ANXA13

gene
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Summary

ANXA13 (annexin A13, HGNC:536) is a protein-coding gene on chromosome 8q24.13, encoding Annexin A13 (P27216). Binds to membranes enriched in phosphatidylserine or phosphatidylglycerol in a calcium-dependent manner.

This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. The specific function of this gene has not yet been determined; however, it is associated with the plasma membrane of undifferentiated, proliferating endothelial cells and differentiated villus enterocytes. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 312 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 82 total — 4 pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_004306

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:536
Approved symbolANXA13
Nameannexin A13
Location8q24.13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000104537
Ensembl biotypeprotein_coding
OMIM602573
Entrez312

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000262219, ENST00000419625, ENST00000519045, ENST00000520519, ENST00000520591, ENST00000523822, ENST00000862979, ENST00000862980, ENST00000862981, ENST00000862982, ENST00000962456

RefSeq mRNA: 2 — MANE Select: NM_004306 NM_001003954, NM_004306

CCDS: CCDS34939, CCDS47917

Canonical transcript exons

ENST00000419625 — 11 exons

ExonStartEnd
ENSE00000703223123688871123688946
ENSE00000703231123695688123695721
ENSE00000703234123698389123698559
ENSE00000871715123693197123693298
ENSE00000871716123693711123693779
ENSE00000981342123702642123702736
ENSE00000981343123695502123695581
ENSE00001292122123737320123737393
ENSE00001308806123684610123684722
ENSE00002134040123680794123681359
ENSE00003576382123712678123712753

Expression profiles

Bgee: expression breadth ubiquitous, 149 present calls, max score 98.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.0216 / max 367.8843, expressed in 57 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
947400.955641
947390.033415
947410.032615

Top tissues by expression

277 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
gall bladderUBERON:000211098.37gold quality
jejunal mucosaUBERON:000039997.14gold quality
duodenumUBERON:000211495.14gold quality
right uterine tubeUBERON:000130294.96gold quality
rectumUBERON:000105290.36gold quality
pancreatic ductal cellCL:000207989.05silver quality
small intestine Peyer’s patchUBERON:000345487.87gold quality
small intestineUBERON:000210887.86gold quality
mucosa of transverse colonUBERON:000499185.02gold quality
mucosa of sigmoid colonUBERON:000499382.23gold quality
C1 segment of cervical spinal cordUBERON:000646981.93gold quality
ileal mucosaUBERON:000033181.76gold quality
seminal vesicleUBERON:000099881.22gold quality
epithelial cell of pancreasCL:000008380.96gold quality
transverse colonUBERON:000115780.09gold quality
colonic mucosaUBERON:000031779.98gold quality
intestineUBERON:000016078.84gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.63gold quality
spinal cordUBERON:000224077.71gold quality
jejunumUBERON:000211576.99gold quality
large intestineUBERON:000005975.61gold quality
colonUBERON:000115575.41gold quality
right lobe of liverUBERON:000111472.12gold quality
sigmoid colonUBERON:000115970.79gold quality
fallopian tubeUBERON:000388969.64gold quality
caput epididymisUBERON:000435868.44gold quality
liverUBERON:000210768.28gold quality
muscle layer of sigmoid colonUBERON:003580568.13gold quality
lower esophagus muscularis layerUBERON:003583367.38gold quality
lower esophagusUBERON:001347367.27gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-CURD-98yes527.09
E-GEOD-125970yes16.18
E-ANND-3yes10.63
E-MTAB-8410yes4.57
E-MTAB-5061no3.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting ANXA13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-477599.9875.006394
HSA-MIR-651-3P99.9473.485177
HSA-MIR-22-3P99.9368.13917
HSA-MIR-105-5P99.5469.242060
HSA-MIR-7853-5P99.5469.302055
HSA-MIR-486-5P99.5170.39707
HSA-MIR-122B-5P99.4670.811457
HSA-MIR-455-5P98.7467.31795
HSA-MIR-6868-3P98.6369.642259
HSA-MIR-6830-3P98.6268.071760
HSA-MIR-318898.5865.60878
HSA-MIR-93-3P98.1566.651309
HSA-MIR-93897.4168.28656

Literature-anchored findings (GeneRIF, showing 7)

