SYT15

synaptotagmin 15, the group of Synaptotagmins

Basic information

Region (hg38): 10:46578216-46594173

Links

ENSG00000204176 ∙ NCBI:83849 ∙ OMIM:608081 ∙ HGNC:17167 ∙ Uniprot:Q9BQS2 ∙ 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 SYT15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT15 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						0
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in SYT15

This is a list of pathogenic ClinVar variants found in the SYT15 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-46580178-G-A		not specified	Uncertain significance (Feb 03, 2022)
10-46580182-T-C		not specified	Uncertain significance (Aug 22, 2022)
10-46580325-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-46580926-C-G		not specified	Likely benign (Sep 21, 2023)
10-46580964-G-C		not specified	Uncertain significance (Apr 06, 2023)
10-46580995-C-T		not specified	Uncertain significance (Jan 26, 2022)
10-46581941-T-C		not specified	Uncertain significance (Oct 03, 2022)
10-46582111-C-A		not specified	Uncertain significance (Sep 30, 2021)
10-46582147-C-T		not specified	Likely benign (Apr 04, 2023)
10-46583775-T-C		not specified	Uncertain significance (Feb 06, 2024)
10-46583861-C-G		not specified	Uncertain significance (Jul 19, 2022)
10-46584498-C-G		not specified	Uncertain significance (Jun 01, 2023)
10-46584577-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-46587613-G-A		not specified	Uncertain significance (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT15	protein_coding	protein_coding	ENST00000374321	8	15957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-15	0.00238	124292	0	373	124665	0.00150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0555	228	226	1.01	0.0000138	2506
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00777	0.00776
Ashkenazi Jewish	0.000806	0.000795
East Asian	0.000167	0.000167
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00182	0.00179
Middle Eastern	0.000167	0.000167
South Asian	0.000328	0.000327
Other	0.00166	0.00165

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0337
• hipred: N
• hipred_score: 0.264
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt15

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
• Cellular component: plasma membrane;integral component of membrane;exocytic vesicle
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;clathrin binding