NM_000282.4(PCCA):c.1962G>A (p.Val654=) AND Propionic acidemia

Clinical significance:Likely benign (Last evaluated: Aug 4, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000282.4(PCCA):c.1962G>A (p.Val654=)]

NM_000282.4(PCCA):c.1962G>A (p.Val654=)

PCCA:propionyl-CoA carboxylase subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000282.4(PCCA):c.1962G>A (p.Val654=)
  • NC_000013.11:g.100515489G>A
  • NG_008768.1:g.431407G>A
  • NM_000282.4:c.1962G>AMANE SELECT
  • NM_001127692.3:c.1884G>A
  • NM_001178004.2:c.1900-12186G>A
  • NM_001352605.2:c.1908G>A
  • NM_001352606.2:c.1818G>A
  • NM_001352607.2:c.1822-12186G>A
  • NM_001352608.2:c.1740G>A
  • NM_001352610.2:c.1017G>A
  • NM_001352611.2:c.963G>A
  • NM_001352612.2:c.873G>A
  • NP_000273.2:p.Val654=
  • NP_001121164.1:p.Val628=
  • NP_001339534.1:p.Val636=
  • NP_001339535.1:p.Val606=
  • NP_001339537.1:p.Val580=
  • NP_001339539.1:p.Val339=
  • NP_001339540.1:p.Val321=
  • NP_001339541.1:p.Val291=
  • NC_000013.10:g.101167743G>A
  • NR_148028.2:n.1971G>A
  • NR_148029.2:n.1893G>A
  • NR_148030.2:n.2074G>A
  • NR_148031.2:n.1887G>A
Molecular consequence:
  • NM_001178004.2:c.1900-12186G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001352607.2:c.1822-12186G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NR_148028.2:n.1971G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148029.2:n.1893G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148030.2:n.2074G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148031.2:n.1887G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000282.4:c.1962G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001127692.3:c.1884G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001352605.2:c.1908G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001352606.2:c.1818G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001352608.2:c.1740G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001352610.2:c.1017G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001352611.2:c.963G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001352612.2:c.873G>A - synonymous variant - [Sequence Ontology: SO:0001819]


Propionic acidemia (PROP)
Propionyl-CoA carboxylase deficiency; PCC deficiency; Glycinemia, ketotic; See all synonyms [MedGen]
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)
SCV001693261Invitaecriteria provided, single submitter
Likely benign
(Aug 4, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



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]

Details of each submission

From Invitae, SCV001693261.1

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

Last Updated: Jun 14, 2021

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