SYT10

synaptotagmin 10, the group of Synaptotagmins

Basic information

Region (hg38): 12:33374237-33439819

Links

ENSG00000110975 ∙ NCBI:341359 ∙ ∙ HGNC:19266 ∙ Uniprot:Q6XYQ8 ∙ 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 SYT10 gene.

• Inborn genetic diseases (23 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT10 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		2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	23	0	3

Variants in SYT10

This is a list of pathogenic ClinVar variants found in the SYT10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-33376847-G-T		not specified	Uncertain significance (Sep 22, 2022)
12-33376853-G-C		not specified	Uncertain significance (Nov 18, 2022)
12-33376888-G-A			Benign (Feb 25, 2018)
12-33379909-C-T		not specified	Uncertain significance (Aug 16, 2022)
12-33379912-C-T		not specified	Uncertain significance (May 11, 2022)
12-33379957-C-T		not specified	Uncertain significance (May 25, 2022)
12-33382351-A-G			Likely benign (Dec 01, 2022)
12-33382460-G-C			Benign (May 17, 2018)
12-33382487-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-33382489-T-G		not specified	Uncertain significance (Dec 08, 2023)
12-33382509-T-C		not specified	Uncertain significance (Jul 19, 2023)
12-33385194-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-33385290-T-C		not specified	Uncertain significance (Oct 04, 2022)
12-33407007-C-T		not specified	Uncertain significance (Jan 11, 2023)
12-33407010-G-T		not specified	Uncertain significance (Dec 12, 2023)
12-33407024-T-G		not specified	Uncertain significance (Mar 29, 2023)
12-33407034-C-A		not specified	Uncertain significance (Aug 01, 2022)
12-33407164-T-G		not specified	Uncertain significance (Dec 28, 2023)
12-33407338-T-A		not specified	Uncertain significance (Jul 08, 2022)
12-33426145-A-T		not specified	Uncertain significance (Apr 09, 2022)
12-33426186-T-C		not specified	Uncertain significance (Jan 21, 2022)
12-33426261-G-C		not specified	Uncertain significance (Dec 15, 2022)
12-33426271-C-T		not specified	Uncertain significance (Jun 18, 2021)
12-33426278-G-A			Benign (Dec 31, 2019)
12-33426308-T-G		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT10	protein_coding	protein_coding	ENST00000228567	7	65582

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000624	0.995	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.452	265	287	0.925	0.0000147	3435
Missense in Polyphen		110	127.1	0.86544		1632
Synonymous	0.370	100	105	0.954	0.00000549	998
Loss of Function	2.48	11	24.2	0.455	0.00000148	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000923	0.0000923
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000761	0.000761
South Asian	0.000233	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ca(2+) sensor specifically required for the Ca(2+)- dependent exocytosis of secretory vesicles containing IGF1 in neurons of the olfactory bulb. Exocytosis of IGF1 is required for sensory perception of smell. Not involved in Ca(2+)-dependent synaptic vesicle exocytosis (By similarity). Acts through Ca(2+) and phospholipid binding to the C2 domain: Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity). {ECO:0000250|UniProtKB:O08625, ECO:0000250|UniProtKB:Q9R0N4}.
• Pathway: Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.775
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.604
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.267

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt10
• Phenotype: normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: chemical synaptic transmission;sensory perception of smell;regulation of dopamine secretion;synaptic vesicle exocytosis;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;positive regulation of calcium ion-dependent exocytosis;cellular response to calcium ion
• Cellular component: plasma membrane;integral component of membrane;transport vesicle membrane;exocytic vesicle;presynapse
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;syntaxin binding;clathrin binding;protein homodimerization activity;protein heterodimerization activity