ANXA1

annexin A1, the group of Annexins|Receptor ligands

Basic information

Region (hg38): 9:73151865-73170629

Previous symbols: [ "ANX1", "LPC1" ]

Links

ENSG00000135046 ∙ NCBI:301 ∙ OMIM:151690 ∙ HGNC:533 ∙ Uniprot:P04083 ∙ 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 ANXA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANXA1 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					2	2
missense			36			36
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			1	1		2
Total	0	0	38	1	2

Variants in ANXA1

This is a list of pathogenic ClinVar variants found in the ANXA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-73158733-G-T		ANXA1-related disorder	Benign (Dec 10, 2018)
9-73158755-A-T		not specified	Uncertain significance (Jan 29, 2024)
9-73158765-C-T		not specified	Uncertain significance (Aug 01, 2024)
9-73159322-T-C		ANXA1-related disorder	Benign (Oct 28, 2019)
9-73159357-TCTAA-T			Uncertain significance (Aug 07, 2018)
9-73159371-A-G		not specified	Uncertain significance (Oct 25, 2024)
9-73159383-G-A		not specified	Uncertain significance (Mar 22, 2023)
9-73159421-A-C		not specified	Uncertain significance (Dec 03, 2024)
9-73159422-A-T		not specified	Uncertain significance (Feb 12, 2025)
9-73160249-CT-C		ANXA1-related disorder	Likely benign (Jan 22, 2020)
9-73160259-G-T			Likely benign (Apr 12, 2018)
9-73160270-A-T		not specified	Uncertain significance (Dec 11, 2023)
9-73160279-T-G		not specified	Uncertain significance (Jun 23, 2021)
9-73160300-A-G		not specified	Uncertain significance (May 23, 2023)
9-73160324-T-C		not specified	Uncertain significance (Feb 24, 2025)
9-73160339-C-T		not specified	Uncertain significance (Jul 02, 2024)
9-73160363-G-A		not specified	Uncertain significance (Jul 16, 2024)
9-73160371-A-T		not specified	Uncertain significance (Jan 29, 2024)
9-73160383-C-T		ANXA1-related disorder	Benign (May 24, 2019)
9-73160812-A-G		not specified	Uncertain significance (Feb 10, 2022)
9-73160831-T-C		not specified	Uncertain significance (Jun 05, 2024)
9-73160868-A-T		not specified	Uncertain significance (Mar 31, 2024)
9-73162812-C-G		not specified	Uncertain significance (May 09, 2022)
9-73162821-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-73163500-G-A		not specified	Uncertain significance (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANXA1	protein_coding	protein_coding	ENST00000376911	12	18637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-7	0.810	125618	0	116	125734	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0490	188	190	0.990	0.00000988	2252
Missense in Polyphen		50	57.299	0.87261		739
Synonymous	0.227	63	65.3	0.964	0.00000351	637
Loss of Function	1.46	14	21.2	0.659	0.00000107	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000653	0.000653
Finnish	0.00148	0.00148
European (Non-Finnish)	0.000372	0.000369
Middle Eastern	0.000653	0.000653
South Asian	0.000689	0.000686
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays important roles in the innate immune response as effector of glucocorticoid-mediated responses and regulator of the inflammatory process. Has anti-inflammatory activity (PubMed:8425544). Plays a role in glucocorticoid-mediated down- regulation of the early phase of the inflammatory response (By similarity). Promotes resolution of inflammation and wound healing (PubMed:25664854). Functions at least in part by activating the formyl peptide receptors and downstream signaling cascades (PubMed:15187149, PubMed:25664854). Promotes chemotaxis of granulocytes and monocytes via activation of the formyl peptide receptors (PubMed:15187149). Contributes to the adaptive immune response by enhancing signaling cascades that are triggered by T- cell activation, regulates differentiation and proliferation of activated T-cells (PubMed:17008549). Promotes the differentiation of T-cells into Th1 cells and negatively regulates differentiation into Th2 cells (PubMed:17008549). Has no effect on unstimulated T cells (PubMed:17008549). Promotes rearrangement of the actin cytoskeleton, cell polarization and cell migration (PubMed:15187149). Negatively regulates hormone exocytosis via activation of the formyl peptide receptors and reorganization of the actin cytoskeleton (PubMed:19625660). Has high affinity for Ca(2+) and can bind up to eight Ca(2+) ions (By similarity). Displays Ca(2+)-dependent binding to phospholipid membranes (PubMed:2532504, PubMed:8557678). Plays a role in the formation of phagocytic cups and phagosomes. Plays a role in phagocytosis by mediating the Ca(2+)-dependent interaction between phagosomes and the actin cytoskeleton (By similarity). {ECO:0000250|UniProtKB:P10107, ECO:0000250|UniProtKB:P19619, ECO:0000269|PubMed:15187149, ECO:0000269|PubMed:17008549, ECO:0000269|PubMed:19625660, ECO:0000269|PubMed:2532504, ECO:0000269|PubMed:25664854, ECO:0000269|PubMed:2936963, ECO:0000269|PubMed:8425544, ECO:0000269|PubMed:8557678}.
• Pathway: Integrated Breast Cancer Pathway;Spinal Cord Injury;VEGFA-VEGFR2 Signaling Pathway;Interleukin-4 and 13 signaling;Prostaglandin Synthesis and Regulation;Smooth Muscle Contraction;Signaling by GPCR;Signal Transduction;corticosteroids and cardioprotection;Formyl peptide receptors bind formyl peptides and many other ligands;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Muscle contraction;EGFR1;G alpha (i) signalling events;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.520

