SYTL5

synaptotagmin like 5, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): X:38006552-38128819

Links

ENSG00000147041 ∙ NCBI:94122 ∙ ∙ HGNC:15589 ∙ Uniprot:Q8TDW5 ∙ 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 SYTL5 gene.

• Inborn genetic diseases (30 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYTL5 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			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	0

Variants in SYTL5

This is a list of pathogenic ClinVar variants found in the SYTL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-38033915-A-G		not specified	Uncertain significance (Nov 09, 2022)
X-38054313-A-T		SYTL5-related disorder • not specified	Conflicting classifications of pathogenicity (Jul 20, 2021)
X-38054315-C-G		not specified	Uncertain significance (May 24, 2023)
X-38054319-G-A		not specified	Uncertain significance (Jan 04, 2024)
X-38054352-A-T		not specified	Uncertain significance (Sep 21, 2021)
X-38054371-G-A		not specified	Uncertain significance (Feb 16, 2023)
X-38054386-A-G		SYTL5-related disorder	Likely benign (Dec 03, 2019)
X-38054388-G-C		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-38072120-G-A		not specified	Uncertain significance (Jul 21, 2021)
X-38073607-A-G		not specified	Uncertain significance (Jan 20, 2023)
X-38073622-C-T		not specified	Likely benign (Nov 29, 2021)
X-38073655-G-A		not specified	Uncertain significance (Dec 01, 2022)
X-38089456-G-A		not specified	Uncertain significance (Dec 03, 2021)
X-38089489-C-T		not specified	Likely benign (Jun 10, 2022)
X-38089496-C-A		not specified	Uncertain significance (Jan 08, 2024)
X-38089499-C-T		not specified	Uncertain significance (Jul 17, 2023)
X-38089511-G-A		not specified	Uncertain significance (Jan 08, 2024)
X-38089583-G-A		not specified	Uncertain significance (Feb 28, 2023)
X-38094302-G-A		not specified	Uncertain significance (Feb 21, 2024)
X-38094307-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-38094368-G-A		SYTL5-related disorder	Benign (Feb 20, 2019)
X-38094377-C-T		not specified	Uncertain significance (Jan 19, 2024)
X-38094395-T-C		not specified	Uncertain significance (Dec 15, 2023)
X-38094410-C-T		SYTL5-related disorder	Likely benign (Jun 14, 2023)
X-38094418-T-C		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYTL5	protein_coding	protein_coding	ENST00000456733	17	122238

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000269	0.999	125722	6	10	125738	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.389	286	268	1.07	0.0000204	4915
Missense in Polyphen		97	89.409	1.0849		1670
Synonymous	-1.24	107	91.8	1.17	0.00000655	1418
Loss of Function	2.99	11	28.1	0.392	0.00000224	509

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000761	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000163
Finnish	0.0000648	0.0000462
European (Non-Finnish)	0.000104	0.0000703
Middle Eastern	0.000224	0.000163
South Asian	0.000160	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as Rab effector protein and play a role in vesicle trafficking. Binds phospholipids.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.741
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.63

Haploinsufficiency Scores

• pHI: 0.234
• hipred: Y
• hipred_score: 0.544
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.697

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sytl5

Gene ontology

• Biological process: intracellular protein transport;exocytosis
• Cellular component: membrane;exocytic vesicle
• Molecular function: protein binding;phospholipid binding;Rab GTPase binding;metal ion binding