  • Genetic Screening Revealed the Negative Regulation of miR-310~313 Cluster Members on Imd Pathway during Gram-Negative Bacterial Infection in Drosophila. (PMID:38790230)
  • The unique, conserved aspects of annexin A13 primary structure, gene organization, and genetic maps identify it as the probable common ancestor of all vertebrate annexins. (PMID:11961095)
  • Ectopic overexpression of Annexin A13 was likewise sufficient to sensitize malignant breast cancer cells to treatment with Rapamycin. (PMID:20701074)
  • High ANXA13 expression is associated with Refractory Lupus Nephritis. (PMID:26110394)
  • ANXA13 is associated with colorectal cancer cell invasion in vitro, and with lymph node metastasis and poor survival in colorectal cancer patients (PMID:28423508)
  • a mechanism for how the association of the ANX A13a isoform with the membrane is regulated (PMID:30610115)
  • Intracellular Transport of Ribosome-Inactivating Proteins Depends on Annexin 13. (PMID:33119820)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioanxa13lENSDARG00000013613
danio_rerioanxa14ENSDARG00000100104
mus_musculusAnxa13ENSMUSG00000055114
rattus_norvegicusAnxa13ENSRNOG00000007980
drosophila_melanogasterAnxB9FBGN0000083
drosophila_melanogasterAnxB11FBGN0030749

Paralogs (12): ANXA10 (ENSG00000109511), ANXA11 (ENSG00000122359), ANXA1 (ENSG00000135046), ANXA7 (ENSG00000138279), ANXA3 (ENSG00000138772), ANXA9 (ENSG00000143412), ANXA5 (ENSG00000164111), ANXA2 (ENSG00000182718), ANXA4 (ENSG00000196975), ANXA6 (ENSG00000197043), ANXA8L1 (ENSG00000264230), ANXA8 (ENSG00000265190)

Protein

Protein identifiers

Annexin A13P27216 (reviewed: P27216)

Alternative names: Annexin XIII, Annexin-13, Intestine-specific annexin

All UniProt accessions (2): E5RIN3, P27216

UniProt curated annotations — full annotation on UniProt →

Function. Binds to membranes enriched in phosphatidylserine or phosphatidylglycerol in a calcium-dependent manner. Half-maximal membrane binding requires about 60 uM calcium. Does not bind to membranes that lack phospholipids with an acidic headgroup. Binds to membranes enriched in phosphatidylserine or phosphatidylglycerol in a calcium-dependent manner, but requires higher calcium levels for membrane binding than isoform A. Half-maximal membrane binding requires about 320 uM calcium.

Subunit / interactions. Monomer and homodimer.

Subcellular location. Apical cell membrane. Cell membrane. Cytoplasmic vesicle.

Tissue specificity. Detected in epithelial cells in colon and jejunum (at protein level). Detected in epithelial cells in jejunum.

Domain organisation. A pair of annexin repeats may form one binding site for calcium and phospholipid.

Similarity. Belongs to the annexin family.

Isoforms (2)

UniProt IDNamesCanonical?
P27216-1A, Anx13A, A13ayes
P27216-2B, Anx13B, A13b

RefSeq proteins (2): NP_001003954, NP_004297* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001464AnnexinFamily
IPR009166ANX13Family
IPR018252Annexin_repeat_CSConserved_site
IPR018502Annexin_repeatRepeat
IPR037104Annexin_sfHomologous_superfamily

Pfam: PF00191

UniProt features (36 total): helix 18, repeat 4, sequence variant 3, mutagenesis site 3, strand 2, initiator methionine 1, chain 1, sequence conflict 1, turn 1, lipid moiety-binding region 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6B3IX-RAY DIFFRACTION2.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P27216-F195.000.92

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 2

Mutagenesis-validated functional residues (3):

PositionPhenotype
2loss of myristoylation. loss of location at the cell membrane.
32–34loss of dimerization. no effect on calcium-dependent membrane binding and location at the cell membrane.
73slightly increased dimerization. decreases calcium-dependent membrane binding and location at the cell membrane.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_VESICLE_MEDIATED_TRANSPORT, MODULE_453, HNF1_Q6, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, PUJANA_CHEK2_PCC_NETWORK, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT, RGTTAMWNATT_HNF1_01, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, GOBP_NEGATIVE_REGULATION_OF_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE

GO Biological Process (3): cell differentiation (GO:0030154), negative regulation of Golgi to plasma membrane protein transport (GO:0042997), positive regulation of Golgi to plasma membrane protein transport (GO:0042998)

GO Molecular Function (4): phosphatidylserine binding (GO:0001786), calcium ion binding (GO:0005509), calcium-dependent phospholipid binding (GO:0005544), phosphatidylglycerol binding (GO:1901611)

GO Cellular Component (13): obsolete extracellular space (GO:0005615), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), plasma membrane (GO:0005886), vesicle membrane (GO:0012506), membrane (GO:0016020), basolateral plasma membrane (GO:0016323), apical plasma membrane (GO:0016324), cytoplasmic vesicle (GO:0031410), membrane raft (GO:0045121), extracellular exosome (GO:0070062), exocytic vesicle (GO:0070382)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
phospholipid binding3
cellular anatomical structure3
regulation of Golgi to plasma membrane protein transport2
Golgi to plasma membrane protein transport2
anion binding2
plasma membrane region2
cellular developmental process1
negative regulation of protein transport1
negative regulation of protein localization to plasma membrane1
positive regulation of protein transport1
positive regulation of protein localization to plasma membrane1
modified amino acid binding1
metal ion binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
membrane1
cell periphery1
organelle membrane1
vesicle1
basal plasma membrane1
apical part of cell1
cytoplasm1
intracellular vesicle1
membrane microdomain1
extracellular vesicle1
transport vesicle1
secretory vesicle1

