SYTL3

protein-coding

synaptotagmin like 3, the group of Synaptotagmin like tandem C2 proteins

Gene summary

The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

MANE transcript

NM_001242394.2

Inheritance

—

ClinVar variants

U:106B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr6:158,650,014-158,764,876

External References & Databases

Ensembl (ENSG00000164674)

Transcript & Mutation Effects

hg38 • Region Span ~114.9 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 SYTL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001242394.2. 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			98 clinvar	5 clinvar		103
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	106	6	0	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001242394.2	RefSeq	NP_001229323.1	15	MANE Select
ENST00000611299.5	Ensembl	ENSP00000483936.1	15	MANE Select
NM_001009991.4	RefSeq	NP_001009991.2	13	Standard
NM_001242384.2	RefSeq	NP_001229313.1	15	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

Biological Process

intracellular protein transport
exocytosis

Molecular Function

calcium-dependent phospholipid binding
Rab GTPase binding
neurexin family protein binding

Cellular Component

extrinsic component of plasma membrane
exocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297239
Coding exons: 15
Length: 114863
Individuals with no LoFs: 125432
Homozygous LoFs: 1
Heterozygous LoFs: 315
Defined: 125748
p: 0.00126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.371	366	347	1.06	0.0000205	3933
Missense (PolyPhen)		116	105.47	1.0999		1291
Synonymous	-0.584	144	135	1.06	0.00000825	1182
Loss of Function	0.477	32	35.0	0.913	0.00000194	388

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.0025	0.0024	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0049	0.0048	notable
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00073	0.00072	rare
South Asian	0.0017	0.0016	notable
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as Rab effector protein and play a role in vesicle trafficking. Binds phospholipids in the presence of calcium ions (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0948

Intolerance Scores

LoFtool: 0.988
RVIS EVS: 0.67
RVIS percentile EVS: 84.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.890

Gene Damage Prediction

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