Provide a comprehensive cross-database identifier and functional mapping reference for human SNCA. This should serve as a definitive lookup resource for researchers. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 1: GENE IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Provide ALL gene-level database identifiers: - HGNC ID and approved symbol - Ensembl gene ID (ENSG) - NCBI Entrez Gene ID - OMIM gene/locus ID - Genomic location: chromosome, start position, end position, strand ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 2: TRANSCRIPT IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ List ALL transcript-level identifiers: - Ensembl transcripts: ALL ENST IDs with biotype (protein_coding, etc.) How many total transcripts? - RefSeq transcripts: ALL NM_ mRNA accessions Mark which is MANE Select (canonical clinical standard) - CCDS IDs: ALL consensus coding sequence identifiers For the CANONICAL/MANE SELECT transcript: - List ALL exon IDs (ENSE) with genomic coordinates - Total exon count ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 3: PROTEIN IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ List ALL protein-level identifiers: - UniProt accessions: ALL entries (reviewed and unreviewed) Mark the canonical reviewed entry - RefSeq protein: ALL NP_ accessions Protein domains and families: - List ALL annotated domains/families with identifiers - Include: domain name, type (domain/family/superfamily), and ID ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 4: STRUCTURE IDENTIFIERS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Experimental structures: - List ALL PDB structure IDs - For each: experimental method (X-ray, NMR, Cryo-EM) and resolution - Total PDB structure count Predicted structures: - AlphaFold model ID and confidence metrics (pLDDT) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 5: CROSS-SPECIES ORTHOLOGS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ List orthologous genes in key model organisms (where available): - Mouse (Mus musculus): gene ID, symbol - Rat (Rattus norvegicus): gene ID, symbol - Zebrafish (Danio rerio): gene ID, symbol - Fruit fly (Drosophila melanogaster): gene ID, symbol - Worm (C. elegans): gene ID, symbol - Yeast (S. cerevisiae): gene ID, symbol ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 6: CLINICAL VARIANTS & AI PREDICTIONS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Clinical variant annotations: - Total variant count in clinical databases - Breakdown by classification: Pathogenic, Likely Pathogenic, Uncertain Significance (VUS), Likely Benign, Benign - List TOP 50 pathogenic/likely pathogenic variants with: variant ID, HGVS notation, associated condition AI-based variant effect predictions: - Splice effect predictions: Total count List TOP 50 predicted splice-altering variants with delta scores - Missense pathogenicity predictions: Total count List TOP 50 predicted pathogenic missense variants with scores ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 7: BIOLOGICAL PATHWAYS & GENE ONTOLOGY ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Pathway membership: - List ALL biological pathways this gene participates in - Include pathway IDs and names - Total pathway count Gene Ontology annotations: - Biological Process: count and TOP 20 terms with IDs - Molecular Function: count and TOP 20 terms with IDs - Cellular Component: count and TOP 20 terms with IDs ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 8: PROTEIN INTERACTIONS & MOLECULAR NETWORKS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Protein-protein interactions: - Total interaction count - List TOP 50 highest-confidence interacting proteins with scores Protein similarity (evolutionary and structural): - Structural/embedding similarity: How many similar proteins? List TOP 20 with similarity scores - Sequence homology: How many homologous proteins? List TOP 20 with identity/similarity scores ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 9: TRANSCRIPTION FACTOR REGULATORY DATA ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ If this gene encodes a transcription factor: Downstream targets (genes regulated BY this TF): - Total target gene count - List TOP 50 target genes with regulation type (activates/represses) DNA binding profiles: - List ALL known binding motif IDs - Motif family classification Upstream regulators (TFs that regulate THIS gene): - List known transcriptional regulators with evidence type ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 10: DRUG & PHARMACOLOGY DATA ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ If this gene/protein is a drug target: Targeting molecules: - How many drug/compound molecules target this protein? - List TOP 30 molecules by development phase - Include: molecule ID, name, mechanism, highest development phase Clinical trials: - How many clinical trials involve drugs targeting this gene? - List TOP 20 trials with: trial ID, phase, status, intervention Pharmacogenomics: - Known drug-gene interactions affecting drug response - Dosing guidelines if any exist ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 11: EXPRESSION PROFILES ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Tissue expression: - Which tissues express this gene most highly? - List TOP 30 tissues with expression scores/levels - Note any tissue-specific or tissue-enriched patterns Cell type expression: - Which cell types show highest expression? - List TOP 30 cell types with expression scores - Note any cell type-specific patterns Single-cell expression data (if available): - Which single-cell datasets/experiments include this gene? - Notable cell population patterns ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ SECTION 12: DISEASE ASSOCIATIONS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Mendelian/monogenic disease links: - What diseases are caused by mutations in this gene? - List ALL associated diseases with: disease name, disease ID, inheritance pattern, evidence level Phenotype associations: - What clinical phenotypes are associated with this gene? - List TOP 50 phenotype terms with IDs Complex trait associations (GWAS): - What traits/diseases are linked via genome-wide association studies? - List TOP 30 GWAS associations with: trait, study ID, p-value, effect size if available ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ FORMATTING REQUIREMENTS ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ - Present each section with clear headers - Use tables for listing multiple items - Always include COUNTS for every category - For lists with 50 items: show total count + TOP 50 - For lists with

Question

Provide a comprehensive cross-database identifier and functional mapping
reference for human SNCA. This should serve as a definitive
lookup resource for researchers.

