ClinVar Genomic variation as it relates to human health
NM_000345.4(SNCA):c.88G>C (p.Ala30Pro)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000345.4(SNCA):c.88G>C (p.Ala30Pro)
Variation ID: 14008 Accession: VCV000014008.5
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4q22.1 4: 89835580 (GRCh38) [ NCBI UCSC ] 4: 90756731 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 30, 2018 Apr 15, 2024 Nov 20, 2020 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000345.4:c.88G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000336.1:p.Ala30Pro missense NM_001146054.2:c.88G>C NP_001139526.1:p.Ala30Pro missense NM_001146055.2:c.88G>C NP_001139527.1:p.Ala30Pro missense NM_001375285.1:c.88G>C NP_001362214.1:p.Ala30Pro missense NM_001375286.1:c.88G>C NP_001362215.1:p.Ala30Pro missense NM_001375287.1:c.88G>C NP_001362216.1:p.Ala30Pro missense NM_001375288.1:c.88G>C NP_001362217.1:p.Ala30Pro missense NM_007308.3:c.88G>C NP_009292.1:p.Ala30Pro missense NR_164674.1:n.166G>C non-coding transcript variant NR_164675.1:n.313G>C non-coding transcript variant NC_000004.12:g.89835580C>G NC_000004.11:g.90756731C>G NG_011851.1:g.7717G>C P37840:p.Ala30Pro - Protein change
- A30P
- Other names
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- Canonical SPDI
- NC_000004.12:89835579:C:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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SNCA | - | - |
GRCh38 GRCh37 |
167 | 207 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Likely pathogenic (2) |
criteria provided, single submitter
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Nov 20, 2020 | RCV000015045.33 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Nov 20, 2020)
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criteria provided, single submitter
Method: clinical testing
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Autosomal dominant Parkinson disease 1
Affected status: unknown
Allele origin:
germline
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Molecular Genetics, Royal Melbourne Hospital
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002503806.2
First in ClinVar: Apr 28, 2022 Last updated: Apr 15, 2024 |
Comment:
This sequence change is predicted to replace alanine with proline at codon 30 of the SNCA protein (p.(Ala30Pro)). The alanine residue is evolutionarily conserved (100 … (more)
This sequence change is predicted to replace alanine with proline at codon 30 of the SNCA protein (p.(Ala30Pro)). The alanine residue is evolutionarily conserved (100 vertebrates, UCSC), and is located in an N-terminal domain helix. There is a small physicochemical difference between alanine and glycine. The variant is absent in a large population cohort (PM2; gnomAD v2.1 and v3.0). It has been shown to co-segregate with Parkinson disease in a single family (PP1; PMID: 11376188). Additionally, mouse models of the variant recapitulate the human Parkinson disease phenotype and brain pathology (PS3; PMID: 21559878, 31267130). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (PP3; 6/6 algorithms). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as a LIKELY PATHOGENIC. Following criteria are met: PS3, PM2, PP1, PP3. (less)
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Pathogenic
(Nov 22, 2013)
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no assertion criteria provided
Method: literature only
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PARKINSON DISEASE 1, AUTOSOMAL DOMINANT
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000035301.8
First in ClinVar: Apr 04, 2013 Last updated: Jul 07, 2022 |
Comment on evidence:
To investigate further the role of alpha-synuclein in familial Parkinson disease (PARK1; 168601), Kruger et al. (1998) undertook mutation analysis of all 5 translated SNCA … (more)
To investigate further the role of alpha-synuclein in familial Parkinson disease (PARK1; 168601), Kruger et al. (1998) undertook mutation analysis of all 5 translated SNCA exons in 192 sporadic cases and in 7 unrelated patients with a family history for Parkinson disease. None of the patients was found to carry the A53T mutation (163890.0001). One patient was found to carry a heterozygous 88G-C transversion in exon 3, resulting in an ala30-to-pro (A30P) substitution. The index patient developed signs of progressive parkinsonism at 52 years of age. His mother presented with symptoms at age 56 and died from the disease at age 60. A younger sib, aged 55, reported impaired motor function in the right arm and neurologic findings of Parkinson disease. The 33-year-old child of the index patient and a 50-year-old sib were carriers of the mutation. Both exhibited subtle neurologic disturbances. The A30P substitution was not found in 1,140 control chromosomes. Kruger et al. (1998) concluded that mutations in the SNCA gene participate in the pathogenesis of some rare cases of Parkinson disease. Kruger et al. (2001) characterized the disease phenotype caused by the A30P mutation and found that it is similar to that of typical PD, including cardinal features of PD and positive and sustained response to L-DOPA therapy. Two affected members of 1 family showed striatal dopaminergic abnormalities on PET scan similar to those in sporadic PD. Cognitive impairment was noted as an early and frequent finding. Seidel et al. (2010) reported neuropathologic findings of a patient with PD due to the A30P mutation. He had onset at age 54 years, had L-DOPA-related complications, and died in a mute, bedridden state at age 69. Postmortem examination showed depigmentation and neuronal loss in the substantia nigra and neuronal loss in the locus ceruleus and dorsal motor vagal nucleus. There were widespread SNCA-positive Lewy bodies, Lewy neurites, and glial aggregates in the cerebral cortex and many other regions of the brain, including the hippocampus, hypothalamus, brainstem, and cerebellum. Biochemical analysis showed a significant load of insoluble SNCA. Chung et al. (2013) generated cortical neurons from iPS cells of patients harboring the A53T alpha-synuclein mutation. Genetic modifiers from unbiased screens in a yeast model of alpha-synuclein toxicity led to identification of early pathogenic phenotypes in patient neurons, including nitrosative stress, accumulation of endoplasmic reticulum-associated degradation substrates, and ER stress. A small molecule, NAB2, identified in a yeast screen (Tardiff et al., 2013), and NEDD4 (602278), the ubiquitin ligase that it affects, reversed pathologic phenotypes in these neurons. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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The A30P α-synuclein mutation decreases subventricular zone proliferation. | Zhang XM | Human molecular genetics | 2019 | PMID: 31267130 |
Yeast reveal a "druggable" Rsp5/Nedd4 network that ameliorates α-synuclein toxicity in neurons. | Tardiff DF | Science (New York, N.Y.) | 2013 | PMID: 24158909 |
Identification and rescue of α-synuclein toxicity in Parkinson patient-derived neurons. | Chung CY | Science (New York, N.Y.) | 2013 | PMID: 24158904 |
Parkinson's disease mouse models in translational research. | Antony PM | Mammalian genome : official journal of the International Mammalian Genome Society | 2011 | PMID: 21559878 |
First appraisal of brain pathology owing to A30P mutant alpha-synuclein. | Seidel K | Annals of neurology | 2010 | PMID: 20437567 |
Familial parkinsonism with synuclein pathology: clinical and PET studies of A30P mutation carriers. | Krüger R | Neurology | 2001 | PMID: 11376188 |
Ala30Pro mutation in the gene encoding alpha-synuclein in Parkinson's disease. | Krüger R | Nature genetics | 1998 | PMID: 9462735 |
Text-mined citations for rs104893878 ...
HelpRecord last updated Apr 15, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.