NM_000282.4(PCCA):c.1850T>C (p.Leu617Pro) AND Propionic acidemia

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Dec 8, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000877589.5

Allele description [Variation Report for NM_000282.4(PCCA):c.1850T>C (p.Leu617Pro)]

NM_000282.4(PCCA):c.1850T>C (p.Leu617Pro)

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.1850T>C (p.Leu617Pro)
HGVS:
  • NC_000013.11:g.100449256T>C
  • NG_008768.1:g.365174T>C
  • NM_000282.4:c.1850T>CMANE SELECT
  • NM_000282.4:c.1850T>CMANE SELECT
  • NM_001127692.3:c.1772T>C
  • NM_001178004.2:c.1850T>C
  • NM_001352605.2:c.1845+23525T>C
  • NM_001352606.2:c.1706T>C
  • NM_001352607.2:c.1772T>C
  • NM_001352608.2:c.1628T>C
  • NM_001352609.2:c.1850T>C
  • NM_001352610.2:c.905T>C
  • NM_001352611.2:c.900+23525T>C
  • NM_001352612.2:c.761T>C
  • NP_000273.2:p.Leu617Pro
  • NP_000273.2:p.Leu617Pro
  • NP_001121164.1:p.Leu591Pro
  • NP_001171475.1:p.Leu617Pro
  • NP_001339535.1:p.Leu569Pro
  • NP_001339536.1:p.Leu591Pro
  • NP_001339537.1:p.Leu543Pro
  • NP_001339538.1:p.Leu617Pro
  • NP_001339539.1:p.Leu302Pro
  • NP_001339541.1:p.Leu254Pro
  • NC_000013.10:g.101101510T>C
  • NC_000013.10:g.101101510T>C
  • NM_000282.3:c.1850T>C
  • NR_148027.2:n.1962T>C
  • NR_148028.2:n.1859T>C
  • NR_148029.2:n.1781T>C
  • NR_148030.2:n.1962T>C
  • NR_148031.2:n.1775T>C
Protein change:
L254P
Links:
dbSNP: rs563417983
NCBI 1000 Genomes Browser:
rs563417983
Molecular consequence:
  • NM_001352605.2:c.1845+23525T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001352611.2:c.900+23525T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000282.4:c.1850T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127692.3:c.1772T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178004.2:c.1850T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352606.2:c.1706T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352607.2:c.1772T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352608.2:c.1628T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352609.2:c.1850T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352610.2:c.905T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001352612.2:c.761T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148027.2:n.1962T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148028.2:n.1859T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148029.2:n.1781T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148030.2:n.1962T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148031.2:n.1775T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Propionic acidemia (PROP)
Synonyms:
Propionyl-CoA carboxylase deficiency; PCC deficiency; Glycinemia, ketotic; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011628; MedGen: C0268579; Orphanet: 35; OMIM: 606054; Human Phenotype Ontology: HP:0003353

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001020341Invitaecriteria provided, single submitter
Benign
(Dec 8, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001269812Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

Citation Link,

SCV001463919Natera, Inc.no assertion criteria providedBenign
(Apr 17, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001020341.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001269812.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001463919.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 24, 2021

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