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 1: GENE IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Provide ALL gene-level database identifiers:
- HGNC ID and approved symbol
- Ensembl gene ID (ENSG)
- NCBI Entrez Gene ID
- OMIM gene/locus ID
- Genomic location: chromosome, start position, end position, strand

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 2: TRANSCRIPT IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
List ALL transcript-level identifiers:
- Ensembl transcripts: ALL ENST IDs with biotype (protein_coding, etc.)
  How many total transcripts?
- RefSeq transcripts: ALL NM_ mRNA accessions
  Mark which is MANE Select (canonical clinical standard)
- CCDS IDs: ALL consensus coding sequence identifiers

For the CANONICAL/MANE SELECT transcript:
- List ALL exon IDs (ENSE) with genomic coordinates
- Total exon count

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 3: PROTEIN IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
List ALL protein-level identifiers:
- UniProt accessions: ALL entries (reviewed and unreviewed)
  Mark the canonical reviewed entry
- RefSeq protein: ALL NP_ accessions

Protein domains and families:
- List ALL annotated domains/families with identifiers
- Include: domain name, type (domain/family/superfamily), and ID

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 4: STRUCTURE IDENTIFIERS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Experimental structures:
- List ALL PDB structure IDs
- For each: experimental method (X-ray, NMR, Cryo-EM) and resolution
- Total PDB structure count

Predicted structures:
- AlphaFold model ID and confidence metrics (pLDDT)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 5: CROSS-SPECIES ORTHOLOGS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
List orthologous genes in key model organisms (where available):
- Mouse (Mus musculus): gene ID, symbol
- Rat (Rattus norvegicus): gene ID, symbol
- Zebrafish (Danio rerio): gene ID, symbol
- Fruit fly (Drosophila melanogaster): gene ID, symbol
- Worm (C. elegans): gene ID, symbol
- Yeast (S. cerevisiae): gene ID, symbol

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 6: CLINICAL VARIANTS & AI PREDICTIONS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Clinical variant annotations:
- Total variant count in clinical databases
- Breakdown by classification: Pathogenic, Likely Pathogenic,
  Uncertain Significance (VUS), Likely Benign, Benign
- List TOP 50 pathogenic/likely pathogenic variants with:
  variant ID, HGVS notation, associated condition

AI-based variant effect predictions:
- Splice effect predictions: Total count
  List TOP 50 predicted splice-altering variants with delta scores
- Missense pathogenicity predictions: Total count
  List TOP 50 predicted pathogenic missense variants with scores

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 7: BIOLOGICAL PATHWAYS & GENE ONTOLOGY
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Pathway membership:
- List ALL biological pathways this gene participates in
- Include pathway IDs and names
- Total pathway count

Gene Ontology annotations:
- Biological Process: count and TOP 20 terms with IDs
- Molecular Function: count and TOP 20 terms with IDs
- Cellular Component: count and TOP 20 terms with IDs

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 8: PROTEIN INTERACTIONS & MOLECULAR NETWORKS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Protein-protein interactions:
- Total interaction count
- List TOP 50 highest-confidence interacting proteins with scores

Protein similarity (evolutionary and structural):
- Structural/embedding similarity: How many similar proteins?
  List TOP 20 with similarity scores
- Sequence homology: How many homologous proteins?
  List TOP 20 with identity/similarity scores

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 9: TRANSCRIPTION FACTOR REGULATORY DATA
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
If this gene encodes a transcription factor:

Downstream targets (genes regulated BY this TF):
- Total target gene count
- List TOP 50 target genes with regulation type (activates/represses)

DNA binding profiles:
- List ALL known binding motif IDs
- Motif family classification

Upstream regulators (TFs that regulate THIS gene):
- List known transcriptional regulators with evidence type

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 10: DRUG & PHARMACOLOGY DATA
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
If this gene/protein is a drug target:

Targeting molecules:
- How many drug/compound molecules target this protein?
- List TOP 30 molecules by development phase
- Include: molecule ID, name, mechanism, highest development phase

Clinical trials:
- How many clinical trials involve drugs targeting this gene?
- List TOP 20 trials with: trial ID, phase, status, intervention

