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NM_000532.5(PCCB):c.1228C>T (p.Arg410Trp)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Apr 29, 2020)
Last evaluated:
Mar 13, 2020
Accession:
VCV000012011.4
Variation ID:
12011
Description:
single nucleotide variant
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NM_000532.5(PCCB):c.1228C>T (p.Arg410Trp)

Allele ID
27050
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q22.3
Genomic location
3: 136327184 (GRCh38) GRCh38 UCSC
3: 136046026 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P05166:p.Arg410Trp
NC_000003.11:g.136046026C>T
NC_000003.12:g.136327184C>T
... more HGVS
Protein change
R410W, R430W
Other names
R412W
Canonical SPDI
NC_000003.12:136327183:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00003
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA343136
UniProtKB: P05166#VAR_000278
OMIM: 232050.0001
dbSNP: rs121964959
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 6 criteria provided, multiple submitters, no conflicts Mar 13, 2020 RCV000012791.26
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCCB - - GRCh38
GRCh37
449 475

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Dec 13, 2016)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: germline
Invitae
Accession: SCV000631912.1
Submitted: (Oct 05, 2017)
Evidence details
Comment:
This sequence change replaces arginine with tryptophan at codon 410 of the PCCB protein (p.Arg410Trp). The arginine residue is highly conserved and there is a … (more)
Likely pathogenic
(Jan 17, 2017)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: unknown
Counsyl
Accession: SCV000789286.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (7)
Pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: unknown
Mendelics
Accession: SCV001136613.1
Submitted: (Oct 22, 2019)
Evidence details
Pathogenic
(Mar 13, 2020)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001339066.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (5)
Comment:
Variant summary: PCCB c.1228C>T (p.Arg410Trp) results in a non-conservative amino acid change located in the Acetyl-coenzyme A carboxyltransferase, C-terminal (IPR011763) of the encoded protein sequence. … (more)
pathologic
(May 17, 2012)
no assertion criteria provided
Method: curation
Propionic Acidemia
Allele origin: not provided
GeneReviews
Accession: SCV000055678.1
Submitted: (Jan 08, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.
Pathogenic
(Jan 01, 1999)
no assertion criteria provided
Method: literature only
PROPIONIC ACIDEMIA
Allele origin: germline
OMIM
Accession: SCV000033031.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (3)

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
Comparison of Methods of Initial Ascertainment in 58 Cases of Propionic Acidemia Enrolled in the Inborn Errors of Metabolism Information System Reveals Significant Differences in Time to Evaluation and Symptoms at Presentation. McCrory NM The Journal of pediatrics 2017 PMID: 27776753
Propionic Acidemia Shchelochkov OA - 2016 PMID: 22593918
Mutation analysis in 54 propionic acidemia patients. Kraus JP Journal of inherited metabolic disease 2012 PMID: 22033733
Characterization of four variant forms of human propionyl-CoA carboxylase expressed in Escherichia coli. Jiang H The Journal of biological chemistry 2005 PMID: 15890657
Mutation spectrum of the PCCA and PCCB genes in Japanese patients with propionic acidemia. Yang X Molecular genetics and metabolism 2004 PMID: 15059621
Functional analysis of PCCB mutations causing propionic acidemia based on expression studies in deficient human skin fibroblasts. Pérez-Cerdá C Biochimica et biophysica acta 2003 PMID: 12757933
Propionic acidemia: analysis of mutant propionyl-CoA carboxylase enzymes expressed in Escherichia coli. Chloupkova M Human mutation 2002 PMID: 12007220
Overview of mutations in the PCCA and PCCB genes causing propionic acidemia. Ugarte M Human mutation 1999 PMID: 10502773
Mutations participating in interallelic complementation in propionic acidemia. Gravel RA American journal of human genetics 1994 PMID: 8023851
Three independent mutations in the same exon of the PCCB gene: differences between Caucasian and Japanese propionic acidaemia. Tahara T Journal of inherited metabolic disease 1993 PMID: 8411997
An unusual insertion/deletion in the gene encoding the beta-subunit of propionyl-CoA carboxylase is a frequent mutation in Caucasian propionic acidemia. Tahara T Proceedings of the National Academy of Sciences of the United States of America 1990 PMID: 2154743

Text-mined citations for rs121964959...

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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 Sep 29, 2021