ANXA2

annexin A2, the group of Annexins

Basic information

Region (hg38): 15:60347133-60402883

Previous symbols: [ "ANX2", "ANX2L4", "CAL1H", "LPC2D" ]

Links

ENSG00000182718 ∙ NCBI:302 ∙ OMIM:151740 ∙ HGNC:537 ∙ Uniprot:P07355 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANXA2 gene.

• Inborn genetic diseases (2 variants)
• not provided (1 variants)

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			2		1	3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	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)
15-60352425-T-C		not specified	Uncertain significance (Dec 12, 2023)
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)
15-60386066-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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