ANXA9

protein-coding

annexin A9, the group of Annexins

Gene summary

The annexins are a family of calcium-dependent phospholipid-binding proteins. Members of the annexin family contain 4 internal repeat domains, each of which includes a type II calcium-binding site. The calcium-binding sites are required for annexins to aggregate and cooperatively bind anionic phospholipids and extracellular matrix proteins. This gene encodes a divergent member of the annexin protein family in which all four homologous type II calcium-binding sites in the conserved tetrad core contain amino acid substitutions that ablate their function. However, structural analysis suggests that the conserved putative ion channel formed by the tetrad core is intact. [provided by RefSeq, Jul 2008]

Previous symbols:

ANX31

MANE transcript

NM_003568.3

Inheritance

—

ClinVar variants

U:61B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr1:150,982,249-150,995,634

External References & Databases

Ensembl (ENSG00000143412)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 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 ANXA9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003568.3. 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			54 clinvar	4 clinvar		58
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	61	4	0	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003568.3	RefSeq	NP_003559.2	12	MANE Select
ENST00000368947.9	Ensembl	ENSP00000357943.4	12	MANE Select
ENST00000887887.1	Ensembl	ENSP00000557946.1	11	Standard
ENST00000887888.1	Ensembl	ENSP00000557947.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell-cell adhesion

Molecular Function

phosphatidylserine binding
calcium ion binding
protein binding
phospholipid binding
calcium-dependent phospholipid binding

Cellular Component

cytosol
cell surface

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368947
Coding exons: 12
Length: 13618
Individuals with no LoFs: 125601
Homozygous LoFs: 0
Heterozygous LoFs: 147
Defined: 125748
p: 0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.344	181	195	0.931	0.0000108	2219
Missense (PolyPhen)		52	61.879	0.84035		748
Synonymous	0.466	75	80.3	0.934	0.00000453	706
Loss of Function	-0.121	25	24.4	1.03	0.00000143	233

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00086	rare
Latino/Admixed American	0.00073	0.00072	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00077	0.00071	rare
Finnish	0.00074	0.00074	rare
European (Non-Finnish)	0.00043	0.00043	rare
South Asian	0.00079	0.00078	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Low affinity receptor for acetylcholine known to be targeted by disease-causing pemphigus vulgaris antibodies in keratinocytes. {ECO:0000269|PubMed:10899159}.;

Recessive Scores

pRec: 0.0977

Intolerance Scores

LoFtool: 0.942
RVIS EVS: 0.53
RVIS percentile EVS: 80.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.770

Gene Damage Prediction

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