Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000282.4(PCCA):c.1423A>G (p.Ile475Val)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000092761.9
Variation ID:
92761
Description:
single nucleotide variant
Help

NM_000282.4(PCCA):c.1423A>G (p.Ile475Val)

Allele ID
98668
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q32.3
Genomic location
13: 100309902 (GRCh38) GRCh38 UCSC
13: 100962156 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P05165:p.Ile475Val
NC_000013.11:g.100309902A>G
NG_008768.1:g.225820A>G
... more HGVS
Protein change
I475V, I401V, I427V, I449V, I112V, I160V
Other names
-
Canonical SPDI
NC_000013.11:100309901:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.01577 (G)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03683
The Genome Aggregation Database (gnomAD), exomes 0.04219
Exome Aggregation Consortium (ExAC) 0.04257
The Genome Aggregation Database (gnomAD) 0.04878
1000 Genomes Project 0.01577
Trans-Omics for Precision Medicine (TOPMed) 0.03345
Links
ClinGen: CA145988
UniProtKB: P05165#VAR_009098
dbSNP: rs35719359
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Mar 29, 2018 RCV000078547.8
Benign/Likely benign 6 criteria provided, multiple submitters, no conflicts Dec 5, 2020 RCV000313421.11
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCCA - - GRCh38
GRCh37
504 593

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 01, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000514038.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Mar 29, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919955.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: PCCA c.1423A>G (p.Ile475Val) results in a conservative amino acid change located in the Biotin carboxylase, C-terminal domain of the encoded protein sequence. Four … (more)
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303450.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Oct 09, 2014)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Study: VKGL Data-share Consensus
Accession: SCV000744069.1
Submitted: (Apr 17, 2018)
Evidence details
Benign
(Sep 14, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110403.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 06, 2018)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000382015.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jul 04, 2020)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001159024.2
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Propionic acidemia
Allele origin: germline
Invitae
Accession: SCV000631898.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
Propionic acidemia
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000733195.1
Submitted: (Apr 04, 2018)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Propionic acidemia
Allele origin: germline
Natera, Inc.
Accession: SCV001455848.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
Propionic acidemia: mutation update and functional and structural effects of the variant alleles. Desviat LR Molecular genetics and metabolism 2004 PMID: 15464417
Genetic heterogeneity in propionic acidemia patients with alpha-subunit defects. Identification of five novel mutations, one of them causing instability of the protein. Richard E Biochimica et biophysica acta 1999 PMID: 10101253
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PCCA - - - -

Text-mined citations for rs35719359...

Help
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 18, 2021