Pharmacogenomics:
- Known drug-gene interactions affecting drug response
- Dosing guidelines if any exist

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 11: EXPRESSION PROFILES
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Tissue expression:
- Which tissues express this gene most highly?
- List TOP 30 tissues with expression scores/levels
- Note any tissue-specific or tissue-enriched patterns

Cell type expression:
- Which cell types show highest expression?
- List TOP 30 cell types with expression scores
- Note any cell type-specific patterns

Single-cell expression data (if available):
- Which single-cell datasets/experiments include this gene?
- Notable cell population patterns

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
SECTION 12: DISEASE ASSOCIATIONS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Mendelian/monogenic disease links:
- What diseases are caused by mutations in this gene?
- List ALL associated diseases with: disease name, disease ID,
  inheritance pattern, evidence level

Phenotype associations:
- What clinical phenotypes are associated with this gene?
- List TOP 50 phenotype terms with IDs

Complex trait associations (GWAS):
- What traits/diseases are linked via genome-wide association studies?
- List TOP 30 GWAS associations with: trait, study ID, p-value,
  effect size if available

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
FORMATTING REQUIREMENTS
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
- Present each section with clear headers
- Use tables for listing multiple items
- Always include COUNTS for every category
- For lists with >50 items: show total count + TOP 50
- For lists with <50 items: show ALL items
- Always include database identifiers (IDs), not just names
- Mark canonical/primary/reviewed entries where applicable
- If a section has no data available, state "No data available"
  rather than omitting the section

Accepted Answer

Now let me compile the comprehensive reference document for human SNCA.
SNCA (Alpha-Synuclein) - Comprehensive Cross-Database Identifier and Functional Mapping Reference Gene: SNCA (synuclein alpha) Species: Homo sapiens (Human) Last Updated: 2026-03-27
Section 1: Gene Identifiers Core Gene Identifiers
DatabaseIdentifierNotes HGNC IDHGNC:11138Approved symbol: SNCA HGNC SymbolSNCAApproved name: synuclein alpha Ensembl Gene IDENSG00000145335GRCh38 NCBI Entrez Gene ID6622 OMIM Gene …

Attribute	Value
Chromosome	4
Cytogenetic Band	4q22.1
Start Position	89,700,345
End Position	89,838,315
Strand	Minus (-)
Genomic Accession	NC_000004.12
Gene Span	~138 kb

Attribute	Values
Previous Symbols	PARK1, PARK4
Aliases	NACP, PD1
Previous Names	Parkinson disease (autosomal dominant, Lewy body) 4; synuclein, alpha (non A4 component of amyloid precursor)
Locus Type	protein-coding gene
Gene Family	Synuclein family

Transcript ID	Biotype	Start	End	Canonical
ENST00000336904	protein_coding	89724099	89838315	Yes (MANE)
ENST00000345009	protein_coding	89725884	89835680
ENST00000394986	protein_coding	89726053	89837139
ENST00000394989	protein_coding	89724105	89837199
ENST00000394991	protein_coding	89724099	89837161
ENST00000420646	protein_coding	89724099	89836976
ENST00000502987	protein_coding	89821849	89835695
ENST00000505199	protein_coding	89726616	89835685
ENST00000506244	protein_coding	89726577	89837168
ENST00000506691	protein_coding	89822352	89837076
ENST00000508895	protein_coding	89726258	89836213
ENST00000611107	protein_coding	89726628	89835667
ENST00000618500	protein_coding	89724099	89836213
ENST00000673718	protein_coding	89724115	89837015
ENST00000673766	protein_coding_CDS_not_defined	89724113	89771957
ENST00000673902	protein_coding	89700345	89837310
ENST00000674129	protein_coding	89725343	89837310
ENST00000889657	protein_coding	89726055	89838265
ENST00000889658	protein_coding	89726055	89838210
ENST00000889659	protein_coding	89726053	89837660
ENST00000889660	protein_coding	89725536	89836262
ENST00000889662	protein_coding	89726055	89836607
ENST00000889663	protein_coding	89726136	89835949
ENST00000912364	protein_coding	89726254	89837016
ENST00000912365	protein_coding	89726055	89836701
ENST00000965186	protein_coding	89726060	89838263
ENST00000965187	protein_coding	89725519	89837189
ENST00000965188	protein_coding	89726060	89837200
ENST00000965189	protein_coding	89726060	89837198
ENST00000965190	protein_coding	89726062	89836979
ENST00000965191	protein_coding	89726137	89836747
ENST00000965192	protein_coding	89726137	89836507

