SYN2

synapsin II, the group of Synapsins

Basic information

Region (hg38): 3:12004387-12192032

Links

ENSG00000157152 ∙ NCBI:6854 ∙ OMIM:600755 ∙ HGNC:11495 ∙ Uniprot:Q92777 ∙ 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 SYN2 gene.

• Inborn genetic diseases (34 variants)
• not provided (7 variants)
• Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYN2 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						0
missense			16	2	1	19
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18	2	1	21
Total	0	0	36	4	2

Variants in SYN2

This is a list of pathogenic ClinVar variants found in the SYN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-12004712-C-T			Likely benign (Jun 01, 2023)
3-12140656-A-G		SYN2-related disorder	Benign (May 24, 2019)
3-12145698-G-A		not specified	Uncertain significance (Nov 29, 2021)
3-12145729-C-T		SYN2-related disorder	Benign (Jun 24, 2019)
3-12145759-T-C		not specified	Uncertain significance (Jul 14, 2021)
3-12151273-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-12151295-A-G		not specified	Uncertain significance (Oct 04, 2022)
3-12153526-C-T		not specified	Likely benign (Nov 17, 2022)
3-12153588-A-G		not specified	Uncertain significance (Nov 09, 2023)
3-12153597-A-G		not specified	Uncertain significance (Feb 23, 2023)
3-12153616-C-T		not specified	Uncertain significance (May 24, 2023)
3-12153699-T-C		not specified	Uncertain significance (Mar 07, 2024)
3-12154365-T-C		not specified	Uncertain significance (Aug 20, 2023)
3-12154371-T-C		not specified	Uncertain significance (Mar 06, 2023)
3-12154401-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-12154402-G-A			Likely benign (May 21, 2018)
3-12154404-T-C		not specified	Uncertain significance (Oct 12, 2022)
3-12154411-G-C		not specified	Uncertain significance (Nov 30, 2021)
3-12154421-A-C		not specified	Uncertain significance (Feb 22, 2023)
3-12156824-C-G		not specified	Uncertain significance (Jan 04, 2022)
3-12156888-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-12157461-C-T		not specified	Uncertain significance (Feb 17, 2022)
3-12158710-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-12158716-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-12158719-A-G		not specified	Uncertain significance (Feb 13, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. May play a role in noradrenaline secretion by sympathetic neurons (By similarity). {ECO:0000250}.
• Disease: DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:15449241}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.
• Pathway: Synaptic Vesicle Pathway;Neuronal System;Dopamine Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses;Serotonin Neurotransmitter Release Cycle (Consensus)

Recessive Scores

• pRec: 0.271

Haploinsufficiency Scores

• pHI: 0.191

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.752

Mouse Genome Informatics

• Gene name: Syn2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: syn2b
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: truncated

Gene ontology

• Biological process: chemical synaptic transmission;neurotransmitter secretion;synaptic vesicle clustering
• Cellular component: plasma membrane;postsynaptic density;cell junction;synaptic vesicle membrane;SNARE complex;myelin sheath;synapse;Schaffer collateral - CA1 synapse;glutamatergic synapse
• Molecular function: ATP binding