in the pathogenesis of various human cancers. The protein encoded by this gene is closely related to the adenomatous polyposis coli (APC) tumor-suppressor protein and has similar tumor-suppressor effects. This gene also plays a role in actin assembly, cell-cell adhesion, and microtubule network formation through its interaction with cytoskeletal proteins. This gene has its highest expression in the central nervous system and is involved in brain development through cytoskeletal regulation in neurons. Alternative splicing produces multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2017]
Expression: Biased expression in brain (RPKM 24.7) and adrenal (RPKM 1.1) See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (1446230..1473244)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (1416241..1443282)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (1450120..1473243)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Reprint of: Recessive APC2 missense variants associated with epilepsies without neurodevelopmental disorders.
Title: Reprint of: Recessive APC2 missense variants associated with epilepsies without neurodevelopmental disorders.
Recessive APC2 missense variants associated with epilepsies without neurodevelopmental disorders.
Title: Recessive APC2 missense variants associated with epilepsies without neurodevelopmental disorders.
High miR-3648 expression and low APC2 expression are associated with shorter survival and tumor progression in NSCLC.
Title: High miR-3648 expression and low APC2 expression are associated with shorter survival and tumor progression in NSCLC.
What are the roles of global DNA and APC 2 gene promotor hypermethylation in multiple myeloma?
Title: What are the roles of global DNA and APC 2 gene promotor hypermethylation in multiple myeloma?
Whole-exome sequencing in adult patients with developmental and epileptic encephalopathy: It is never too late.
Title: Whole-exome sequencing in adult patients with developmental and epileptic encephalopathy: It is never too late.
METTL3 promotes tumour development by decreasing APC expression mediated by APC mRNA N(6)-methyladenosine-dependent YTHDF binding.
Title: METTL3 promotes tumour development by decreasing APC expression mediated by APC mRNA N(6)-methyladenosine-dependent YTHDF binding.
miR-3648 Promotes Prostate Cancer Cell Proliferation by Inhibiting Adenomatous Polyposis Coli 2.
Title: miR-3648 Promotes Prostate Cancer Cell Proliferation by Inhibiting Adenomatous Polyposis Coli 2.
findings identify APC2 as a radiographically distinguishable recessive form of lissencephaly
Title: Bi-allelic Loss of Human APC2, Encoding Adenomatous Polyposis Coli Protein 2, Leads to Lissencephaly, Subcortical Heterotopia, and Global Developmental Delay.
Hsa_circ_0009361 acted as a tumor suppressive sponge of miR-582, which could up-regulate the expression of APC2, inhibit the Wnt/beta-catenin signaling, and suppress the growth and metastasis of colorectal cancer
Title: Hsa_circ_0009361 acts as the sponge of miR-582 to suppress colorectal cancer progression by regulating APC2 expression.
These results demonstrate that the circ-PKD2/miR-204-3p/APC2 axis represents a novel pathway involved in the pathogenesis of oral squamous cell carcinoma (OSCC) and may serve as a novel therapeutic target of OSCC.
Title: circ-PKD2 inhibits carcinogenesis via the miR-204-3p/APC2 axis in oral squamous cell carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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

Associated conditions

Description	Tests
Cortical dysplasia, complex, with other brain malformations 10 MedGen: C5231458 OMIM: 618677 GeneReviews: Not available	Compare labs
Intellectual developmental disorder, autosomal recessive 74 MedGen: C4310684 OMIM: 617169 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2S2123 (e-PCR)
- UniSTS:154149

A009Q48 (e-PCR)
- UniSTS:35146

G32795 (e-PCR)
- UniSTS:117374

WI-14332 (e-PCR)
- UniSTS:49868

RH39051 (e-PCR)
- UniSTS:91382

RH36570 (e-PCR)
- UniSTS:49911

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables beta-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables gamma-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in activation of GTPase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in microtubule cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of microtubule depolymerization	IBA Inferred from Biological aspect of Ancestor more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in pattern specification process	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in actin filament	IDA Inferred from Direct Assay more info	PubMed
part_of beta-catenin destruction complex	IBA Inferred from Biological aspect of Ancestor more info
part_of beta-catenin destruction complex	NAS Non-traceable Author Statement more info	PubMed
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
part_of catenin complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with cytoplasmic microtubule	IBA Inferred from Biological aspect of Ancestor more info
colocalizes_with cytoplasmic microtubule	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
part_of filamentous actin	IDA Inferred from Direct Assay more info	PubMed
located_in intercellular bridge	IDA Inferred from Direct Assay more info
located_in lamellipodium membrane	IDA Inferred from Direct Assay more info	PubMed
located_in microtubule cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in midbody	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in postsynapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: adenomatous polyposis coli protein 2

Names: APC2, WNT signaling pathway regulator; adenomatosis polyposis coli 2; adenomatous polyposis coli like

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.

Genomic

NG_055243.1 RefSeqGene

Range

8854..31977

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001351273.1 → NP_001338202.1 adenomatous polyposis coli protein 2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate, in-frame splice site in the 5' coding region, compared to variant 1. This difference results in a protein (isoform 2) that is one amino acid shorter than isoform 1.

