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NM_000282.4(PCCA):c.2040G>A (p.Ala680=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Mar 16, 2021)
Last evaluated:
Mar 16, 2021
Accession:
VCV000218256.3
Variation ID:
218256
Description:
single nucleotide variant
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NM_000282.4(PCCA):c.2040G>A (p.Ala680=)

Allele ID
214899
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q32.3
Genomic location
13: 100515567 (GRCh38) GRCh38 UCSC
13: 101167821 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.101167821G>A
NC_000013.11:g.100515567G>A
NM_000282.4:c.2040G>A MANE Select NP_000273.2:p.Ala680= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000013.11:100515566:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Links
ClinGen: CA7033876
dbSNP: rs369982920
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Mar 16, 2021 RCV000236921.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCCA - - GRCh38
GRCh37
510 599

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 01, 2012)
criteria provided, single submitter
Method: research
Propionic Acidemia
Allele origin: germline
Institute of Medical Genetics and Genomics,Sir Ganga Ram Hospital
Study: ORGANIC ACIDURIAS
Accession: SCV000256847.1
Submitted: (Nov 04, 2015)
Comment:
Synonymous change
Evidence details
Publications
PubMed (1)
Uncertain significance
(Mar 27, 2018)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: unknown
Counsyl
Accession: SCV000800685.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(Feb 17, 2021)
criteria provided, single submitter
Method: research, in vitro
Propionic acidemia
Allele origin: germline, not applicable
Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics
Accession: SCV001482008.1
Submitted: (Feb 19, 2021)
Evidence details
Comment:
PS3, PM2, PM3_supportive, PP3, PP4
Pathogenic
(Mar 16, 2021)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
(Autosomal recessive inheritance)
Allele origin: germline
Centre for Inherited Metabolic Diseases, Karolinska University Hospital
Accession: SCV001519662.1
Submitted: (Mar 16, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Seventeen Novel Mutations in PCCA and PCCB Genes in Indian Propionic Acidemia Patients, and Their Outcomes. Gupta D Genetic testing and molecular biomarkers 2016 PMID: 27227689

Text-mined citations for rs369982920...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 22, 2021