SYT7

synaptotagmin 7, the group of Synaptotagmins

Basic information

Region (hg38): 11:61513714-61581148

Previous symbols: [ "PCANAP7" ]

Links

ENSG00000011347 ∙ NCBI:9066 ∙ OMIM:604146 ∙ HGNC:11514 ∙ Uniprot:O43581 ∙ 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 SYT7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT7 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		1
missense			23	1	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in SYT7

This is a list of pathogenic ClinVar variants found in the SYT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61518658-G-A		not specified	Uncertain significance (May 14, 2024)
11-61523103-T-C		not specified	Likely benign (Oct 05, 2023)
11-61523170-C-T		not specified	Uncertain significance (Aug 26, 2024)
11-61523236-G-A		not specified	Uncertain significance (Sep 20, 2024)
11-61523260-C-A		not specified	Uncertain significance (Jan 16, 2024)
11-61523862-C-T		not specified	Uncertain significance (Aug 23, 2021)
11-61523863-G-A		not specified	Uncertain significance (Oct 07, 2024)
11-61523908-A-G		not specified	Uncertain significance (Feb 22, 2024)
11-61523937-C-T		not specified	Uncertain significance (Dec 01, 2022)
11-61524455-G-A		not specified	Uncertain significance (Aug 15, 2023)
11-61528014-C-T		not specified	Uncertain significance (Jan 03, 2022)
11-61528078-G-A			Likely benign (Jan 01, 2023)
11-61528139-C-T		not specified	Uncertain significance (May 24, 2023)
11-61528162-A-C		not specified	Uncertain significance (Feb 23, 2023)
11-61533045-C-T		not specified	Uncertain significance (Aug 10, 2021)
11-61533113-C-T		not specified	Uncertain significance (Jun 29, 2023)
11-61542439-C-T			Benign (Feb 01, 2023)
11-61551406-G-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
11-61551454-A-C		not specified	Uncertain significance (May 06, 2024)
11-61551457-G-A		not specified	Uncertain significance (May 24, 2024)
11-61556133-C-T		not specified	Uncertain significance (Dec 14, 2023)
11-61556139-G-A		not specified	Uncertain significance (Jan 17, 2024)
11-61556139-G-C		not specified	Uncertain significance (Dec 26, 2023)
11-61556142-C-G		not specified	Uncertain significance (Nov 12, 2021)
11-61556190-C-A		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT7	protein_coding	protein_coding	ENST00000540677	10	65836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0366	125090	0	2	125092	0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	189	296	0.638	0.0000203	3094
Missense in Polyphen		28	76.981	0.36373		827
Synonymous	0.174	130	133	0.981	0.0000103	955
Loss of Function	3.63	2	19.1	0.105	9.86e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000893	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ca(2+) sensor involved in Ca(2+)-dependent exocytosis of secretory and synaptic vesicles through Ca(2+) and phospholipid binding to the C2 domain (By similarity). Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity). SYT7 binds Ca(2+) with high affinity and slow kinetics compared to other synaptotagmins (By similarity). Involved in Ca(2+)-triggered lysosomal exocytosis, a major component of the plasma membrane repair (PubMed:11342594). Ca(2+)- regulated delivery of lysosomal membranes to the cell surface is also involved in the phagocytic uptake of particles by macrophages (By similarity). Ca(2+)-triggered lysosomal exocytosis also plays a role in bone remodeling by regulating secretory pathways in osteoclasts and osteoblasts (By similarity). In case of infection, involved in participates cell invasion by Trypanosoma cruzi via Ca(2+)-triggered lysosomal exocytosis (PubMed:11342594, PubMed:15811535). Involved in cholesterol transport from lysosome to peroxisome by promoting membrane contacts between lysosomes and peroxisomes: probably acts by promoting vesicle fusion by binding phosphatidylinositol-4,5-bisphosphate on peroxisomal membranes (By similarity). Acts as a key mediator of synaptic facilitation, a process also named short-term synaptic potentiation: synaptic facilitation takes place at synapses with a low initial release probability and is caused by influx of Ca(2+) into the axon terminal after spike generation, increasing the release probability of neurotransmitters (By similarity). Probably mediates synaptic facilitation by directly increasing the probability of release (By similarity). May also contribute to synaptic facilitation by regulating synaptic vesicle replenishment, a process required to ensure that synaptic vesicles are ready for the arrival of the next action potential: SYT7 is required for synaptic vesicle replenishment by acting as a sensor for Ca(2+) and by forming a complex with calmodulin (By similarity). Also acts as a regulator of Ca(2+)-dependent insulin and glucagon secretion in beta-cells (By similarity). Triggers exocytosis by promoting fusion pore opening and fusion pore expansion in chromaffin cells (By similarity). Also regulates the secretion of some non-synaptic secretory granules of specialized cells (By similarity). {ECO:0000250|UniProtKB:Q62747, ECO:0000250|UniProtKB:Q9R0N7, ECO:0000269|PubMed:11342594, ECO:0000269|PubMed:15811535}.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.139
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.882
• ghis: 0.681

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt7
• Phenotype: muscle phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; normal phenotype

Zebrafish Information Network

• Gene name: syt7b
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: physical object quality

Gene ontology

• Biological process: plasma membrane repair;phagocytosis;regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;synaptic vesicle recycling;regulation of bone remodeling;calcium ion-regulated exocytosis of neurotransmitter;regulation of phagocytosis;regulation of insulin secretion;regulation of glucagon secretion;cellular response to calcium ion;vesicle-mediated cholesterol transport;phagosome-lysosome fusion;calcium-dependent activation of synaptic vesicle fusion;regulation of synaptic vesicle endocytosis;short-term synaptic potentiation;calcium ion regulated lysosome exocytosis
• Cellular component: lysosome;lysosomal membrane;peroxisome;peroxisomal membrane;cytosol;plasma membrane;synaptic vesicle;cell junction;axon;dendrite;phagocytic vesicle membrane;synaptic vesicle membrane;dense core granule;early phagosome;neuron projection;neuronal cell body;axon terminus;extracellular exosome;exocytic vesicle;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;GABA-ergic synapse;integral component of presynaptic membrane
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;protein binding;calmodulin binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;syntaxin binding;clathrin binding