SYT17

synaptotagmin 17, the group of Synaptotagmins

Basic information

Region (hg38): 16:19167971-19268332

Links

ENSG00000103528 ∙ NCBI:51760 ∙ ∙ HGNC:24119 ∙ Uniprot:Q9BSW7 ∙ 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 SYT17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT17 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			39			39
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	40	0	0

Variants in SYT17

This is a list of pathogenic ClinVar variants found in the SYT17 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-19172760-T-C		not specified	Likely benign (Jan 01, 2025)
16-19172767-C-G		not specified	Uncertain significance (Jan 24, 2024)
16-19172770-T-C		not specified	Uncertain significance (May 09, 2024)
16-19173463-T-A		not specified	Uncertain significance (Oct 08, 2024)
16-19173485-G-T		not specified	Uncertain significance (Oct 22, 2024)
16-19173500-A-G		not specified	Uncertain significance (Aug 01, 2022)
16-19173559-G-T		not specified	Uncertain significance (Oct 14, 2023)
16-19180402-G-A		not specified	Uncertain significance (Jan 09, 2024)
16-19180413-A-C		not specified	Uncertain significance (Jun 02, 2023)
16-19180443-G-A		not specified	Uncertain significance (Mar 12, 2024)
16-19180474-C-T		not specified	Uncertain significance (Oct 06, 2022)
16-19180528-G-A		not specified	Uncertain significance (Dec 17, 2021)
16-19183528-G-A		not specified	Uncertain significance (Jan 14, 2025)
16-19183596-G-A		not specified	Uncertain significance (Jun 17, 2022)
16-19183607-G-C		not specified	Uncertain significance (Jan 24, 2024)
16-19183621-C-T		not specified	Uncertain significance (Apr 03, 2023)
16-19183650-G-A		not specified	Uncertain significance (Mar 05, 2025)
16-19183725-G-A		not specified	Uncertain significance (Jan 06, 2023)
16-19183730-G-C		not specified	Uncertain significance (Mar 01, 2024)
16-19183779-G-A		not specified	Uncertain significance (Nov 06, 2023)
16-19183806-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-19183821-A-G		not specified	Uncertain significance (Jan 19, 2024)
16-19183831-C-T		not specified	Uncertain significance (Nov 25, 2024)
16-19183855-C-T		not specified	Uncertain significance (Dec 04, 2023)
16-19183858-G-A		not specified	Uncertain significance (Oct 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT17	protein_coding	protein_coding	ENST00000355377	8	100360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000110	0.948	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	231	287	0.804	0.0000189	3106
Missense in Polyphen		57	80.605	0.70715		943
Synonymous	0.243	118	121	0.972	0.00000859	945
Loss of Function	1.81	11	19.7	0.559	9.06e-7	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000272	0.000272
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000269|PubMed:23999003}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.620
• rvis_EVS: -1.27
• rvis_percentile_EVS: 5.24

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.454
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.741

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt17

Gene ontology

• Biological process: regulation of dopamine secretion;synaptic vesicle exocytosis;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;synaptic vesicle endocytosis;calcium ion-regulated exocytosis of neurotransmitter;cellular response to calcium ion;positive regulation of dendrite extension
• Cellular component: trans-Golgi network;plasma membrane;exocytic vesicle;presynapse
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;protein binding;calcium-dependent phospholipid binding;syntaxin binding;clathrin binding