SYT11

synaptotagmin 11, the group of Synaptotagmins

Basic information

Region (hg38): 1:155859567-155885199

Links

ENSG00000132718

∙ NCBI:23208 ∙ OMIM:608741 ∙ HGNC:19239 ∙ Uniprot:Q9BT88 ∙ 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 SYT11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT11 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			20 clinvar	1 clinvar		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in SYT11

This is a list of pathogenic ClinVar variants found in the SYT11 region.

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

Position	Phenotype	Significance	ClinVar
1-155867985-G-A	not specified	Uncertain significance (Jul 06, 2021)	2235281
1-155868018-G-A	not specified	Uncertain significance (Nov 10, 2022)	2325259
1-155868030-G-A	not specified	Uncertain significance (Sep 03, 2024)	3452146
1-155868052-A-G	not specified	Uncertain significance (Dec 10, 2024)	2404987
1-155868126-C-T	not specified	Uncertain significance (Oct 02, 2023)	3172951
1-155868247-G-A	not specified	Likely benign (Apr 18, 2024)	3324020
1-155868259-C-T	not specified	Uncertain significance (Mar 20, 2023)	2527316
1-155868264-G-A	not specified	Uncertain significance (Mar 20, 2024)	3324019
1-155868285-A-G	not specified	Uncertain significance (Apr 07, 2022)	2227657
1-155868474-C-T	not specified	Uncertain significance (Aug 02, 2021)	2240215
1-155868477-G-A	not specified	Uncertain significance (Dec 28, 2022)	2340048
1-155868493-A-G	not specified	Uncertain significance (Sep 29, 2023)	3172952
1-155868555-C-T	not specified	Uncertain significance (Apr 26, 2024)	3324021
1-155868655-T-C	not specified	Uncertain significance (Jul 11, 2023)	2610326
1-155868657-C-T	not specified	Uncertain significance (Dec 17, 2021)	2267785
1-155868690-C-G	not specified	Uncertain significance (Jan 18, 2022)	2272174
1-155868777-A-C	not specified	Uncertain significance (Jun 22, 2021)	3172953
1-155881227-G-A	not specified	Uncertain significance (Dec 28, 2022)	2275298
1-155881285-T-C	not specified	Uncertain significance (Dec 20, 2023)	3172949
1-155881308-G-A	not specified	Uncertain significance (Feb 06, 2023)	2458861
1-155881359-G-A	not specified	Uncertain significance (Oct 02, 2023)	3172950

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT11	protein_coding	protein_coding	ENST00000368324	4	25691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.927	0.0732	125735	0	2	125737	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	178	253	0.703	0.0000142	2826
Missense in Polyphen		68	114.03	0.59632		1280
Synonymous	0.962	90	102	0.879	0.00000600	882
Loss of Function	3.05	1	12.7	0.0784	6.29e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. {ECO:0000250}.;
Pathway: Parkinsons Disease Pathway;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

pRec: 0.149

Intolerance Scores

loftool: 0.0933
rvis_EVS: -0.25
rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

pHI: 0.519
hipred: Y
hipred_score: 0.673
ghis: 0.582

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Syt11
Phenotype: normal phenotype;

Gene ontology

Biological process: plasma membrane repair;regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;negative regulation of neurotransmitter secretion;calcium ion-regulated exocytosis of neurotransmitter;negative regulation of phagocytosis;protein homotetramerization;cellular response to calcium ion;negative regulation of interleukin-6 secretion;negative regulation of clathrin-dependent endocytosis;negative regulation of synaptic vesicle endocytosis;regulation of defense response to bacterium;negative regulation of tumor necrosis factor secretion;negative regulation of membrane invagination;regulation of phagosome maturation;positive regulation of protein localization to phagocytic vesicle;negative regulation of clathrin-coated pit assembly;calcium ion regulated lysosome exocytosis
Cellular component: phagocytic cup;lysosome;plasma membrane;synaptic vesicle;postsynaptic density;cell junction;integral component of synaptic vesicle membrane;axon;early phagosome;neuron projection;terminal bouton;dendritic spine;cell body;phagocytic vesicle;perinuclear region of cytoplasm;presynaptic active zone membrane;recycling endosome;excitatory synapse;inhibitory synapse;exocytic vesicle;Schaffer collateral - CA1 synapse;presynapse;integral component of presynaptic active zone membrane
Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;protein binding;calcium-dependent phospholipid binding;clathrin binding;translation initiation factor binding;ubiquitin protein ligase binding;protein homodimerization activity;beta-tubulin binding