SYT8

synaptotagmin 8, the group of Synaptotagmins

Basic information

Region (hg38): 11:1828307-1837521

Links

ENSG00000149043 ∙ NCBI:90019 ∙ OMIM:607719 ∙ HGNC:19264 ∙ Uniprot:Q8NBV8 ∙ 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 SYT8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT8 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			35	1	2	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	2

Variants in SYT8

This is a list of pathogenic ClinVar variants found in the SYT8 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-1835109-G-T		not specified	Uncertain significance (Jan 22, 2024)
11-1835128-C-T		not specified	Uncertain significance (Aug 08, 2023)
11-1835301-C-T		not specified	Uncertain significance (May 27, 2022)
11-1835302-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-1835332-C-T		not specified	Uncertain significance (Nov 14, 2023)
11-1835361-T-C		not specified	Uncertain significance (Jun 26, 2024)
11-1835374-G-A		not specified	Uncertain significance (Aug 19, 2024)
11-1835422-G-C		not specified	Uncertain significance (Aug 28, 2024)
11-1835436-C-T		not specified	Uncertain significance (Apr 06, 2023)
11-1835451-A-C		not specified	Uncertain significance (Mar 29, 2022)
11-1835887-T-G		not specified	Uncertain significance (Dec 19, 2023)
11-1835920-C-T		not specified	Uncertain significance (May 08, 2023)
11-1835932-A-T		not specified	Uncertain significance (Aug 04, 2024)
11-1835939-G-C		not specified	Uncertain significance (Jan 04, 2024)
11-1835967-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-1835970-T-A			Benign (Feb 26, 2018)
11-1835977-G-A		not specified	Uncertain significance (Mar 23, 2023)
11-1836142-G-C		not specified	Uncertain significance (Feb 14, 2024)
11-1836174-G-A		not specified	Uncertain significance (Sep 29, 2023)
11-1836204-A-G		not specified	Uncertain significance (Aug 28, 2024)
11-1836211-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-1836247-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-1836253-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-1836258-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-1836435-C-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT8	protein_coding	protein_coding	ENST00000381968	9	10043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.89e-25	0.00000492	125435	1	250	125686	0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.237	261	250	1.04	0.0000166	2504
Missense in Polyphen		54	53.012	1.0186		711
Synonymous	-1.68	135	112	1.20	0.00000760	884
Loss of Function	-2.41	30	18.7	1.60	0.00000102	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00409	0.00406
Ashkenazi Jewish	0.00	0.00
East Asian	0.000280	0.000272
Finnish	0.000148	0.000139
European (Non-Finnish)	0.000936	0.000898
Middle Eastern	0.000280	0.000272
South Asian	0.000539	0.000523
Other	0.00120	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 4 may play a role in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues. Mediates Ca(2+)-regulation of exocytosis acrosomal reaction in sperm. May mediate Ca(2+)-regulation of exocytosis in insulin secreted cells (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.820
• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.63

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.146
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Syt8

Gene ontology

• Biological process: acrosome reaction;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
• Cellular component: acrosomal vesicle;plasma membrane;integral component of membrane;axon;synaptic vesicle membrane;dense core granule;exocytic vesicle
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;calcium-dependent phospholipid binding;syntaxin binding;clathrin binding;calcium-dependent protein binding