ANXA2
annexin A2, the group of Annexins
Basic information
Region (hg38): 15:60347134-60402883
Previous symbols: [ "ANX2", "ANX2L4", "CAL1H", "LPC2D" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANXA2 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in ANXA2
This is a list of pathogenic ClinVar variants found in the ANXA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-60349159-C-A | not specified | Uncertain significance (Oct 20, 2021) | ||
| 15-60351196-C-T | not specified | Uncertain significance (May 10, 2024) | ||
| 15-60351247-C-A | not specified | Uncertain significance (Jul 16, 2024) | ||
| 15-60351753-C-T | not specified | Uncertain significance (Nov 13, 2024) | ||
| 15-60352407-G-A | not specified | Uncertain significance (Jun 11, 2024) | ||
| 15-60352425-T-C | not specified | Uncertain significance (Dec 12, 2023) | ||
| 15-60355935-A-G | not specified | Uncertain significance (May 01, 2024) | ||
| 15-60355940-C-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 15-60357154-T-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 15-60357233-G-T | not specified | Uncertain significance (Mar 01, 2024) | ||
| 15-60361006-C-A | Benign (Feb 23, 2021) | |||
| 15-60364471-C-G | not specified | Uncertain significance (Feb 21, 2024) | ||
| 15-60382402-A-G | not specified | Uncertain significance (Apr 15, 2024) | ||
| 15-60382432-G-T | not specified | Uncertain significance (Jul 27, 2024) | ||
| 15-60386066-C-T | not specified | Uncertain significance (Aug 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ANXA2 | protein_coding | protein_coding | ENST00000332680 | 13 | 55750 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000977 | 0.988 | 125729 | 0 | 19 | 125748 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.284 | 186 | 197 | 0.943 | 0.0000106 | 2329 |
| Missense in Polyphen | 33 | 42.305 | 0.78005 | 613 | ||
| Synonymous | -1.06 | 90 | 78.1 | 1.15 | 0.00000454 | 655 |
| Loss of Function | 2.22 | 10 | 21.0 | 0.476 | 9.67e-7 | 275 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000416 | 0.000416 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000704 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-regulated membrane-binding protein whose affinity for calcium is greatly enhanced by anionic phospholipids. It binds two calcium ions with high affinity. May be involved in heat-stress response. Inhibits PCSK9-enhanced LDLR degradation, probably reduces PCSK9 protein levels via a translational mechanism but also competes with LDLR for binding with PCSK9 (PubMed:18799458, PubMed:24808179, PubMed:22848640). {ECO:0000269|PubMed:18799458, ECO:0000269|PubMed:22848640, ECO:0000269|PubMed:24808179}.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Prostaglandin Synthesis and Regulation;Smooth Muscle Contraction;Neutrophil degranulation;Dissolution of Fibrin Clot;TCR;Innate Immune System;Immune System;Muscle contraction;EGFR1;Hemostasis;Gastrin
(Consensus)
Recessive Scores
- pRec
- 0.851
Intolerance Scores
- loftool
- 0.776
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.379
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.529
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Anxa2
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system 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);
Gene ontology
- Biological process
- angiogenesis;membrane raft assembly;positive regulation of receptor recycling;positive regulation of protein phosphorylation;growth plate cartilage development;vesicle budding from membrane;body fluid secretion;regulation of plasminogen activation;collagen fibril organization;biomineral tissue development;positive regulation of vesicle fusion;positive regulation of chondrocyte differentiation;negative regulation of low-density lipoprotein particle receptor catabolic process;interleukin-12-mediated signaling pathway;osteoclast development;fibrinolysis;negative regulation of catalytic activity;neutrophil degranulation;positive regulation of vacuole organization;negative regulation of development of symbiont involved in interaction with host;positive regulation by host of viral process;positive regulation of fibroblast proliferation;protein heterotetramerization;regulation of cytosolic calcium ion concentration;positive regulation of calcium ion transport;catabolism by host of symbiont protein;negative regulation by host of symbiont molecular function;endocardial cell differentiation;calcium ion transmembrane transport;protein localization to plasma membrane;response to thyroid hormone;cell-cell adhesion;positive regulation of viral life cycle;positive regulation of low-density lipoprotein particle clearance;positive regulation of low-density lipoprotein particle receptor binding;positive regulation of low-density lipoprotein receptor activity;positive regulation of receptor-mediated endocytosis involved in cholesterol transport
- Cellular component
- ruffle;extracellular region;basement membrane;extracellular space;nucleus;cytoplasm;lysosomal membrane;endosome;early endosome;lipid droplet;cytosol;plasma membrane;cell-cell adherens junction;cell cortex;cell surface;membrane;basolateral plasma membrane;extrinsic component of plasma membrane;midbody;late endosome membrane;vesicle;azurophil granule lumen;myelin sheath adaxonal region;sarcolemma;melanosome;Schmidt-Lanterman incisure;macropinosome;membrane raft;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome;PCSK9-AnxA2 complex
- Molecular function
- phosphatidylserine binding;protease binding;RNA binding;calcium channel activity;calcium ion binding;protein binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;cytoskeletal protein binding;Rab GTPase binding;phospholipase A2 inhibitor activity;identical protein binding;S100 protein binding;bone sialoprotein binding;virion binding;calcium-dependent protein binding;cadherin binding involved in cell-cell adhesion;molecular function regulator;voltage-gated calcium channel activity involved in regulation of cytosolic calcium levels