Source sequence(s)

AC027307

Conserved Domains (8) summary

smart00185
Location:613 → 653

ARM; Armadillo/beta-catenin-like repeats

pfam16689
Location:6 → 57

APC_N_CC; Coiled-coil N-terminus of APC, dimerisation domain

sd00043
Location:526 → 559

ARM; armadillo repeat [structural motif]

pfam05923
Location:1259 → 1280

APC_r; APC repeat

pfam05956
Location:1785 → 2111

APC_basic; APC basic domain

pfam11414
Location:124 → 204

Suppressor_APC; Adenomatous polyposis coli tumor suppressor protein

pfam16629
Location:696 → 943

Arm_APC_u3; Armadillo-associated region on APC

cl26464
Location:1314 → 1910

Atrophin-1; Atrophin-1 family
NM_005883.3 → NP_005874.1 adenomatous polyposis coli protein 2 isoform 1

See identical proteins and their annotated locations for NP_005874.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC027307, BC032573

Consensus CDS

CCDS12068.1

UniProtKB/Swiss-Prot

O95996, Q05BW4, Q9UBZ1, Q9UEM8, Q9UQJ8, Q9UQJ9, Q9Y632

Related

ENSP00000467073.2, ENST00000590469.6

Conserved Domains (8) summary

cd00020
Location:576 → 694

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:1260 → 1281

APC_crr; APC cysteine-rich region

pfam05924
Location:1626 → 1643

SAMP; SAMP Motif

pfam05956
Location:1786 → 2112

APC_basic; APC basic domain

pfam11414
Location:124 → 205

Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein

pfam16629
Location:697 → 944

Arm_APC_u3; Armadillo-associated region on APC

pfam16689
Location:6 → 57

APC_N_CC; Coiled-coil N-terminus of APC, dimerization domain

sd00043
Location:527 → 560

ARM; armadillo repeat [structural motif]

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

1446230..1473244

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005259475.3 → XP_005259532.1 adenomatous polyposis coli protein 2 isoform X3

See identical proteins and their annotated locations for XP_005259532.1

Conserved Domains (8) summary

cd00020
Location:600 → 718

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:1284 → 1305

APC_crr; APC cysteine-rich region

pfam05924
Location:1650 → 1667

SAMP; SAMP Motif

pfam05956
Location:1810 → 2136

APC_basic; APC basic domain

pfam11414
Location:148 → 229

Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein

pfam16629
Location:721 → 968

Arm_APC_u3; Armadillo-associated region on APC

pfam16689
Location:30 → 81

APC_N_CC; Coiled-coil N-terminus of APC, dimerization domain

sd00043
Location:551 → 584

ARM; armadillo repeat [structural motif]
XM_006722607.3 → XP_006722670.1 adenomatous polyposis coli protein 2 isoform X4

Conserved Domains (8) summary

cd00020
Location:599 → 717

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:1283 → 1304

APC_crr; APC cysteine-rich region

pfam05924
Location:1649 → 1666

SAMP; SAMP Motif

pfam05956
Location:1809 → 2135

APC_basic; APC basic domain

pfam11414
Location:148 → 228

Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein

pfam16629
Location:720 → 967

Arm_APC_u3; Armadillo-associated region on APC

pfam16689
Location:30 → 81

APC_N_CC; Coiled-coil N-terminus of APC, dimerization domain

sd00043
Location:550 → 583

ARM; armadillo repeat [structural motif]
XM_047438031.1 → XP_047293987.1 adenomatous polyposis coli protein 2 isoform X2
XM_006722608.4 → XP_006722671.3 adenomatous polyposis coli protein 2 isoform X1

UniProtKB/Swiss-Prot

O95996, Q05BW4, Q9UBZ1, Q9UEM8, Q9UQJ8, Q9UQJ9, Q9Y632
XM_006722610.4 → XP_006722673.3 adenomatous polyposis coli protein 2 isoform X2
XM_006722609.4 → XP_006722672.1 adenomatous polyposis coli protein 2 isoform X1

See identical proteins and their annotated locations for XP_006722672.1

UniProtKB/Swiss-Prot

O95996, Q05BW4, Q9UBZ1, Q9UEM8, Q9UQJ8, Q9UQJ9, Q9Y632

Related

ENSP00000442954.1, ENST00000535453.5

Conserved Domains (8) summary

cd00020
Location:576 → 694

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:1260 → 1281

APC_crr; APC cysteine-rich region

pfam05924
Location:1626 → 1643

SAMP; SAMP Motif

pfam05956
Location:1786 → 2112

APC_basic; APC basic domain

pfam11414
Location:124 → 205

Suppressor_APC; Adenomatous polyposis coli tumour suppressor protein

pfam16629
Location:697 → 944

Arm_APC_u3; Armadillo-associated region on APC

pfam16689
Location:6 → 57

APC_N_CC; Coiled-coil N-terminus of APC, dimerization domain

sd00043
Location:527 → 560

ARM; armadillo repeat [structural motif]
XM_047438032.1 → XP_047293988.1 adenomatous polyposis coli protein 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

1416241..1443282

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054319499.1 → XP_054175474.1 adenomatous polyposis coli protein 2 isoform X4
XM_054319498.1 → XP_054175473.1 adenomatous polyposis coli protein 2 isoform X3
XM_054319496.1 → XP_054175471.1 adenomatous polyposis coli protein 2 isoform X5
XM_054319497.1 → XP_054175472.1 adenomatous polyposis coli protein 2 isoform X6
XM_054319501.1 → XP_054175476.1 adenomatous polyposis coli protein 2 isoform X2
XM_054319502.1 → XP_054175477.1 adenomatous polyposis coli protein 2 isoform X2
XM_054319500.1 → XP_054175475.1 adenomatous polyposis coli protein 2 isoform X1

UniProtKB/Swiss-Prot

O95996, Q05BW4, Q9UBZ1, Q9UEM8, Q9UQJ8, Q9UQJ9, Q9Y632