RefSeq ID	Type	Status	MANE Select
NM_000345	mRNA	REVIEWED	Yes ✓
NM_001146054	mRNA	REVIEWED	No
NM_001146055	mRNA	REVIEWED	No
NM_001375285	mRNA	REVIEWED	No
NM_001375286	mRNA	REVIEWED	No
NM_001375287	mRNA	REVIEWED	No
NM_001375288	mRNA	REVIEWED	No
NM_001375290	mRNA	REVIEWED	No
NM_007308	mRNA	REVIEWED	No
NR_164674-NR_164676	ncRNA	REVIEWED	No

Exon ID	Start	End	Strand
ENSE00001484185	89838252	89838315	-
ENSE00001407446	89835547	89835692	-
ENSE00000970012	89828143	89828184	-
ENSE00000970013	89822246	89822388	-
ENSE00000970014	89729194	89729277	-
ENSE00003902180	89724099	89726660	-

SNCA Gene Complete Identifier and Functional Mapping Reference

Structured Data Sources

Database	Identifier	Notes
HGNC ID	HGNC:11138	Approved symbol: SNCA
HGNC Symbol	SNCA	Approved name: synuclein alpha
Ensembl Gene ID	ENSG00000145335	GRCh38
NCBI Entrez Gene ID	6622
OMIM Gene ID	163890	Gene/locus

UniProt ID	Status	Name	Notes
P37840	Reviewed (Swiss-Prot)	Alpha-synuclein	Canonical ✓
A0A669KB41	Unreviewed (TrEMBL)		Isoform
A0A669KBH5	Unreviewed (TrEMBL)		Isoform
D6RA31	Unreviewed (TrEMBL)		Isoform
E7EPV7	Unreviewed (TrEMBL)		Isoform
H6UYS0	Unreviewed (TrEMBL)		Isoform
H6UYS5	Unreviewed (TrEMBL)		Isoform
H6UYS7	Unreviewed (TrEMBL)		Isoform

Property	Value
Protein Name	Alpha-synuclein
Alternative Names	Non-A beta component of AD amyloid; Non-A4 component of amyloid precursor
Length	140 amino acids
Molecular Mass	14,460 Da

RefSeq Protein ID	Status	MANE Select
NP_000336	REVIEWED	Yes ✓
NP_001139526	REVIEWED	No
NP_001139527	REVIEWED	No
NP_001362214	REVIEWED	No
NP_001362215	REVIEWED	No
NP_001362216	REVIEWED	No
NP_001362217	REVIEWED	No
NP_001362219	REVIEWED	No
NP_009292	REVIEWED	No

Database	ID	Name	Type
InterPro	IPR001058	Synuclein	Family
InterPro	IPR002460	Synuclein_alpha	Family
Pfam	PF01387	Synuclein	Domain

PDB ID	Method	Resolution	Title
1XQ8	Solution NMR	-	Human micelle-bound alpha-synuclein
2KKW	NMR/EPR	-	SLAS-micelle bound alpha-synuclein
2N0A	Solid-state NMR	-	Atomic-resolution structure of alpha-synuclein fibrils
3Q25	X-ray	1.90 Å	Alpha-synuclein (1-19) fused to MBP
3Q26	X-ray	1.54 Å	Alpha-synuclein (10-42) fused to MBP
3Q27	X-ray	1.30 Å	Alpha-synuclein (32-57) fused to MBP
3Q28	X-ray	1.60 Å	Alpha-synuclein (58-79) fused to MBP
6A6B	Cryo-EM	3.07 Å	Alpha-synuclein fiber
6CU7	Cryo-EM	3.50 Å	Alpha-synuclein fibril - Rod Polymorph
6CU8	Cryo-EM	3.60 Å	Alpha-synuclein fibril - Twister Polymorph
6H6B	Cryo-EM	3.40 Å	Alpha-synuclein fibrils
6I42	X-ray	1.38 Å	Alpha-synuclein PreNAC/Cyclophilin A complex
6OSJ	Cryo-EM	2.80 Å	N-terminally acetylated full length alpha-synuclein fibrils
6UFR	Cryo-EM	2.50 Å	E46K alpha-synuclein fibrils
6XYO	Cryo-EM	2.60 Å	Multiple system atrophy Type I alpha-synuclein filament
7E0F	Cryo-EM	3.02 Å	G51D alpha-synuclein amyloid fibril
7LRQ	Cryo-EM	3.49 Å	A53T alpha-synuclein amyloid fibril
8A9L	Cryo-EM	2.20 Å	Alpha-synuclein filaments from Parkinson's disease/DLB
8BQV	Cryo-EM	2.00 Å	Alpha-synuclein from Juvenile-onset synucleinopathy
9EUU	Cryo-EM	1.93 Å	Recombinant alpha-synuclein fibrils 1B (highest res)

