SYT4

synaptotagmin 4, the group of Synaptotagmins

Basic information

Region (hg38): 18:43267891-43277535

Links

ENSG00000132872 ∙ NCBI:6860 ∙ OMIM:600103 ∙ HGNC:11512 ∙ Uniprot:Q9H2B2 ∙ 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 SYT4 gene.

• Inborn genetic diseases (13 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT4 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			13	1	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	1

Variants in SYT4

This is a list of pathogenic ClinVar variants found in the SYT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-43270415-C-T		not specified	Uncertain significance (Jun 07, 2023)
18-43270537-T-C		not specified	Uncertain significance (Apr 04, 2023)
18-43271747-C-T		not specified	Uncertain significance (Sep 29, 2023)
18-43271819-C-T		not specified	Uncertain significance (Dec 20, 2022)
18-43273616-C-A		not specified	Uncertain significance (Nov 17, 2022)
18-43273651-G-A		not specified	Uncertain significance (Dec 02, 2022)
18-43273777-C-G		not specified	Uncertain significance (Mar 22, 2022)
18-43273788-G-A		not specified	Uncertain significance (Jun 06, 2023)
18-43273867-T-A		not specified	Uncertain significance (Dec 07, 2021)
18-43273924-C-T			Benign (Mar 29, 2018)
18-43273935-A-T			Likely benign (Dec 31, 2019)
18-43274208-C-G		not specified	Uncertain significance (Aug 02, 2021)
18-43274210-A-T		not specified	Uncertain significance (Dec 19, 2022)
18-43274224-T-C		not specified	Uncertain significance (Jun 29, 2023)
18-43274362-C-T		not specified	Uncertain significance (Jan 10, 2023)
18-43277277-G-A		not specified	Uncertain significance (May 18, 2022)
18-43277280-AT-A			not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT4	protein_coding	protein_coding	ENST00000255224	4	9773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.439	0.560	125688	0	18	125706	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0635	213	216	0.988	0.0000102	2779
Missense in Polyphen		74	86.452	0.85596		1161
Synonymous	-1.17	100	86.2	1.16	0.00000431	831
Loss of Function	2.74	3	14.1	0.212	7.19e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000124
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000616
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

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 (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000250|UniProtKB:P50232, ECO:0000269|PubMed:23999003}.

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.609
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.305
• hipred: Y
• hipred_score: 0.712
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: brain development;memory;positive regulation of glutamate secretion;regulation of dopamine secretion;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of calcium ion-dependent exocytosis;regulation of endocytosis;negative regulation of vesicle fusion;negative regulation of catecholamine secretion;negative regulation of calcium ion-dependent exocytosis;positive regulation of calcium ion-dependent exocytosis;negative regulation of short-term neuronal synaptic plasticity;calcium ion-regulated exocytosis of neurotransmitter;negative regulation of protein secretion;vesicle fusion with vesicle;secretory granule maturation;cellular response to calcium ion;regulation of presynaptic dense core granule exocytosis;trans-synaptic signaling by BDNF, modulating synaptic transmission;positive regulation of dendrite extension;negative regulation of dense core granule exocytosis;positive regulation of dense core granule exocytosis;negative regulation of retrograde trans-synaptic signaling by neuropeptide;negative regulation of synaptic vesicle exocytosis
• Cellular component: plasma membrane;cell junction;integral component of Golgi membrane;integral component of synaptic vesicle membrane;axon;dendrite;dense core granule membrane;neuron projection;neuronal cell body;intracellular membrane-bounded organelle;neuron projection terminus;perinuclear region of cytoplasm;exocytic vesicle;astrocyte projection;glutamatergic synapse;integral component of neuronal dense core vesicle membrane;microvesicle
• Molecular function: SNARE binding;phosphatidylserine binding;calcium ion binding;protein binding;calcium-dependent phospholipid binding;syntaxin-1 binding;clathrin binding;syntaxin-3 binding;protein homodimerization activity;protein heterodimerization activity