SYT3

synaptotagmin 3, the group of Synaptotagmins

Basic information

Region (hg38): 19:50621307-50639881

Links

ENSG00000213023 ∙ NCBI:84258 ∙ OMIM:600327 ∙ HGNC:11511 ∙ Uniprot:Q9BQG1 ∙ 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 SYT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT3 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			45		1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	45	1	2

Variants in SYT3

This is a list of pathogenic ClinVar variants found in the SYT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50622695-C-T		not specified	Uncertain significance (Jun 16, 2023)
19-50625206-C-T		not specified	Uncertain significance (Jun 27, 2022)
19-50625233-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-50625248-C-T		not specified	Uncertain significance (Jun 28, 2024)
19-50625412-C-A		not specified	Uncertain significance (Mar 01, 2023)
19-50625946-G-A			Likely benign (Apr 01, 2022)
19-50629308-C-T		not specified	Uncertain significance (Apr 04, 2023)
19-50629325-G-A		not specified	Uncertain significance (Jul 11, 2023)
19-50629380-C-A		not specified	Uncertain significance (Oct 29, 2024)
19-50629380-C-T		not specified	Uncertain significance (Mar 20, 2023)
19-50629488-C-T		not specified	Uncertain significance (Nov 24, 2024)
19-50629521-G-C			Benign (May 24, 2018)
19-50629851-T-C		not specified	Uncertain significance (Feb 08, 2023)
19-50629897-C-T		not specified	Uncertain significance (Nov 20, 2023)
19-50629984-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-50630100-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-50630101-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-50630116-G-A		not specified	Uncertain significance (Mar 07, 2023)
19-50630157-G-A		not specified	Uncertain significance (Sep 14, 2022)
19-50630170-A-G			Benign (Jul 13, 2018)
19-50632296-G-T		not specified	Uncertain significance (Mar 17, 2023)
19-50632311-C-A		not specified	Uncertain significance (Apr 01, 2024)
19-50632329-C-G		not specified	Uncertain significance (Mar 19, 2024)
19-50632361-A-T		not specified	Uncertain significance (Dec 18, 2023)
19-50632385-C-T		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT3	protein_coding	protein_coding	ENST00000338916	8	47088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.808	0.192	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	261	365	0.714	0.0000238	3732
Missense in Polyphen		53	109.01	0.48621		1164
Synonymous	0.952	153	169	0.907	0.0000117	1306
Loss of Function	3.67	4	23.0	0.174	0.00000131	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000197	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000342	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ca(2+) sensor involved in Ca(2+)-dependent exocytosis of secretory vesicles 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). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000250|UniProtKB:P40748, ECO:0000269|PubMed:23999003}.

Recessive Scores

• pRec: 0.0928

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.37

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.726
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.603

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt3
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;cellular response to calcium ion;positive regulation of dendrite extension
• Cellular component: endosome;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;syntaxin binding;clathrin binding