ANXA3

annexin A3, the group of Annexins

Basic information

Region (hg38): 4:78551746-78610451

Previous symbols: [ "ANX3" ]

Links

ENSG00000138772 ∙ NCBI:306 ∙ OMIM:106490 ∙ HGNC:541 ∙ Uniprot:P12429 ∙ 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 ANXA3 gene.

• Inborn genetic diseases (15 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANXA3 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			14	2	2	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	2

Variants in ANXA3

This is a list of pathogenic ClinVar variants found in the ANXA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-78554483-A-C		not specified	Uncertain significance (Nov 27, 2023)
4-78554487-G-C		not specified	Uncertain significance (Jan 18, 2023)
4-78573220-G-A			Benign (Dec 31, 2019)
4-78573221-C-A		not specified	Uncertain significance (Feb 12, 2024)
4-78573264-A-T		not specified	Uncertain significance (Dec 12, 2023)
4-78579062-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-78579092-G-T		not specified	Uncertain significance (Aug 22, 2023)
4-78582249-C-G		not specified	Uncertain significance (Aug 23, 2021)
4-78586263-G-A		not specified	Likely benign (Feb 15, 2023)
4-78586315-G-A		not specified	Uncertain significance (Oct 20, 2023)
4-78591555-A-G		not specified	Uncertain significance (Jun 23, 2023)
4-78591562-G-A		not specified	Uncertain significance (Jul 08, 2022)
4-78591579-G-A		not specified	Uncertain significance (Apr 05, 2023)
4-78595393-G-A		not specified	Uncertain significance (Apr 27, 2022)
4-78595800-T-C		not specified	Uncertain significance (May 25, 2022)
4-78595815-A-G		not specified	Uncertain significance (Jun 24, 2022)
4-78595828-C-A		not specified	Uncertain significance (Dec 08, 2023)
4-78595833-G-A		not specified	Uncertain significance (May 03, 2023)
4-78597321-T-A		not specified	Uncertain significance (Jan 03, 2024)
4-78597340-T-A			Benign (Apr 10, 2018)
4-78597346-A-C		not specified	Uncertain significance (Feb 06, 2023)
4-78601545-G-A		not specified	Uncertain significance (Jul 05, 2023)
4-78604308-G-C		not specified	Uncertain significance (Apr 13, 2022)
4-78610057-C-T		not specified	Uncertain significance (Oct 25, 2022)
4-78610081-T-C			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANXA3	protein_coding	protein_coding	ENST00000264908	12	58925

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.52e-12	0.123	125580	0	164	125744	0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.109	166	170	0.977	0.00000838	2102
Missense in Polyphen		62	65.236	0.9504		814
Synonymous	-0.206	65	62.9	1.03	0.00000324	589
Loss of Function	0.603	19	22.1	0.861	0.00000123	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00201	0.00201
Ashkenazi Jewish	0.00417	0.00418
East Asian	0.000873	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000274	0.000264
Middle Eastern	0.000873	0.000870
South Asian	0.000459	0.000457
Other	0.000823	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of phospholipase A2, also possesses anti- coagulant properties. Also cleaves the cyclic bond of inositol 1,2-cyclic phosphate to form inositol 1-phosphate.
• Pathway: Prostaglandin Synthesis and Regulation (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.912
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.35

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.199
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.736

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anxa3
• Phenotype: limbs/digits/tail phenotype; vision/eye 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: phagocytosis;homophilic cell adhesion via plasma membrane adhesion molecules;positive regulation of endothelial cell migration;hippocampus development;animal organ regeneration;defense response to bacterium;negative regulation of catalytic activity;neutrophil degranulation;positive regulation of angiogenesis;positive regulation of DNA metabolic process;positive regulation of DNA-binding transcription factor activity;response to glucocorticoid;response to growth factor;regulation of NMDA receptor activity
• Cellular component: cytoplasm;cytosol;plasma membrane;membrane;axon;dendrite;phagocytic vesicle membrane;specific granule;neuronal cell body;extracellular exosome
• Molecular function: calcium ion binding;calcium-dependent phospholipid binding;phospholipase A2 inhibitor activity;calcium-dependent protein binding