Species	Gene ID	Symbol	Genome
Mouse (Mus musculus)	ENSMUSG00000025889	Snca	mus_musculus
Rat (Rattus norvegicus)	ENSRNOG00000008656	Snca	rattus_norvegicus
Zebrafish (Danio rerio)	No direct ortholog	-	-
Fruit fly (Drosophila)	No ortholog	-	-
C. elegans	No ortholog	-	-
Yeast (S. cerevisiae)	No ortholog	-	-

Classification	Count
Pathogenic	~5
Likely pathogenic	~3
Pathogenic/Likely pathogenic (CNV)	~3
Uncertain Significance (VUS)	~45
Likely Benign	~55
Benign	~35
Conflicting classifications	~5

ClinVar ID	HGVS Notation	Classification	Condition
14007	NM_000345.4:c.157G>A (p.Ala53Thr)	Pathogenic	Parkinson disease
14010	NM_000345.4:c.136G>A (p.Glu46Lys)	Pathogenic	Parkinson disease
14008	NM_000345.4:c.88G>C (p.Ala30Pro)	Likely pathogenic	Parkinson disease
1120010	4q22.1 copy number gain	Pathogenic	Parkinson disease
1454898	SNCA duplication	Pathogenic	Parkinson disease

Variant	Position	Pathogenicity Score	Classification
A140D	4:89726632	0.807	Likely pathogenic
A140P	4:89726633	0.699	Likely pathogenic

CCDS ID
CCDS3634
CCDS43252

Variant	Effect	Delta Score
4:89726487:T>TA	Donor gain	0.90
4:89726657:CTTC>C	Acceptor gain	0.87
4:89726601:T>TG	Acceptor gain	0.80
4:89725343:A>T	Acceptor gain	0.76
4:89725341:C>T	Acceptor gain	0.74
4:89726656:CCTTC>C	Acceptor gain	0.73
4:89726528:ACTTT>A	Acceptor gain	0.68
4:89725337:A>T	Acceptor gain	0.65
4:89725345:A>T	Acceptor gain	0.64
4:89726530:T>A	Acceptor gain	0.62

Pathway ID	Pathway Name	Disease Pathway
R-HSA-977225	Amyloid fiber formation	No
R-HSA-9833482	PKR-mediated signaling	No
R-HSA-1169410	Antimicrobial mechanism of IFN-stimulated genes	No
R-HSA-1280215	Cytokine Signaling in Immune system	No
R-HSA-168256	Immune System	No
R-HSA-392499	Metabolism of proteins	No
R-HSA-913531	Interferon Signaling	No

GO ID	Term
GO:0005515	protein binding
GO:0042802	identical protein binding
GO:0008289	lipid binding
GO:0005543	phospholipid binding
GO:0008017	microtubule binding
GO:0003779	actin binding
GO:0000149	SNARE binding
GO:0048156	tau protein binding
GO:0005507	copper ion binding
GO:0005509	calcium ion binding
GO:0008270	zinc ion binding
GO:0008198	ferrous iron binding
GO:0000287	magnesium ion binding
GO:0004857	enzyme inhibitor activity
GO:0004860	protein kinase inhibitor activity
GO:0004869	cysteine-type endopeptidase inhibitor activity
GO:0042393	histone binding
GO:0019894	kinesin binding
GO:0043014	alpha-tubulin binding
GO:0048487	beta-tubulin binding

GO ID	Term
GO:0007268	chemical synaptic transmission
GO:0016079	synaptic vesicle exocytosis
GO:0016082	synaptic vesicle priming
GO:0007269	neurotransmitter secretion
GO:0042416	dopamine biosynthetic process
GO:0042417	dopamine metabolic process
GO:0001963	synaptic transmission, dopaminergic
GO:0035493	SNARE complex assembly
GO:0048489	synaptic vesicle transport
GO:0048488	synaptic vesicle endocytosis
GO:0043066	negative regulation of apoptotic process
GO:0043065	positive regulation of apoptotic process
GO:0051259	protein complex oligomerization
GO:1990000	amyloid fibril formation
GO:0034599	cellular response to oxidative stress
GO:0007006	mitochondrial membrane organization
GO:0042775	mitochondrial ATP synthesis coupled electron transport
GO:0050808	synapse organization
GO:0014059	regulation of dopamine secretion
GO:0031115	negative regulation of microtubule polymerization

GO ID	Term
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0045202	synapse
GO:0098793	presynapse
GO:0008021	synaptic vesicle
GO:0030672	synaptic vesicle membrane
GO:0043195	terminal bouton
GO:0030424	axon
GO:0043679	axon terminus
GO:0043025	neuronal cell body
GO:0005739	mitochondrion
GO:0005743	mitochondrial inner membrane
GO:0005741	mitochondrial outer membrane
GO:0005634	nucleus
GO:0016234	inclusion body
GO:0099512	supramolecular fiber
GO:0005764	lysosome
GO:0030426	growth cone
GO:0005576	extracellular region

