SYT9

synaptotagmin 9, the group of Synaptotagmins

Basic information

Region (hg38): 11:7238777-7469043

Links

ENSG00000170743 ∙ NCBI:143425 ∙ OMIM:613528 ∙ HGNC:19265 ∙ Uniprot:Q86SS6 ∙ 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 SYT9 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT9 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in SYT9

This is a list of pathogenic ClinVar variants found in the SYT9 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-7252196-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-7252236-C-T		not specified	Uncertain significance (Nov 03, 2022)
11-7252295-C-G		not specified	Uncertain significance (Nov 21, 2023)
11-7303042-T-C		not specified	Uncertain significance (Mar 24, 2023)
11-7303110-G-A		not specified	Uncertain significance (Jun 22, 2021)
11-7303195-A-G		not specified	Uncertain significance (Apr 25, 2023)
11-7303212-A-G		not specified	Uncertain significance (Aug 08, 2023)
11-7303232-G-C		not specified	Uncertain significance (Oct 24, 2023)
11-7303236-T-C		not specified	Uncertain significance (Oct 14, 2023)
11-7303347-G-A		not specified	Likely benign (Dec 13, 2022)
11-7303350-C-T		not specified	Uncertain significance (Jun 29, 2023)
11-7313461-A-C		not specified	Uncertain significance (Aug 03, 2022)
11-7313534-G-A		not specified	Uncertain significance (Jan 31, 2024)
11-7313541-G-A		not specified	Likely benign (Sep 26, 2023)
11-7313699-C-T		not specified	Uncertain significance (May 31, 2023)
11-7313744-C-G		not specified	Uncertain significance (Jun 21, 2023)
11-7313841-G-A		not specified	Uncertain significance (Nov 09, 2021)
11-7416060-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-7416114-A-G		not specified	Uncertain significance (Mar 04, 2024)
11-7418093-A-T		not specified	Uncertain significance (Apr 12, 2022)
11-7418127-C-T		not specified	Uncertain significance (Sep 09, 2021)
11-7420507-G-A		not specified	Uncertain significance (Dec 13, 2022)
11-7420519-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-7420574-A-T		not specified	Uncertain significance (Mar 04, 2024)
11-7420600-C-T		not specified	Uncertain significance (Aug 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT9	protein_coding	protein_coding	ENST00000318881	7	230265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.309	0.691	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	211	272	0.776	0.0000155	3216
Missense in Polyphen		77	118.84	0.64792		1414
Synonymous	-0.117	115	113	1.01	0.00000696	956
Loss of Function	3.29	5	21.4	0.233	0.00000128	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Neuronal System;Clathrin-mediated endocytosis;Neurexins and neuroligins;Cargo recognition for clathrin-mediated endocytosis;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.546
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.359
• hipred: Y
• hipred_score: 0.749
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt9

Gene ontology

• Biological process: regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;regulation of insulin secretion;membrane organization;cellular response to calcium ion;calcium-dependent activation of synaptic vesicle fusion
• Cellular component: plasma membrane;cell junction;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;secretory granule membrane;dense core granule;exocytic vesicle;hippocampal mossy fiber to CA3 synapse
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;syntaxin binding;clathrin binding;identical protein binding