SNCB

synuclein beta, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 5:176620081-176630556

Links

ENSG00000074317

∙ NCBI:6620 ∙ OMIM:602569 ∙ HGNC:11140 ∙ Uniprot:Q16143 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Lewy body dementia (Moderate), mode of inheritance: Unknown
Lewy body dementia (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dementia with Lewy bodies	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	15365127

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNCB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNCB 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				1 clinvar		1
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1 clinvar	7 clinvar	8
Total	0	0	6	2	7

Variants in SNCB

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

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

Position	Phenotype	Significance	ClinVar
5-176620760-G-A		Benign (May 15, 2021)	1222753
5-176620840-C-T	not specified	Uncertain significance (Aug 26, 2022)	2309219
5-176620954-C-T		Benign (May 17, 2021)	1178596
5-176621205-C-T	SNCB-related disorder	Likely benign (Jul 10, 2019)	3050307
5-176621218-G-T	Lewy body dementia • SNCB-related disorder	Conflicting classifications of pathogenicity (Dec 30, 2023)	7026
5-176626335-GGT-G		Benign (May 15, 2021)	1282871
5-176626335-GGTGT-G		Benign (May 15, 2021)	1253251
5-176626411-G-A	Lewy body dementia	Uncertain significance (-)	3024092
5-176626449-G-C	not specified	Uncertain significance (Sep 29, 2022)	2314526
5-176626472-C-T	Lewy body dementia	Pathogenic (Sep 14, 2004)	7025
5-176626621-G-A		Benign (May 15, 2021)	1267656
5-176626644-C-G		Benign (May 15, 2021)	1257127
5-176629528-A-G	not specified • Lewy body dementia	Benign (Jul 15, 2021)	1174817
5-176629547-G-A	not specified	Likely benign (Oct 27, 2023)	2637515
5-176629555-T-C	Lewy body dementia	Uncertain significance (Dec 02, 2020)	1333743
5-176629618-C-G	Lewy body dementia	Uncertain significance (Jul 01, 2020)	2436214
5-176629648-C-T	not specified	Uncertain significance (Sep 23, 2023)	3166954
5-176629805-C-T	not specified	Benign (May 15, 2021)	1181147

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNCB	protein_coding	protein_coding	ENST00000310112	5	10446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0681	0.877	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.952	50	72.9	0.686	0.00000332	853
Missense in Polyphen		12	19.075	0.62911		214
Synonymous	-0.279	31	29.1	1.07	0.00000143	262
Loss of Function	1.63	3	7.94	0.378	3.93e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Non-amyloid component of senile plaques found in Alzheimer disease. Could act as a regulator of SNCA aggregation process. Protects neurons from staurosporine and 6-hydroxy dopamine (6OHDA)-stimulated caspase activation in a p53/TP53- dependent manner. Contributes to restore the SNCA anti-apoptotic function abolished by 6OHDA. Not found in the Lewy bodies associated with Parkinson disease.;
Pathway: MTF1 activates gene expression;MTF1 activates gene expression;Response to metal ions;Cellular responses to external stimuli (Consensus)

Recessive Scores

pRec: 0.221

Intolerance Scores

loftool: 0.375
rvis_EVS: -0.05
rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

pHI: 0.489
hipred: Y
hipred_score: 0.589
ghis: 0.654

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.637

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sncb
Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); skeleton phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Zebrafish Information Network

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

Gene ontology

Biological process: chemical synaptic transmission;response to metal ion;dopamine metabolic process;negative regulation of catalytic activity;negative regulation of neuron apoptotic process;synaptic vesicle endocytosis;synapse organization
Cellular component: cytosol;inclusion body;presynapse
Molecular function: phospholipase inhibitor activity;calcium ion binding;transition metal ion binding;cuprous ion binding