Interactor	UniProt	Confidence Score
SNCA (self)	P37840	999
PRKN (Parkin)	O60260	999
DJPC1 (DJ-1)	Q9Y6H5	998
TARDBP	Q13148	995
PARK7	Q99497	986
PRNP (Prion)	P04156	984
HTT (Huntingtin)	P42858	983
SNCAIP (Synphilin-1)	Q9Y6H5	980
TOMM22	Q15388	980
TH (Tyrosine Hydroxylase)	P07101	975
LRRK2	Q5S007	973
VDAC1	P21796	972
MAPT (Tau)	P10636	971
HSPA4	P34932	970
APOE	P02649	967
HSPA8	P11142	962
CALM1	P02593	955
APP	P05067	954
PINK1	Q9BXM7	947
UCHL1	P09936	940

Interactor	Type	Confidence
SNCA (homo-oligomer)	direct interaction	0.99
APOE	physical association	0.81
SNCAIP	physical association	0.80
TPPP	direct interaction	0.72
SERF1A	direct interaction	0.65
VAMP2	physical association	0.63
CLU (Clusterin)	physical association	0.66
APP	physical association	0.66
APOA1	physical association	0.62

UniProt ID	Top Similarity	Average Similarity
P61138	1.000	0.983
P61139	1.000	0.983
P61140	1.000	0.983
P61141-P61145	1.000	0.983
B3EWG3	1.000	0.976
O55042 (Mouse)	0.9999	0.981
P37377 (Beta-syn)	0.9999	0.981
Q16143 (Gamma-syn)	0.999	0.983
P33567	0.999	0.982
O76070	0.9996	0.984

UniProt ID	Identity	BitScore
P37840	100%	139
P61138-P61145	99-100%	137-149
O55042 (Mouse Snca)	99.3%	158
P37377 (Mouse/Rat)	99.3%	158
P61147	90.7%	147
Q16143 (SNCG, Gamma)	93.3%	109

TF Gene	Regulation	Confidence
YY1	Activation	High
NR4A2 (NURR1)	Activation	-
GATA2	Unknown	High
BATF	-	High
IRF9	-	High
ISL1	-	High
NFATC1	-	High
PARP1	-	High
PRDM1	-	High
ZNF219	-	High
CEBPB	Unknown	-
ESR1	-	Low
BCL6	-	Low
PAX6	-	Low
NONO	-	Low
TBX21	-	Low
ZNF436	-	Low
ZSCAN21	Unknown	-
SRF	-	-
VPS35	Repression	-
OPRD1	Repression	-

Kinase	Effect	Mechanism	Score
SNCAIP	Up-regulates activity	Binding	0.80
ROS	Up-regulates quantity	-	0.70
GRK5	Down-regulates activity	Phosphorylation	0.64
LRRK2	Down-regulates activity	Phosphorylation	0.62
DYRK1A	Up-regulates	Phosphorylation	0.56
SYK	Down-regulates	Phosphorylation	0.53
CSNK2A1	Down-regulates activity	Phosphorylation	0.51
PLK2	Down-regulates activity	Phosphorylation	0.48
ABL1	Up-regulates quantity	Phosphorylation	0.42
CSNK1A1	Down-regulates activity	Phosphorylation	0.37

Effect	Mechanism
Lewy body formation	Up-regulates
ER stress	Up-regulates
VAMP2 quantity	Down-regulates (binding)
CADPS2 expression	Down-regulates (transcriptional)

ChEMBL Target ID	Type	Target Name
CHEMBL6152	Single Protein	Alpha-synuclein
CHEMBL5465209	PPI	Cereblon/Alpha-synuclein
CHEMBL5465232	PPI	VHL/Alpha-synuclein
CHEMBL5483090	PPI	cIAP1/Alpha-synuclein

ChEMBL ID	Name	Type	Highest Phase
CHEMBL135	ESTRADIOL	Small molecule	Phase 4 (Approved)
CHEMBL1405	ESTRONE	Small molecule	Phase 4 (Approved)
CHEMBL1440	TETRACYCLINE	Small molecule	Phase 4 (Approved)
CHEMBL1550	PHYTONADIONE	Small molecule	Phase 4 (Approved)
CHEMBL161	CEFTRIAXONE	Small molecule	Phase 4 (Approved)
CHEMBL1908919	FLORBETAPIR	Small molecule	Phase 4 (Approved)
CHEMBL193482	ESTRIOL	Small molecule	Phase 4 (Approved)
CHEMBL140	CURCUMIN	Small molecule	Phase 3
CHEMBL259223	MENATETRENONE	Small molecule	Phase 3
CHEMBL286494	HYPERICIN	Small molecule	Phase 3
CHEMBL297453	EGCG	Small molecule	Phase 3
CHEMBL1368322	PARAROSANILINE	Small molecule	Phase 2
CHEMBL151	LUTEOLIN	Small molecule	Phase 2
CHEMBL288114	GALLIC ACID	Small molecule	Phase 2
CHEMBL164	MYRICETIN	Small molecule	Preclinical
CHEMBL125743	GALLOCATECHIN	Small molecule	Preclinical
CHEMBL129451	CATECHINGALLATE	Small molecule	Preclinical
CHEMBL224392	THIOFLAVIN T	Small molecule	Preclinical

