SYT6

synaptotagmin 6, the group of Synaptotagmins

Basic information

Region (hg38): 1:114089291-114153880

Links

ENSG00000134207 ∙ NCBI:148281 ∙ OMIM:607718 ∙ HGNC:18638 ∙ Uniprot:Q5T7P8 ∙ 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 SYT6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT6 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in SYT6

This is a list of pathogenic ClinVar variants found in the SYT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-114093793-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-114097771-C-T		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
1-114097773-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-114097821-A-G		not specified	Uncertain significance (Oct 22, 2021)
1-114097857-A-G		not specified	Uncertain significance (Dec 28, 2022)
1-114099119-G-A		not specified	Uncertain significance (Sep 22, 2023)
1-114099229-C-A		not specified	Uncertain significance (Mar 08, 2024)
1-114099230-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-114137514-T-A		not specified	Uncertain significance (Jun 10, 2022)
1-114137604-C-A		not specified	Uncertain significance (Aug 08, 2023)
1-114137604-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-114137638-G-A		not specified	Uncertain significance (Apr 18, 2024)
1-114137677-T-C		not specified	Uncertain significance (Nov 10, 2022)
1-114137736-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-114137737-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-114137774-G-T		not specified	Uncertain significance (Mar 25, 2024)
1-114137778-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-114137808-G-A		not specified	Uncertain significance (Apr 17, 2023)
1-114137901-G-T		not specified	Uncertain significance (Jan 04, 2022)
1-114137958-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-114138037-G-A		not specified	Uncertain significance (Oct 26, 2021)
1-114138045-G-T		not specified	Uncertain significance (Jan 09, 2024)
1-114139646-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-114139655-G-A		not specified	Uncertain significance (Apr 08, 2024)
1-114139663-C-T		not specified	Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT6	protein_coding	protein_coding	ENST00000609117	6	64629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00812	0.979	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.168	254	262	0.971	0.0000159	2810
Missense in Polyphen		108	132.06	0.81782		1415
Synonymous	0.108	101	102	0.986	0.00000604	831
Loss of Function	2.19	6	15.2	0.395	7.05e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00150
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000502	0.000489

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. May mediate Ca(2+)- regulation of exocytosis in acrosomal reaction in sperm (By similarity). {ECO:0000250|UniProtKB:Q9R0N8}.

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.463
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.884
• hipred: Y
• hipred_score: 0.506
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt6
• Phenotype: normal phenotype

Gene ontology

• Biological process: regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;acrosomal vesicle exocytosis;cellular response to calcium ion;presynaptic dense core vesicle exocytosis
• Cellular component: cytosol;plasma membrane;integral component of membrane;extrinsic component of membrane;cell junction;synaptic vesicle membrane;exocytic vesicle;perinuclear endoplasmic reticulum;glutamatergic synapse;integral component of synaptic membrane
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;syntaxin binding;clathrin binding;protein homodimerization activity;calcium-dependent protein binding