Protein interactions and networks

STRING

636 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ANXA13CSMD3Q7Z407833
ANXA13EXT1Q16394742
ANXA13TRPS1Q9UHF7726
ANXA13NKX3-2P78367411
ANXA13SGCAQ16586410
ANXA13DYSFO75923404
ANXA13LMO2P25791386
ANXA13ANXA5P08758386
ANXA13COL9A2Q14055361
ANXA13DLX2Q07687353
ANXA13APOBEC2Q9Y235353
ANXA13ACRBPQ8NEB7352
ANXA13ZPBP2Q6X784352
ANXA13SPACA3Q8IXA5352
ANXA13CYB5R2Q6BCY4348

IntAct

16 interactions, top by confidence:

ABTypeScore
DEUP1HIP1psi-mi:“MI:0914”(association)0.530
SCCPDHRPN1psi-mi:“MI:0914”(association)0.530
ARMC8VWA8psi-mi:“MI:0914”(association)0.350
EDARUPK3BL1psi-mi:“MI:0914”(association)0.350
DEFB109BCHST10psi-mi:“MI:0914”(association)0.350
SIRT3SRCpsi-mi:“MI:0914”(association)0.350
ARMS2PRKCApsi-mi:“MI:0914”(association)0.350
APBB1IPANXA13psi-mi:“MI:0914”(association)0.350
MSI2ANXA13psi-mi:“MI:0914”(association)0.350
ANXA2ANXA13psi-mi:“MI:0914”(association)0.350
SRPRAANXA13psi-mi:“MI:0914”(association)0.350
ZNF200ANXA13psi-mi:“MI:0914”(association)0.350
YIPF3EI24psi-mi:“MI:0914”(association)0.350
BCL2L12MCM3APpsi-mi:“MI:0914”(association)0.350
ANXA13NMT2psi-mi:“MI:0914”(association)0.350

BioGRID (33): ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS), ANXA13 (Affinity Capture-MS)

ESM2 similar proteins: A2SW69, A5A6L7, A6NMY6, O35639, O35640, O97529, P04272, P07355, P07356, P08132, P08758, P09525, P12429, P13214, P13928, P14668, P14669, P14824, P14950, P17153, P17785, P19620, P22464, P24551, P24801, P26256, P27006, P27216, P48036, P50994, P51074, P55260, P70075, P81287, P93157, P97429, Q07936, Q29471, Q2Q1M6, Q3SWX7

Diamond homologs: A2SW69, A5A6L7, A5A6M2, A6NMY6, C0HJG9, C1L7Y4, C4QH88, O35639, O35640, O76027, O97529, P04083, P04272, P07150, P07355, P07356, P08132, P08133, P08758, P09525, P10107, P12429, P13214, P13928, P14087, P14668, P14669, P14824, P14950, P17153, P17785, P19619, P19620, P20072, P20073, P22464, P22465, P24551, P24639, P24801

SIGNOR signaling

1 interactions.

AEffectBMechanism
ANXA13“up-regulates quantity”NEDD4relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 24 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Hemostasis511.3×8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

82 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic4
Likely pathogenic0
Uncertain significance67
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
144138GRCh38/hg38 8q24.13-24.21(chr8:122454392-128513076)x3Pathogenic
154743GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3Pathogenic
2671975GRCh37/hg19 8q24.13-24.21(chr8:124534271-129054138)x4Pathogenic
3245610NC_000008.10:g.(?124515613)(126379127_?)delPathogenic

SpliceAI

2212 predictions. Top by Δscore:

