SYT15

protein-coding

synaptotagmin 15, the group of Synaptotagmins

Gene summary

This gene encodes a member of the Synaptotagmin (Syt) family of membrane trafficking proteins. Members of this family contain a transmembrane region and a C-terminal-type tandem C2 domain. Unlike related family members, the encoded protein may be involved in membrane trafficking in non-neuronal tissues. Two trancript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_031912.5

Inheritance

—

ClinVar variants

U:76B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.26

Max pathogenic AF

—

Genomic locus

chr10:46,578,217-46,594,173

External References & Databases

Ensembl (ENSG00000204176)

Transcript & Mutation Effects

hg38 • Region Span ~16.0 kb

Loading mutation effect viewer...

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 SYT15 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 80

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031912.5. 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						0
missense			73 clinvar	7 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	76	7	0	83

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031912.5	RefSeq	NP_114118.2	8	MANE Select
ENST00000374321.9	Ensembl	ENSP00000363441.4	8	MANE Select
NM_181519.3	RefSeq	NP_852660.1	8	Standard
ENST00000374323.8	Ensembl	ENSP00000363443.3	7	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
clathrin binding

Cellular Component

plasma membrane
integral component of membrane
exocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374321
Coding exons: 8
Length: 15957
Individuals with no LoFs: 124292
Homozygous LoFs: 0
Heterozygous LoFs: 373
Defined: 124665
p: 0.00150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0555	228	226	1.01	0.0000138	2506
Missense (PolyPhen)		67	65.197	1.0277		856
Synonymous	-0.202	102	99.4	1.03	0.00000630	779
Loss of Function	-0.953	20	15.9	1.26	7.65e-7	187

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0069	0.0069	notable
Latino/Admixed American	0.00090	0.00090	rare
Ashkenazi Jewish	0.00081	0.00080	rare
East Asian	0.00017	0.00017	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0018	0.0018	notable
South Asian	0.00033	0.00033	rare
Other	0.0017	0.0017	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues. {ECO:0000250}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

LoFtool: 0.990
RVIS EVS: 0.78
RVIS percentile EVS: 87.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.199

Gene Damage Prediction

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