Intolerance Scores

• loftool: 0.826
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.797
• hipred: Y
• hipred_score: 0.765
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Anxa1
• Phenotype: skeleton phenotype; immune system 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); digestive/alimentary phenotype; neoplasm; 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); 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; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: neutrophil homeostasis;adaptive immune response;monocyte chemotaxis;regulation of leukocyte migration;phagocytosis;inflammatory response;signal transduction;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;regulation of cell shape;response to X-ray;myoblast migration involved in skeletal muscle regeneration;peptide cross-linking;cytokine-mediated signaling pathway;insulin secretion;keratinocyte differentiation;prostate gland development;endocrine pancreas development;positive regulation of vesicle fusion;positive regulation of prostaglandin biosynthetic process;actin cytoskeleton reorganization;response to estradiol;DNA duplex unwinding;regulation of interleukin-1 production;positive regulation of interleukin-2 production;positive regulation of neutrophil apoptotic process;cellular response to vascular endothelial growth factor stimulus;gliogenesis;positive regulation of T cell proliferation;regulation of cell population proliferation;response to drug;negative regulation of apoptotic process;response to peptide hormone;estrous cycle;innate immune response;positive regulation of T-helper 1 cell differentiation;negative regulation of T-helper 2 cell differentiation;negative regulation of exocytosis;alpha-beta T cell differentiation;regulation of hormone secretion;arachidonic acid secretion;regulation of inflammatory response;cellular response to hydrogen peroxide;hepatocyte differentiation;prolactin secretion;response to interleukin-1;cellular response to glucocorticoid stimulus;granulocyte chemotaxis;positive regulation of cell migration involved in sprouting angiogenesis;positive regulation of wound healing;neutrophil clearance;cell-cell adhesion;positive regulation of G1/S transition of mitotic cell cycle;negative regulation of phospholipase A2 activity;negative regulation of interleukin-8 secretion
• Cellular component: cornified envelope;phagocytic cup;extracellular region;extracellular space;nucleus;nucleoplasm;cytoplasm;endosome;cytosol;actin filament;plasma membrane;cell-cell adherens junction;focal adhesion;cell surface;basolateral plasma membrane;apical plasma membrane;lateral plasma membrane;extrinsic component of membrane;cytoplasmic vesicle membrane;extrinsic component of external side of plasma membrane;extrinsic component of endosome membrane;motile cilium;early endosome membrane;mitochondrial membrane;vesicle;protein-containing complex;sarcolemma;mast cell granule;collagen-containing extracellular matrix;extracellular exosome;synaptic membrane
• Molecular function: single-stranded DNA binding;single-stranded RNA binding;signaling receptor binding;structural molecule activity;calcium ion binding;protein binding;phospholipid binding;calcium-dependent phospholipid binding;phospholipase A2 inhibitor activity;protein binding, bridging;double-stranded DNA-dependent ATPase activity;protein homodimerization activity;calcium-dependent protein binding;cadherin binding involved in cell-cell adhesion;DNA/DNA annealing activity