SYTL2

synaptotagmin like 2, the group of Synaptotagmin like tandem C2 proteins|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 11:85694223-85811159

Links

ENSG00000137501 ∙ NCBI:54843 ∙ OMIM:612880 ∙ HGNC:15585 ∙ Uniprot:Q9HCH5 ∙ 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 SYTL2 gene.

• Inborn genetic diseases (75 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYTL2 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				3	1	4
missense			72	6	4	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	72	9	5

Variants in SYTL2

This is a list of pathogenic ClinVar variants found in the SYTL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-85695256-T-C		not specified	Uncertain significance (Jan 19, 2024)
11-85695273-C-A		not specified	Uncertain significance (Dec 06, 2021)
11-85695275-T-C		not specified	Uncertain significance (Apr 07, 2022)
11-85696200-C-T		not specified	Uncertain significance (Jan 05, 2022)
11-85696204-G-T		not specified	Uncertain significance (Jan 23, 2023)
11-85696356-C-T		not specified	Uncertain significance (Mar 02, 2023)
11-85696378-G-A		not specified	Uncertain significance (Oct 22, 2021)
11-85698035-C-G		not specified	Uncertain significance (Jan 12, 2024)
11-85698049-G-A		not specified	Uncertain significance (Apr 25, 2023)
11-85698061-T-C		not specified	Uncertain significance (May 25, 2022)
11-85704862-C-T		not specified	Uncertain significance (Mar 12, 2024)
11-85704871-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-85704895-T-A		not specified	Uncertain significance (Jun 29, 2023)
11-85704932-C-T		not specified	Uncertain significance (Mar 17, 2023)
11-85704956-G-A		not specified	Uncertain significance (May 11, 2022)
11-85707441-G-A			Likely benign (Nov 01, 2022)
11-85709340-C-T		not specified	Uncertain significance (Sep 27, 2022)
11-85709341-G-A		not specified	Uncertain significance (Dec 09, 2023)
11-85709436-A-G		not specified	Uncertain significance (Feb 22, 2023)
11-85709507-G-A			Likely benign (Oct 01, 2022)
11-85711173-C-G			Benign (Jul 06, 2018)
11-85714416-A-C		not specified	Uncertain significance (Nov 30, 2022)
11-85714424-G-C		not specified	Uncertain significance (Jun 21, 2021)
11-85714486-G-T		not specified	Uncertain significance (Nov 09, 2023)
11-85718804-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYTL2	protein_coding	protein_coding	ENST00000354566	13	116918

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.26e-21	0.123	125667	2	78	125747	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.20	725	639	1.13	0.0000305	8354
Missense in Polyphen		192	172.33	1.1142		2277
Synonymous	0.839	216	232	0.930	0.0000115	2421
Loss of Function	1.49	38	49.3	0.771	0.00000227	683

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00114	0.00103
Finnish	0.00	0.00
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.00114	0.00103
South Asian	0.000753	0.000752
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 acts as a RAB27A effector protein and plays a role in cytotoxic granule exocytosis in lymphocytes. It is required for cytotoxic granule docking at the immunologic synapse. Isoform 4 binds phosphatidylserine (PS) and phosphatidylinositol- 4,5-bisphosphate (PIP2) and promotes the recruitment of glucagon- containing granules to the cell membrane in pancreatic alpha cells. Binding to PS is inhibited by Ca(2+) while binding to PIP2 is Ca(2+) insensitive. {ECO:0000269|PubMed:17182843, ECO:0000269|PubMed:18266782, ECO:0000269|PubMed:18812475}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer (Consensus)

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• loftool: 0.995
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.23

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.123
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sytl2
• Phenotype: digestive/alimentary phenotype

Gene ontology

• Biological process: intracellular protein transport;exocytosis;vesicle docking involved in exocytosis;negative regulation of phosphatase activity;vesicle-mediated transport;positive regulation of mucus secretion;protein localization to plasma membrane
• Cellular component: cytoplasm;plasma membrane;membrane;extrinsic component of plasma membrane;melanosome;exocytic vesicle
• Molecular function: phosphatidylserine binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;Rab GTPase binding;phosphatase binding;neurexin family protein binding