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

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Feb 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000313421.35

Allele description [Variation Report for NM_000282.4(PCCA):c.1423A>G (p.Ile475Val)]

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

Gene:

PCCA:propionyl-CoA carboxylase subunit alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q32.3

Genomic location:

Preferred name:

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

HGVS:

NC_000013.11:g.100309902A>G
NG_008768.1:g.225820A>G
NM_000282.4:c.1423A>GMANE SELECT
NM_001127692.3:c.1345A>G
NM_001178004.2:c.1423A>G
NM_001352605.2:c.1423A>G
NM_001352606.2:c.1279A>G
NM_001352607.2:c.1345A>G
NM_001352608.2:c.1201A>G
NM_001352609.2:c.1423A>G
NM_001352610.2:c.478A>G
NM_001352611.2:c.478A>G
NM_001352612.2:c.334A>G
NP_000273.2:p.Ile475Val
NP_000273.2:p.Ile475Val
NP_001121164.1:p.Ile449Val
NP_001171475.1:p.Ile475Val
NP_001339534.1:p.Ile475Val
NP_001339535.1:p.Ile427Val
NP_001339536.1:p.Ile449Val
NP_001339537.1:p.Ile401Val
NP_001339538.1:p.Ile475Val
NP_001339539.1:p.Ile160Val
NP_001339540.1:p.Ile160Val
NP_001339541.1:p.Ile112Val
NC_000013.10:g.100962156A>G
NM_000282.3:c.1423A>G
NR_148027.2:n.1535A>G
NR_148028.2:n.1535A>G
NR_148029.2:n.1457A>G
NR_148030.2:n.1535A>G
NR_148031.2:n.1451A>G
P05165:p.Ile475Val

Protein change:

I112V

Links:

UniProtKB: P05165#VAR_009098; dbSNP: rs35719359

NCBI 1000 Genomes Browser:

rs35719359

Molecular consequence:

NM_000282.4:c.1423A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127692.3:c.1345A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001178004.2:c.1423A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352605.2:c.1423A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352606.2:c.1279A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352607.2:c.1345A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352608.2:c.1201A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352609.2:c.1423A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352610.2:c.478A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352611.2:c.478A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352612.2:c.334A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148027.2:n.1535A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148028.2:n.1535A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148029.2:n.1457A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148030.2:n.1535A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148031.2:n.1451A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Propionic acidemia (PROP)
Synonyms:: Glycinemia, ketotic; Hyperglycinemia with ketoacidosis and leukopenia; Ketotic hyperglycinemia
Identifiers:: MONDO: MONDO:0011628; MedGen: C0268579; Orphanet: 35; OMIM: 606054; Human Phenotype Ontology: HP:0003571

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000382015	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Mar 6, 2018)	germline	clinical testing	Citation Link,
SCV000631898	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000733195	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV000744069	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Oct 9, 2014)	germline	clinical testing	Citation Link,
SCV001159024	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Oct 26, 2023)	germline	clinical testing	Citation Link,
SCV001455848	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000382015.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000631898.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733195.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000744069.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001159024.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001455848.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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