SYN3

synapsin III, the group of Synapsins

Basic information

Region (hg38): 22:32507820-33058381

Links

ENSG00000185666 ∙ NCBI:8224 ∙ OMIM:602705 ∙ HGNC:11496 ∙ Uniprot:O14994 ∙ 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 SYN3 gene.

• not provided (3 variants)
• Sorsby fundus dystrophy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYN3 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				2	2	4
missense			30	6	2	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	3	3	141	62	40	249
Total	3	3	171	70	44

Variants in SYN3

This is a list of pathogenic ClinVar variants found in the SYN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-32513733-G-A		not specified	Uncertain significance (Dec 20, 2023)
22-32513756-T-G		not specified	Uncertain significance (Jan 23, 2023)
22-32513768-G-T		not specified	Uncertain significance (Jul 14, 2022)
22-32518080-C-G			Benign (Jun 29, 2018)
22-32518106-C-A		not specified	Uncertain significance (Apr 08, 2024)
22-32518185-C-T		not specified	Uncertain significance (Sep 16, 2021)
22-32518208-GG-AA		Generalized hypotonia;Visual impairment;Global developmental delay;Cerebellar vermis atrophy;Seizure	Pathogenic (-)
22-32518222-C-A			Likely benign (Dec 31, 2019)
22-32518233-C-G		not specified	Uncertain significance (Dec 02, 2021)
22-32518233-C-T		not specified	Uncertain significance (Aug 13, 2021)
22-32518235-G-C		not specified	Uncertain significance (Mar 19, 2024)
22-32518325-C-T			Benign/Likely benign (Jul 01, 2023)
22-32527922-C-T			Likely benign (Jun 28, 2018)
22-32527933-G-A		not specified	Uncertain significance (Jan 10, 2022)
22-32527986-G-A			Uncertain significance (-)
22-32528896-G-A		not specified	Likely benign (Jun 10, 2022)
22-32528952-C-T			Likely benign (Sep 25, 2018)
22-32528981-C-G		not specified	Uncertain significance (Apr 15, 2024)
22-32533816-C-T		not specified	Uncertain significance (Apr 03, 2023)
22-32538049-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-32541589-G-T		not specified	Uncertain significance (May 17, 2023)
22-32541647-C-T		not specified	Uncertain significance (Jun 10, 2024)
22-32541659-C-T			Likely benign (Jun 01, 2018)
22-32541671-C-T		not specified	Likely benign (Jan 24, 2024)
22-32541673-C-T		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYN3	protein_coding	protein_coding	ENST00000358763	13	545820

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00189	0.998	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	289	343	0.842	0.0000197	3774
Missense in Polyphen		37	41.224	0.89754		429
Synonymous	1.96	113	143	0.792	0.00000877	1172
Loss of Function	3.26	10	28.9	0.346	0.00000140	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000130
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.000462	0.000416
European (Non-Finnish)	0.000182	0.000176
Middle Eastern	0.000164	0.000163
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of neurotransmitter release and synaptogenesis.
• 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: 0.145

Intolerance Scores

• loftool: 0.147
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

• pHI: 0.108
• hipred: Y
• hipred_score: 0.527
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syn3
• Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; 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)

Gene ontology

• Biological process: neurotransmitter secretion;regulation of synaptic transmission, GABAergic;synaptic vesicle clustering
• Cellular component: synaptic vesicle;postsynaptic density;cell junction;synaptic vesicle membrane;glutamatergic synapse
• Molecular function: ATP binding