ANXA4

annexin A4, the group of Annexins

Basic information

Region (hg38): 2:69644425-69827112

Previous symbols: [ "ANX4" ]

Links

ENSG00000196975 ∙ NCBI:307 ∙ OMIM:106491 ∙ HGNC:542 ∙ Uniprot:P09525 ∙ 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 ANXA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANXA4 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	2

Variants in ANXA4

This is a list of pathogenic ClinVar variants found in the ANXA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-69781573-T-C		not specified	Uncertain significance (Mar 07, 2024)
2-69788133-A-C		not specified	Uncertain significance (Jan 18, 2022)
2-69804559-G-A		not specified	Uncertain significance (Sep 22, 2022)
2-69804572-G-A		not specified	Uncertain significance (Oct 12, 2023)
2-69804614-G-C		not specified	Likely benign (Dec 21, 2022)
2-69806427-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-69806447-G-C		not specified	Uncertain significance (Jun 16, 2023)
2-69806458-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-69807912-G-A		not specified	Uncertain significance (Apr 27, 2023)
2-69807919-A-G		not specified	Uncertain significance (Sep 01, 2021)
2-69810594-A-G		not specified	Uncertain significance (May 26, 2023)
2-69810600-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-69810609-T-C		not specified	Uncertain significance (Nov 27, 2023)
2-69810614-G-T		not specified	Uncertain significance (Oct 20, 2023)
2-69810659-G-A		not specified	Uncertain significance (Feb 13, 2024)
2-69812682-C-T			Benign (Feb 08, 2018)
2-69812692-G-A		not specified	Likely benign (Aug 22, 2023)
2-69816183-A-T		not specified	Uncertain significance (Oct 13, 2023)
2-69818603-T-A		not specified	Uncertain significance (Jan 18, 2022)
2-69818605-A-G		not specified	Uncertain significance (Apr 19, 2024)
2-69818669-C-T			Benign (Jul 30, 2018)
2-69819331-C-T		not specified	Uncertain significance (May 18, 2023)
2-69820732-G-C		not specified	Uncertain significance (Apr 26, 2024)
2-69825498-T-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANXA4	protein_coding	protein_coding	ENST00000394295	12	182040

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-8	0.794	125668	0	79	125747	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.855	160	193	0.827	0.0000114	2093
Missense in Polyphen		60	81.844	0.73311		898
Synonymous	0.617	68	74.8	0.909	0.00000468	608
Loss of Function	1.50	16	23.9	0.669	0.00000152	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000674	0.000673
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000272	0.000272
South Asian	0.000751	0.000752
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium/phospholipid-binding protein which promotes membrane fusion and is involved in exocytosis. {ECO:0000250}.
• Pathway: Prostaglandin Synthesis and Regulation;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.196

Intolerance Scores

• loftool: 0.873
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• pHI: 0.198
• hipred: N
• hipred_score: 0.492
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.819

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Anxa4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: anxa4
• Affected structure: liver
• Phenotype tag: abnormal
• Phenotype quality: increased process quality

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;signal transduction;Notch signaling pathway;epithelial cell differentiation;negative regulation of NF-kappaB transcription factor activity;negative regulation of apoptotic process;negative regulation of catalytic activity;negative regulation of interleukin-8 secretion
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;cell surface;vesicle membrane;nuclear membrane;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: phospholipase inhibitor activity;calcium ion binding;protein binding;calcium-dependent phospholipid binding;heparin binding;chondroitin sulfate binding;identical protein binding;calcium-dependent protein binding;NF-kappaB binding