SNCB synuclein beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNCBprovided by HGNC
Official Full Name: synuclein betaprovided by HGNC
Primary source: HGNC:HGNC:11140
See related: Ensembl:ENSG00000074317 MIM:602569; AllianceGenome:HGNC:11140
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
Summary: This gene encodes a member of a small family of proteins that inhibit phospholipase D2 and may function in neuronal plasticity. The encoded protein is abundant in lesions of patients with Alzheimer disease. A mutation in this gene was found in individuals with dementia with Lewy bodies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Expression: Restricted expression toward brain (RPKM 60.7) See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (176620082..176630534, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (177166665..177177114, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (176047083..176057535, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Understanding Genetic Risks: Computational Exploration of Human beta-Synuclein nsSNPs and their Potential Impact on Structural Alteration.
Title: Understanding Genetic Risks: Computational Exploration of Human β-Synuclein nsSNPs and their Potential Impact on Structural Alteration.
Serum beta-synuclein, neurofilament light chain and glial fibrillary acidic protein as prognostic biomarkers in moderate-to-severe acute ischemic stroke.
Title: Serum β-synuclein, neurofilament light chain and glial fibrillary acidic protein as prognostic biomarkers in moderate-to-severe acute ischemic stroke.
Plasma beta-synuclein, GFAP, and neurofilaments in patients with malignant gliomas undergoing surgical and adjuvant therapy.
Title: Plasma β-synuclein, GFAP, and neurofilaments in patients with malignant gliomas undergoing surgical and adjuvant therapy.
Blood beta-Synuclein and Neurofilament Light Chain During the Course of Prion Disease.
Title: Blood β-Synuclein and Neurofilament Light Chain During the Course of Prion Disease.
Dementia with Lewy bodies-associated ss-synuclein mutations V70M and P123H cause mutation-specific neuropathological lesions.
Title: Dementia with Lewy bodies-associated ß-synuclein mutations V70M and P123H cause mutation-specific neuropathological lesions.
Effect of Disease-Associated P123H and V70M Mutations on beta-Synuclein Fibrillation.
Title: Effect of Disease-Associated P123H and V70M Mutations on β-Synuclein Fibrillation.
beta-synuclein-specific T cells were enriched in patients with chronic-progressive multiple sclerosis; findings reveal a previously unrecognized role of beta-synuclein in provoking T-cell-mediated pathology of the central nervous system
Title: β-Synuclein-reactive T cells induce autoimmune CNS grey matter degeneration.
This analyzed identify functional insertion and deletion (INDEL) variations upstream of SNCB, determined SNCB expression levels, and correlated INDEL lengths with expression levels.
Title: INDEL Length and Haplotypes in the β-Synuclein Gene: A Key to Differentiate Dementia with Lewy Bodies?
Vibrational Circular Dichroism Sheds New Light on the Competitive Effects of Crowding and beta-Synuclein on the Fibrillation Process of alpha-Synuclein.
Title: Vibrational Circular Dichroism Sheds New Light on the Competitive Effects of Crowding and β-Synuclein on the Fibrillation Process of α-Synuclein.
Results show that the non-amyloid-beta component domain of SNCB is the primary determinant of self-association leading to fibril formation, while the N- and C-terminal domains play critical roles in the fibril inhibition process. These data provide evidence that all three domains together contribute to providing effective inhibition.
Title: Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein.

Submit: New GeneRIF Correction See all GeneRIFs (48)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Lewy body dementia MedGen: C0752347 OMIM: 127750 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

SNCB_7881 (e-PCR)
- UniSTS:466464

D5S2595 (e-PCR)
- UniSTS:24496

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables cuprous ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables cuprous ion binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables phospholipase inhibitor activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transition metal ion binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in dopamine metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in synapse organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle endocytosis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in axon terminus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in inclusion body	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuronal cell body	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: beta-synuclein

Names: I(2)-synuclein

NCBI Reference Sequences (RefSeq)

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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_012131.1 RefSeqGene

Range

5023..15475

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001001502.3 → NP_001001502.1 beta-synuclein isoform 1

See identical proteins and their annotated locations for NP_001001502.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 2 and 7 encode the same protein (isoform 1).

Source sequence(s)

AC091934, BC002902, BM543516, BQ184193, S69965

Consensus CDS

CCDS4406.1

UniProtKB/Swiss-Prot

Q16143, Q6IAX7

Related

ENSP00000308057.3, ENST00000310112.7

Conserved Domains (1) summary

pfam01387
Location:1 → 121

Synuclein
NM_001318034.2 → NP_001304963.1 beta-synuclein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 3 and 5 encode the same protein (isoform 2).

Source sequence(s)

AC091934, BQ184193, JF960950

Consensus CDS

CCDS83048.1

UniProtKB/TrEMBL

G4Y816

Related

ENSP00000479489.1, ENST00000614675.4

Conserved Domains (1) summary

pfam01387
Location:1 → 76

Synuclein; Synuclein
NM_001318035.2 → NP_001304964.1 beta-synuclein isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Both variants 4 and 6 encode the same protein (isoform 3).

Source sequence(s)

AC091934, BQ184193, JF960951

UniProtKB/TrEMBL

G4Y815

Conserved Domains (1) summary

pfam01387
Location:1 → 97

Synuclein
NM_001318036.2 → NP_001304965.1 beta-synuclein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks exons in the 5' UTR and coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 3 and 5 encode the same isoform (2).

Source sequence(s)

AC091934, BQ184193, JF960952

Consensus CDS

CCDS83048.1

UniProtKB/TrEMBL

G4Y816

Conserved Domains (1) summary

pfam01387
Location:1 → 76

Synuclein; Synuclein
NM_001318037.2 → NP_001304966.1 beta-synuclein isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks exons in the 5' UTR and coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Variants 4 and 6 encode the same isoform (3).

Source sequence(s)

AC091934, BQ184193, JF960953

UniProtKB/TrEMBL

G4Y815

Conserved Domains (1) summary

pfam01387
Location:1 → 97

Synuclein
NM_001363140.2 → NP_001350069.1 beta-synuclein isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks a segment in the 5' UTR compared to variant 1. Variants 1, 2 and 7 encode the same protein (isoform 1).

Source sequence(s)

AC091934

Consensus CDS

CCDS4406.1

UniProtKB/Swiss-Prot

Q16143, Q6IAX7

Conserved Domains (1) summary

pfam01387
Location:1 → 121

Synuclein
NM_003085.5 → NP_003076.1 beta-synuclein isoform 1

See identical proteins and their annotated locations for NP_003076.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1, 2 and 7 encode the same protein (isoform 1).

Source sequence(s)

AC091934, BC002902, BM543516, BQ184193, S69965

Consensus CDS

CCDS4406.1

UniProtKB/Swiss-Prot

Q16143, Q6IAX7

Related

ENSP00000377296.2, ENST00000393693.7

Conserved Domains (1) summary

pfam01387
Location:1 → 121

Synuclein