SYT3

protein-coding

synaptotagmin 3, the group of Synaptotagmins

Gene summary

Predicted to enable several functions, including calcium ion sensor activity; phospholipid binding activity; and protein dimerization activity. Involved in positive regulation of dendrite extension. Located in endosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001160329.2

Inheritance

—

ClinVar variants

U:86B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr19:50,621,307-50,639,881

External References & Databases

Ensembl (ENSG00000213023)

Transcript & Mutation Effects

hg38 • Region Span ~18.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYT3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001160329.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			84 clinvar	2 clinvar	1 clinvar	87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	86	4	1	91

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001160329.2	RefSeq	NP_001153801.1	8	MANE Select
ENST00000600079.6	Ensembl	ENSP00000469398.1	8	MANE Select
NM_001160328.2	RefSeq	NP_001153800.1	8	Standard
NM_001424344.1	RefSeq	NP_001411273.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of dopamine secretion
vesicle-mediated transport
calcium ion regulated exocytosis
regulation of calcium ion-dependent exocytosis
cellular response to calcium ion

Molecular Function

SNARE binding
phosphatidylserine binding
calcium ion binding
calcium-dependent phospholipid binding
syntaxin binding

Cellular Component

endosome
plasma membrane
integral component of membrane
transport vesicle membrane
exocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000338916
Coding exons: 8
Length: 47088
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125745
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.94	261	365	0.714	0.0000238	3732
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000020	0.000018	rare
South Asian	0.000034	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.603

Gene Damage Prediction

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