ANXA11

annexin A11, the group of Annexins

Basic information

Region (hg38): 10:80150888-80205572

Previous symbols: [ "ANX11" ]

Links

ENSG00000122359 ∙ NCBI:311 ∙ OMIM:602572 ∙ HGNC:535 ∙ Uniprot:P50995 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis type 23 (Strong), mode of inheritance: AD
• amyotrophic lateral sclerosis type 23 (Moderate), mode of inheritance: AD
• amyotrophic lateral sclerosis (Supportive), mode of inheritance: AD
• amyotrophic lateral sclerosis type 23 (Strong), mode of inheritance: AD
• inclusion body myopathy and brain white matter abnormalities (Limited), mode of inheritance: AD
• amyotrophic lateral sclerosis type 23 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amytrophic lateral sclerosis 23; Inclusion body myopathy and brain white matter abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	28469040; 34048612

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANXA11 gene.

• not provided (226 variants)
• Inborn genetic diseases (27 variants)
• Inclusion body myopathy and brain white matter abnormalities (27 variants)
• ANXA11-related condition (14 variants)
• Amyotrophic lateral sclerosis type 23 (6 variants)
• Amyotrophic lateral sclerosis (4 variants)
• Oculopharyngeal muscular dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANXA11 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			1	31	13	45
missense	2	2	92	8	12	116
nonsense			7			7
start loss			1			1
frameshift			5	1		6
inframe indel			4	1		5
splice donor/acceptor (+/-2bp)			1			1
splice region			6	7	3	16
non coding			1	15	40	56
Total	2	2	112	56	65

Highest pathogenic variant AF is 0.0000460

Variants in ANXA11

This is a list of pathogenic ClinVar variants found in the ANXA11 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80155849-C-A		ANXA11-related disorder	Likely benign (Apr 26, 2019)
10-80155860-T-C			Uncertain significance (May 09, 2021)
10-80155890-C-T		Amyotrophic lateral sclerosis	Uncertain significance (Jan 01, 2022)
10-80155891-G-A			Uncertain significance (Oct 23, 2021)
10-80155900-C-T			Uncertain significance (Feb 22, 2023)
10-80155902-G-T			Uncertain significance (Dec 09, 2022)
10-80155930-G-A			Likely benign (Jun 26, 2023)
10-80156034-T-C			Benign (May 10, 2021)
10-80157564-G-A		Inclusion body myopathy and brain white matter abnormalities	Benign (Dec 05, 2021)
10-80157634-C-T			Likely benign (Mar 06, 2023)
10-80157636-C-T			Uncertain significance (Oct 10, 2023)
10-80157637-G-A			Benign (Dec 04, 2023)
10-80157642-G-A		ANXA11-related disorder • Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
10-80157649-C-G			Uncertain significance (Mar 09, 2021)
10-80157650-G-A			Likely benign (Mar 24, 2023)
10-80157656-C-T			Likely benign (May 17, 2022)
10-80157665-GC-G			Uncertain significance (May 04, 2023)
10-80157674-C-T			Likely benign (Jun 01, 2021)
10-80157675-C-T		Amyotrophic lateral sclerosis type 23	Uncertain significance (Sep 03, 2023)
10-80157676-G-A			Uncertain significance (Sep 26, 2023)
10-80157695-G-A			Likely benign (Jun 04, 2023)
10-80157706-C-T			Uncertain significance (Nov 14, 2023)
10-80157717-C-T			Uncertain significance (Apr 12, 2022)
10-80157730-T-C			Benign (Feb 01, 2024)
10-80157734-A-C			Uncertain significance (Aug 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANXA11	protein_coding	protein_coding	ENST00000438331	14	54684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.70e-10	0.813	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.249	311	299	1.04	0.0000179	3197
Missense in Polyphen		118	123.95	0.95202		1243
Synonymous	-0.0192	121	121	1.00	0.00000772	1023
Loss of Function	1.64	19	28.5	0.668	0.00000153	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.000879	0.000870
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000160	0.000141
Middle Eastern	0.000879	0.000870
South Asian	0.000237	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds specifically to calcyclin in a calcium-dependent manner (By similarity). Required for midbody formation and completion of the terminal phase of cytokinesis. {ECO:0000250, ECO:0000269|PubMed:15197175}.
• Disease: DISEASE: Amyotrophic lateral sclerosis 23 (ALS23) [MIM:617839]: A form of amyotrophic lateral sclerosis, a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. ALS23 is an autosomal dominant form with incomplete penetrance. {ECO:0000269|PubMed:28469040}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.933
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.61

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.570
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Anxa11

Gene ontology

• Biological process: phagocytosis;cytokinetic process;response to calcium ion
• Cellular component: nuclear envelope;nucleoplasm;cytoplasm;spindle;cytosol;membrane;midbody;melanosome;specific granule;azurophil granule;phagocytic vesicle;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: RNA binding;calcium ion binding;protein binding;calcium-dependent phospholipid binding;phosphatidylethanolamine binding;MHC class II protein complex binding;S100 protein binding;calcium-dependent protein binding