SYT6 synaptotagmin 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYT6provided by HGNC
Official Full Name: synaptotagmin 6provided by HGNC
Primary source: HGNC:HGNC:18638
See related: Ensembl:ENSG00000134207 MIM:607718; AllianceGenome:HGNC:18638
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: sytVI
Summary: The protein encoded by this gene belongs to the synaptotagmin family. Synaptotagmins share a common domain structure that includes a transmembrane domain and a cytoplasmic region composed of 2 C2 domains, and are involved in calcium-dependent exocytosis of synaptic vesicles. This protein has been shown to be a key component of the secretory machinery involved in acrosomal exocytosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2011]
Expression: Biased expression in brain (RPKM 2.6), kidney (RPKM 0.8) and 6 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 1p13.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (114089292..114153869, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (114100938..114165509, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (114631914..114696491, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

synaptotagmin must be dephosphorylated at a specific window of time and phosphorylated synaptotagmin has an active role at early stages of the acrosomal exocytosis.
Title: Calcineurin-mediated dephosphorylation of synaptotagmin VI is necessary for acrosomal exocytosis.
SYT6 is hypermethylated in renal cell carcinoma.
Title: Identification of novel epigenetic markers for clear cell renal cell carcinoma.
Acrosomal exocytosis is regulated through the PKC-mediated phosphorylation of conserved threonines in the polybasic regions of synaptotagmin VI.
Title: Protein kinase C-mediated phosphorylation of the two polybasic regions of synaptotagmin VI regulates their function in acrosomal exocytosis.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

SHGC-75349 (e-PCR)
- UniSTS:54023

Cda16g01 (e-PCR)
- UniSTS:26633

NoName (e-PCR)
- UniSTS:483106

WI-14735 (e-PCR)
- UniSTS:83533

G43675 (e-PCR)
- UniSTS:95085

SHGC-149045 (e-PCR)
- UniSTS:176762

SHGC-147387 (e-PCR)
- UniSTS:175786

SHGC-75351 (e-PCR)
- UniSTS:37060

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion sensor activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables calcium-dependent phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables clathrin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables syntaxin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in acrosomal vesicle exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of calcium ion-dependent exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasmic side of plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: synaptotagmin-6

Names: synaptotagmin VI

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_050730.1 RefSeqGene

Range

4982..69559

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001253772.2 → NP_001240701.1 synaptotagmin-6 isoform a

Status: REVIEWED

Source sequence(s)

AL162594

Consensus CDS

CCDS91027.1

UniProtKB/Swiss-Prot

B1AMB8, B3KPK1, Q5T7P8

UniProtKB/TrEMBL

A0A286YEX2

Related

ENSP00000476396.1, ENST00000610222.3

Conserved Domains (2) summary

cd08385
Location:230 → 354

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:363 → 496

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
NM_001270805.2 → NP_001257734.1 synaptotagmin-6 isoform b

See identical proteins and their annotated locations for NP_001257734.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longer transcript. Variants 2 and 3 encode the same protein.

Source sequence(s)

AL162594, BC044948, N50928

Consensus CDS

CCDS871.1

UniProtKB/TrEMBL

A0A286YEX2, I6L9C3

Conserved Domains (2) summary

cd08385
Location:145 → 269

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:278 → 411

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
NM_001366223.1 → NP_001353152.1 synaptotagmin-6 isoform b

Status: REVIEWED

Source sequence(s)

AL162594

Consensus CDS

CCDS871.1

UniProtKB/TrEMBL

A0A286YEX2, I6L9C3

Related

ENSP00000477344.1, ENST00000609117.5

Conserved Domains (2) summary

cd08385
Location:145 → 269

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:278 → 411

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
NM_001366224.1 → NP_001353153.1 synaptotagmin-6 isoform c

Status: REVIEWED

Source sequence(s)

AL162594

Consensus CDS

CCDS91026.1

UniProtKB/TrEMBL

A0A7I2PMW4

Related

ENSP00000358560.2, ENST00000369547.6

Conserved Domains (2) summary

cd08385
Location:230 → 354

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:363 → 496

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
NM_001366225.1 → NP_001353154.1 synaptotagmin-6 isoform d

Status: REVIEWED

Source sequence(s)

AL162594

UniProtKB/TrEMBL

A0A286YEX2

Related

ENSP00000493062.2, ENST00000641643.2

Conserved Domains (2) summary

cd08385
Location:230 → 354

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:363 → 496

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
NM_001366226.1 → NP_001353155.1 synaptotagmin-6 isoform e

Status: REVIEWED

Source sequence(s)

AL162594

UniProtKB/TrEMBL

A0A286YEX2

Conserved Domains (2) summary

cd08385
Location:145 → 269

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:278 → 411

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
NM_205848.4 → NP_995320.1 synaptotagmin-6 isoform b

See identical proteins and their annotated locations for NP_995320.1

Status: REVIEWED

Source sequence(s)

AK056448, AK096744, AL162594, BC044948, BX431128, N50928

Consensus CDS

CCDS871.1

UniProtKB/TrEMBL

A0A286YEX2, I6L9C3

Related

ENSP00000476507.1, ENST00000607941.5

Conserved Domains (2) summary

cd08385
Location:145 → 269

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:278 → 411

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

114089292..114153869 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024453337.2 → XP_024309105.1 synaptotagmin-6 isoform X1

UniProtKB/TrEMBL

A0A286YEX2

Conserved Domains (2) summary

cd08385
Location:145 → 269

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08403
Location:278 → 411

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
XM_047446760.1 → XP_047302716.1 synaptotagmin-6 isoform X2

UniProtKB/Swiss-Prot

B1AMB8, B3KPK1, Q5T7P8