Metric	Value
Expression Breadth	Ubiquitous
Total Present Calls	280
Total Absent Calls	9
Total Conditions	289
Max Expression Score	99.43
Average Expression Score	83.97
Gold Quality Conditions	257

Rank	Tissue/Structure	Expression Score	Quality
1	Trabecular bone tissue	99.43	Gold
2	Orbitofrontal cortex	99.38	Gold
3	Pons	99.25	Gold
4	Brodmann area 46	99.09	Gold
5	Brodmann area 23	98.76	Gold
6	Tendon of biceps brachii	98.74	Gold
7	Postcentral gyrus	98.72	Gold
8	Parietal lobe	98.69	Gold
9	Middle temporal gyrus	98.65	Gold
10	Substantia nigra pars compacta	98.58	Gold
11	Superior frontal gyrus	98.58	Gold
12	Brodmann area 9	98.58	Gold
13	Olfactory bulb	98.47	Gold
14	Entorhinal cortex	98.30	Gold
15	Right frontal lobe	98.20	Gold
16	Cranial nerve II	98.04	Gold
17	Substantia nigra pars reticulata	98.01	Gold
18	Prefrontal cortex	97.98	Gold
19	Amygdala	97.68	Gold
20	Cerebellar hemisphere	97.65	Gold
21	Temporal lobe	97.63	Gold
22	Dorsolateral prefrontal cortex	97.61	Gold
23	Substantia nigra	97.55	Gold
24	Ammon's horn (Hippocampus)	97.55	Gold
25	Cerebellar cortex	97.52	Gold
26	Right cerebellar hemisphere	97.51	Gold
27	Tibial nerve	97.42	Gold
28	C1 cervical spinal cord	97.35	Gold
29	Midbrain	97.25	Gold
30	Blood	97.15	Gold

Cell Type	Expression Score	Quality
Endothelial cell	98.76	Gold
Monocyte	98.59	Gold
Mononuclear cell	98.25	Gold

Dataset ID	Description	Cell Count
E-CURD-122	Cross-tissue immune cell analysis	356,580
E-MTAB-7407	Human fetal liver, skin, kidney	473,803
E-HCAD-4	Census of Immune Cells	791,344
E-CURD-98	Human Fetal Liver	197,943
E-CURD-114	Human airway epithelium	81,801
E-CURD-112	Fetal bone marrow	56,592
E-HCAD-23	First-trimester placenta/decidua	41,132
E-MTAB-9221	COVID-19 blood	27,943
E-MTAB-8205	hPSC endothelial-to-haematopoietic	25,764
E-HCAD-5	Organoid inter-individual variation	25,049

Disease	Disease ID	Inheritance	Classification	Submitter
Parkinson disease	MONDO:0005180	AD	Definitive	Ambry Genetics
AD Parkinson disease 4	OMIM:605543	AD	Definitive	Ambry Genetics
AD Parkinson disease 1	OMIM:168601	AD	Strong	Genomics England
AD Parkinson disease 4	OMIM:605543	AD	Strong	Genomics England
Lewy body dementia	OMIM:127750	AD	Strong	Genomics England
AD Parkinson disease 4	OMIM:605543	AD	Strong	Labcorp
Lewy body dementia	OMIM:127750	AD	Strong	Labcorp
Hereditary late-onset PD	ORPHA:411602	AD	Supportive	Orphanet
Parkinsonian-pyramidal syndrome	ORPHA:171695	AR	Supportive	Orphanet

Orphanet ID	Disease Name	Type	Gene Count
171695	Parkinsonian-pyramidal syndrome	Disease	2
2828	Young-onset Parkinson disease	Disease	11
411602	Hereditary late-onset Parkinson disease	Disease	7

