SYTL1

synaptotagmin like 1, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): 1:27342020-27353937

Links

ENSG00000142765 ∙ NCBI:84958 ∙ OMIM:608042 ∙ HGNC:15584 ∙ Uniprot:Q8IYJ3 ∙ 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 SYTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYTL1 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			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	1	0

Variants in SYTL1

This is a list of pathogenic ClinVar variants found in the SYTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27345362-G-A		not specified	Uncertain significance (Oct 27, 2022)
1-27345414-A-C		not specified	Uncertain significance (Feb 15, 2023)
1-27345455-G-A		not specified	Uncertain significance (Sep 09, 2024)
1-27345519-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-27347462-T-C		not specified	Uncertain significance (Dec 17, 2024)
1-27347491-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-27347549-G-A		not specified	Uncertain significance (Sep 04, 2024)
1-27347843-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-27347850-T-G		not specified	Likely benign (Jan 26, 2023)
1-27347999-T-G		not specified	Uncertain significance (Jul 06, 2021)
1-27349099-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-27349404-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-27349404-G-T		not specified	Uncertain significance (Aug 04, 2024)
1-27349430-G-C		not specified	Uncertain significance (Nov 14, 2024)
1-27349451-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-27349463-G-T		not specified	Uncertain significance (Sep 17, 2021)
1-27349475-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-27349481-C-G		not specified	Uncertain significance (Dec 21, 2022)
1-27349695-C-G		not specified	Uncertain significance (Mar 29, 2023)
1-27349703-G-A		not specified	Uncertain significance (Aug 23, 2021)
1-27349704-A-C		not specified	Uncertain significance (Jul 13, 2021)
1-27349715-G-C		not specified	Uncertain significance (May 07, 2024)
1-27350012-C-A		not specified	Uncertain significance (Jan 30, 2024)
1-27350012-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-27350027-G-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYTL1	protein_coding	protein_coding	ENST00000543823	14	11909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-11	0.506	125701	0	42	125743	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	248	313	0.793	0.0000186	3542
Missense in Polyphen		90	120.53	0.74669		1240
Synonymous	0.169	129	131	0.981	0.00000768	1137
Loss of Function	1.32	21	28.6	0.734	0.00000148	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000913	0.0000912
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000129	0.0000924
European (Non-Finnish)	0.000254	0.000246
Middle Eastern	0.00	0.00
South Asian	0.000304	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicle trafficking (By similarity). Binds phosphatidylinositol 3,4,5-trisphosphate. Acts as a RAB27A effector protein and may play a role in cytotoxic granule exocytosis in lymphocytes (By similarity). {ECO:0000250, ECO:0000269|PubMed:11278853, ECO:0000269|PubMed:18266782}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.946
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• pHI: 0.364
• hipred: N
• hipred_score: 0.277
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sytl1
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; reproductive system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: intracellular protein transport;exocytosis
• Cellular component: plasma membrane;extrinsic component of plasma membrane;microvillus membrane;melanosome;extracellular exosome;exocytic vesicle
• Molecular function: protein binding;Rab GTPase binding;neurexin family protein binding