SNCG

synuclein gamma

Basic information

Region (hg38): 10:86958599-86963258

Links

ENSG00000173267 ∙ NCBI:6623 ∙ OMIM:602998 ∙ HGNC:11141 ∙ Uniprot:O76070 ∙ 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 SNCG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNCG 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
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	2

Variants in SNCG

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

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

Position	Type	Phenotype	Significance	ClinVar
10-86958727-C-A			Benign (Jun 14, 2018)
10-86959665-G-A		not specified	Uncertain significance (Apr 20, 2024)
10-86960030-G-A		not specified	Uncertain significance (Nov 10, 2024)
10-86960033-G-C		not specified	Uncertain significance (Dec 28, 2023)
10-86960057-G-A		not specified	Uncertain significance (Apr 07, 2022)
10-86960094-A-G		not specified	Uncertain significance (Oct 25, 2024)
10-86960103-C-T		not specified	Likely benign (Jun 24, 2022)
10-86960116-G-A			Benign (Jul 06, 2018)
10-86960124-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-86962653-A-G		not specified	Uncertain significance (Apr 08, 2024)
10-86962661-G-C		not specified	Uncertain significance (Sep 26, 2022)
10-86962673-G-A		not specified	Uncertain significance (Sep 08, 2024)
10-86962974-G-A		not specified	Uncertain significance (Oct 05, 2022)
10-86962974-G-T		not specified	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNCG	protein_coding	protein_coding	ENST00000372017	5	4643

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000847	0.572	125673	0	7	125680	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.226	72	77.6	0.928	0.00000457	814
Missense in Polyphen		22	28.581	0.76975		299
Synonymous	-0.972	42	34.7	1.21	0.00000272	234
Loss of Function	0.440	5	6.18	0.809	2.60e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000918	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000900	0.00000880
Middle Eastern	0.0000544	0.0000544
South Asian	0.000100	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in neurofilament network integrity. May be involved in modulating axonal architecture during development and in the adult. In vitro, increases the susceptibility of neurofilament-H to calcium-dependent proteases (By similarity). May also function in modulating the keratin network in skin. Activates the MAPK and Elk-1 signal transduction pathway (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.154
• rvis_EVS: 1.01
• rvis_percentile_EVS: 90.84

Haploinsufficiency Scores

• pHI: 0.376
• hipred: Y
• hipred_score: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sncg
• Phenotype: cellular phenotype; homeostasis/metabolism 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)

Zebrafish Information Network

• Gene name: sncgb
• Affected structure: larval locomotory behavior
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: chemical synaptic transmission;adult locomotory behavior;protein secretion;regulation of dopamine secretion;regulation of neurotransmitter secretion;synapse organization
• Cellular component: cytoplasm;microtubule organizing center;spindle;axon;neuronal cell body;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding