ANXA3

protein-coding

annexin A3, the group of Annexins

Gene summary

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. This protein functions in the inhibition of phopholipase A2 and cleavage of inositol 1,2-cyclic phosphate to form inositol 1-phosphate. This protein may also play a role in anti-coagulation. [provided by RefSeq, Jul 2008]

Previous symbols:

ANX3

MANE transcript

NM_005139.3

Inheritance

—

ClinVar variants

U:67B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr4:78,551,747-78,610,451

External References & Databases

Ensembl (ENSG00000138772)

Transcript & Mutation Effects

hg38 • Region Span ~58.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ANXA3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005139.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			62 clinvar	2 clinvar	2 clinvar	66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	67	2	2	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005139.3	RefSeq	NP_005130.1	12	MANE Select
ENST00000264908.11	Ensembl	ENSP00000264908.6	12	MANE Select
ENST00000503570.6	Ensembl	ENSP00000421015.2	10	Standard
ENST00000503570.7	Ensembl	ENSP00000421015.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prostaglandin Synthesis and Regulation

Biological Process

phagocytosis
homophilic cell adhesion via plasma membrane adhesion molecules
positive regulation of endothelial cell migration
hippocampus development
animal organ regeneration

Molecular Function

calcium ion binding
calcium-dependent phospholipid binding
phospholipase A2 inhibitor activity
calcium-dependent protein binding

Cellular Component

cytoplasm
cytosol
plasma membrane
membrane
axon

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264908
Coding exons: 12
Length: 58925
Individuals with no LoFs: 125580
Homozygous LoFs: 0
Heterozygous LoFs: 164
Defined: 125744
p: 0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.109	166	170	0.977	0.00000838	2102
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.0042	0.0042	notable
East Asian	0.00087	0.00087	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00046	0.00046	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.170

Intolerance Scores

LoFtool: 0.912
RVIS EVS: 1.24
RVIS percentile EVS: 93.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.736

Gene Damage Prediction

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