HPO ID	Phenotype
HP:0001300	Parkinsonism
HP:0002548	Parkinsonism with favorable response to dopaminergic medication
HP:0002067	Bradykinesia
HP:0002063	Rigidity
HP:0001337	Tremor
HP:0002322	Resting tremor
HP:0002080	Intention tremor
HP:0002172	Postural instability
HP:0001288	Gait disturbance
HP:0002141	Gait imbalance
HP:0002362	Shuffling gait
HP:0002359	Frequent falls
HP:0002304	Akinesia
HP:0002375	Hypokinesia
HP:0001332	Dystonia
HP:0100660	Dyskinesia
HP:0001336	Myoclonus
HP:0000726	Dementia
HP:0001268	Mental deterioration
HP:0100543	Cognitive impairment
HP:0000727	Frontal lobe dementia
HP:0000738	Hallucinations
HP:0002367	Visual hallucination
HP:0000746	Delusion
HP:0011999	Paranoia
HP:0100753	Schizophrenia
HP:0000716	Depression
HP:0000739	Anxiety
HP:0025269	Panic attack
HP:0000741	Apathy
HP:0000713	Agitation
HP:0100710	Impulsivity
HP:0001260	Dysarthria
HP:0031435	Monotonic speech
HP:0031908	Micrographia
HP:0002015	Dysphagia
HP:0001278	Orthostatic hypotension
HP:0004926	Orthostatic hypotension due to autonomic dysfunction
HP:0012332	Abnormal autonomic nervous system physiology
HP:0002019	Constipation
HP:0012450	Chronic constipation
HP:0002578	Gastroparesis
HP:0002360	Sleep disturbance
HP:0100785	Insomnia
HP:0012452	Restless legs
HP:0004409	Hyposmia
HP:0100315	Lewy bodies
HP:0002171	Gliosis
HP:0011960	Substantia nigra gliosis
HP:0002120	Cerebral cortical atrophy

GWAS ID	Trait	P-value	Mapped Gene
GCST004902_48	Parkinson's disease	5×10⁻¹²³	SNCA
GCST009325_4	PD or first-degree relative	4×10⁻¹⁵⁴	SNCA
GCST009325_94	PD or first-degree relative	5×10⁻¹⁴⁹	SNCA
GCST002544_19	Parkinson's disease	4×10⁻⁷³	SNCA
GCST001445_5	Parkinson's disease	6×10⁻⁶⁵	SNCA
GCST003984_5	Parkinson's disease	1×10⁻⁵⁶	SNCA
GCST009325_93	PD or first-degree relative	1×10⁻⁴⁸	SNCA
GCST000959_7	Parkinson's disease	2×10⁻⁴⁷	SNCA
GCST010049_1	Parkinson's disease	2×10⁻³⁷	SNCA
GCST009325_5	PD or first-degree relative	1×10⁻³⁶	SNCA
GCST001430_2	Parkinson's disease	8×10⁻³⁵	SNCA
GCST003922_2	Parkinson's disease	1×10⁻³²	SNCA
GCST006585_2238	Blood protein levels	8×10⁻³⁰	SNCA
GCST001126_2	Parkinson's disease	2×10⁻¹⁹	SNCA
GCST003800_1	Bupropion response in depression	3×10⁻⁸	GPRIN3-SNCA
GCST000530_1	Parkinson's disease	7×10⁻¹⁷	SNCA
GCST000528_4	Parkinson's disease	2×10⁻¹⁶	SNCA
GCST000855_3	Parkinson's disease	9×10⁻¹⁶	SNCA
GCST005276_2	Dementia with Lewy bodies	9×10⁻¹³	SNCA
GCST007780_1	PD age of onset	2×10⁻¹²	SNCA
GCST012354_9	Anxiety	4×10⁻¹¹	SNCA
GCST000772_1	Parkinson's disease	3×10⁻¹¹	SNCA
GCST009373_1	PD in GBA mutation carriers	2×10⁻¹¹	SNCA
GCST002353_3	Parkinson's disease	3×10⁻¹¹	SNCA
GCST001445_6	Parkinson's disease	5×10⁻¹¹	SNCA-AS1
GCST006940_38	Neuroticism	2×10⁻¹⁰	SNCA
GCST006948_44	Feeling nervous	1×10⁻⁹	SNCA
GCST006585_643	Blood protein levels	1×10⁻⁹	SNCA
GCST002353_2	Parkinson's disease	1×10⁻⁹	SNCA
GCST009512_1	Parkinson's disease	2×10⁻⁹	SNCA

Section	Primary Databases
Gene IDs	HGNC, Ensembl, NCBI Entrez, OMIM
Transcripts	Ensembl, RefSeq, CCDS
Proteins	UniProt, RefSeq, InterPro, Pfam
Structures	PDB, AlphaFold
Orthologs	Ensembl Compara
Variants	ClinVar, AlphaMissense, SpliceAI
Pathways	Reactome, Gene Ontology
Interactions	STRING, IntAct, BioGRID, SIGNOR
Regulation	CollecTRI
Drugs	ChEMBL, DrugBank, PharmGKB
Expression	Bgee, Single Cell Expression Atlas
Disease	GenCC, OMIM, Orphanet, HPO, GWAS Catalog