SYTL1

protein-coding

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

Gene summary

Predicted to enable neurexin family protein binding activity. Involved in exocytosis. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001193308.2

Inheritance

—

ClinVar variants

U:89B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr1:27,342,020-27,353,937

External References & Databases

Ensembl (ENSG00000142765)

Transcript & Mutation Effects

hg38 • Region Span ~11.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYTL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 87

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001193308.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			86 clinvar	3 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	4	0	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001193308.2	RefSeq	NP_001180237.1	14	MANE Select
ENST00000616558.5	Ensembl	ENSP00000481032.1	14	MANE Select
NM_032872.3	RefSeq	NP_116261.1	14	Standard
ENST00000318074.10	Ensembl	ENSP00000316464.5	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Deregulation of Rab and Rab Effector Genes in Bladder Cancer
Vesicle-mediated transport
TBC/RABGAPs
Membrane Trafficking
Rab regulation of trafficking

Biological Process

intracellular protein transport
exocytosis

Molecular Function

protein binding
Rab GTPase binding
neurexin family protein binding

Cellular Component

plasma membrane
extrinsic component of plasma membrane
microvillus membrane
melanosome
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000543823
Coding exons: 14
Length: 11909
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125743
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.30	248	313	0.793	0.0000186	3542
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00013	0.000092	rare
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00030	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.152

Intolerance Scores

LoFtool: 0.946
RVIS EVS: -0.27
RVIS percentile EVS: 34.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.246

Gene Damage Prediction

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