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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 23.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001193308.2	NP_001180237.1	14	yes	-
ENST00000616558.5	ENSP00000481032.1	14	yes	-
NM_032872.3	NP_116261.1	14	-	-
ENST00000543823.1	ENSP00000440704.1	14	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYTL1 gene.

• not_specified (87 variants)

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. These statistics are base on transcript: NM_001193308.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	1		3
missense			86	3		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	89	4	0

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
		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

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

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