SYTL3

synaptotagmin like 3, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): 6:158650013-158764876

Links

ENSG00000164674 ∙ NCBI:94120 ∙ ∙ HGNC:15587 ∙ Uniprot:Q4VX76 ∙ 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 SYTL3 gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYTL3 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				1		1
missense			17	2		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	17	3	0

Variants in SYTL3

This is a list of pathogenic ClinVar variants found in the SYTL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-158663288-T-A		not specified	Uncertain significance (Jul 06, 2022)
6-158663316-G-C		not specified	Uncertain significance (Nov 21, 2023)
6-158663377-C-T		not specified	Uncertain significance (Dec 18, 2023)
6-158665475-C-T		not specified	Uncertain significance (May 11, 2022)
6-158665484-A-G		not specified	Uncertain significance (Mar 01, 2024)
6-158665514-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-158665541-G-A		not specified	Uncertain significance (Nov 22, 2021)
6-158665550-C-T		not specified	Uncertain significance (Jun 23, 2023)
6-158665606-G-C		not specified	Uncertain significance (Aug 09, 2021)
6-158708345-C-T		not specified	Uncertain significance (Feb 27, 2023)
6-158718102-A-G		not specified	Uncertain significance (Jul 30, 2023)
6-158718107-G-A		not specified	Uncertain significance (Dec 26, 2023)
6-158718192-C-T		not specified	Uncertain significance (Jun 01, 2023)
6-158725554-T-C		not specified	Likely benign (Sep 14, 2022)
6-158725603-C-T		not specified	Uncertain significance (Dec 13, 2023)
6-158725627-G-T		not specified	Uncertain significance (Sep 16, 2021)
6-158745498-G-A		not specified	Likely benign (May 09, 2023)
6-158745565-T-C		not specified	Uncertain significance (Jul 11, 2023)
6-158745574-G-T		not specified	Uncertain significance (Oct 03, 2022)
6-158757242-G-A		not specified	Uncertain significance (Oct 18, 2021)
6-158757260-T-C		not specified	Uncertain significance (Feb 21, 2024)
6-158757359-G-A		not specified	Uncertain significance (Feb 06, 2024)
6-158760641-C-T		not specified	Uncertain significance (Dec 08, 2023)
6-158760661-G-A		not specified	Uncertain significance (Sep 15, 2021)
6-158760708-C-T			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYTL3	protein_coding	protein_coding	ENST00000297239	15	114863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-20	0.00672	125432	1	315	125748	0.00126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.371	366	347	1.06	0.0000205	3933
Missense in Polyphen		116	105.47	1.0999		1291
Synonymous	-0.584	144	135	1.06	0.00000825	1182
Loss of Function	0.477	32	35.0	0.913	0.00000194	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00276	0.00276
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00494	0.00480
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.000727	0.000721
Middle Eastern	0.00494	0.00480
South Asian	0.00167	0.00163
Other	0.000988	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as Rab effector protein and play a role in vesicle trafficking. Binds phospholipids in the presence of calcium ions (By similarity). {ECO:0000250}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer (Consensus)

Recessive Scores

• pRec: 0.0948

Intolerance Scores

• loftool: 0.988
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.7

Haploinsufficiency Scores

• pHI: 0.0390
• hipred: N
• hipred_score: 0.167
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sytl3

Gene ontology

• Biological process: intracellular protein transport;exocytosis
• Cellular component: extrinsic component of plasma membrane;exocytic vesicle
• Molecular function: calcium-dependent phospholipid binding;Rab GTPase binding;neurexin family protein binding