VariantEffectΔscore
8:123681360:C:CCacceptor_gain1.0000
8:123684604:TCTTA:Tdonor_loss1.0000
8:123684605:CTTAC:Cdonor_loss1.0000
8:123684606:TTA:Tdonor_loss1.0000
8:123684607:TA:Tdonor_loss1.0000
8:123684608:A:AGdonor_loss1.0000
8:123684719:CTCA:Cacceptor_gain1.0000
8:123684720:TCA:Tacceptor_gain1.0000
8:123684721:CA:Cacceptor_gain1.0000
8:123684721:CAC:Cacceptor_gain1.0000
8:123684723:C:CCacceptor_gain1.0000
8:123684728:C:CTacceptor_gain1.0000
8:123684729:A:Tacceptor_gain1.0000
8:123693717:CAGAT:Cdonor_gain1.0000
8:123695599:A:Tacceptor_gain1.0000
8:123712680:ATT:Adonor_gain1.0000
8:123735753:A:ACdonor_gain1.0000
8:123735754:C:CCdonor_gain1.0000
8:123735754:CAGG:Cdonor_gain1.0000
8:123737315:CTT:Cdonor_loss1.0000
8:123737317:TA:Tdonor_loss1.0000
8:123737318:A:ACdonor_gain1.0000
8:123737318:A:AGdonor_loss1.0000
8:123737319:C:CTdonor_gain1.0000
8:123737319:CATGA:Cdonor_gain1.0000
8:123681356:CCAC:Cacceptor_gain0.9900
8:123681357:CAC:Cacceptor_gain0.9900
8:123681357:CACC:Cacceptor_gain0.9900
8:123681358:ACC:Aacceptor_loss0.9900
8:123681360:C:Aacceptor_loss0.9900

AlphaMissense

2072 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:123681330:G:CF287L0.983
8:123681330:G:TF287L0.983
8:123681332:A:GF287L0.983
8:123693298:C:GA181P0.977
8:123693728:C:GA175P0.973
8:123702681:C:AR49S0.971
8:123702681:C:GR49S0.971
8:123693718:A:GL178P0.970
8:123698462:A:GL95P0.969
8:123693727:G:TA175D0.966
8:123695554:A:TV140D0.964
8:123681295:A:TV299D0.962
8:123693773:G:TR160S0.962
8:123693260:G:CF193L0.960
8:123693260:G:TF193L0.960
8:123693262:A:GF193L0.960
8:123693212:A:CF209L0.958
8:123693212:A:TF209L0.958
8:123693214:A:GF209L0.958
8:123695566:A:TL136H0.958
8:123702706:A:GL41S0.957
8:123698406:A:GC114R0.953
8:123702662:A:CY56D0.953
8:123693739:G:TA171D0.951
8:123681270:G:CF307L0.950
8:123681270:G:TF307L0.950
8:123681272:A:GF307L0.950
8:123688918:A:TI224N0.950
8:123693225:A:GL205S0.950
8:123698454:C:GA98P0.949

dbSNP variants (sampled 300 via entrez): RS1000022725 (8:123739135 C>A,T), RS1000055906 (8:123719321 C>G,T), RS1000076265 (8:123703757 A>G), RS1000146174 (8:123703492 T>A,C), RS1000153981 (8:123692666 T>A), RS1000234375 (8:123737689 G>A), RS1000258636 (8:123735974 G>A,T), RS1000269342 (8:123696591 G>A), RS1000370391 (8:123725557 T>C), RS1000433082 (8:123733498 A>C), RS1000623714 (8:123737584 G>A), RS1000657141 (8:123708810 G>A), RS1000730742 (8:123686422 T>C), RS1000731880 (8:123703548 A>T), RS1000768167 (8:123694442 C>G)

Disease associations

OMIM: gene MIM:602573 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): distal trisomy 8q (MONDO:0019882)

Orphanet (1): Distal duplication 8q syndrome (Orphanet:96100)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST000857_3Event-related brain oscillations9.000000e-06
GCST003225_15Pelvic organ prolapse (moderate/severe)9.000000e-06
GCST005076_17Breast cancer (estrogen-receptor negative)2.000000e-08
GCST005077_8Breast cancer2.000000e-11
GCST006979_369Heel bone mineral density1.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004358event-related brain oscillation
EFO:0009270heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6196076 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophendecreases expression2
Tetrachlorodibenzodioxindecreases expression, affects expression, affects cotreatment2
propionaldehydedecreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
titanium dioxidedecreases expression1
beta-lapachonedecreases expression1
sodium arseniteaffects methylation1
butyraldehydedecreases expression1
butylbenzyl phthalatedecreases expression1
pentanaldecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
nutlin 3increases expression1
abrinedecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Irinotecandecreases expression1
Air Pollutantsdecreases expression1
Aldehydesdecreases expression1
Catechinaffects cotreatment, decreases expression1
Cisplatinincreases expression, affects cotreatment1
Dimethyl Sulfoxideincreases expression1
Endosulfanaffects cotreatment, decreases expression1
Folic Acidaffects expression1
Hydrogen Peroxideaffects expression1
Silicon Dioxidedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Aciddecreases expression1
Cyclosporinedecreases expression1

ChEMBL screening assays

6 unique, capped per target: 6 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL6106837BindingInduction of ANXA13 degradation in human MDA-MB-231 cells at 0.5 to 6 uM incubated for 24 hrs by Western blot analysis relative to controlDiscovery of a Novel 1,4-Benzodiazepine Derivative as a Highly Selective ANXA3 Degrader for the Treatment of Triple-Negative Breast Cancer. — J Med Chem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.