NM_000282.4(PCCA):c.1312G>T (p.Gly438Ter) AND Propionic acidemia

Clinical significance:Pathogenic (Last evaluated: Apr 5, 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.1312G>T (p.Gly438Ter)]

NM_000282.4(PCCA):c.1312G>T (p.Gly438Ter)

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.1312G>T (p.Gly438Ter)
  • NC_000013.11:g.100307219G>T
  • NG_008768.1:g.223137G>T
  • NM_000282.4:c.1312G>TMANE SELECT
  • NM_001127692.3:c.1234G>T
  • NM_001178004.2:c.1312G>T
  • NM_001352605.2:c.1312G>T
  • NM_001352606.2:c.1168G>T
  • NM_001352607.2:c.1234G>T
  • NM_001352608.2:c.1090G>T
  • NM_001352609.2:c.1312G>T
  • NM_001352610.2:c.367G>T
  • NM_001352611.2:c.367G>T
  • NM_001352612.2:c.223G>T
  • NP_000273.2:p.Gly438Ter
  • NP_001121164.1:p.Gly412Ter
  • NP_001171475.1:p.Gly438Ter
  • NP_001339534.1:p.Gly438Ter
  • NP_001339535.1:p.Gly390Ter
  • NP_001339536.1:p.Gly412Ter
  • NP_001339537.1:p.Gly364Ter
  • NP_001339538.1:p.Gly438Ter
  • NP_001339539.1:p.Gly123Ter
  • NP_001339540.1:p.Gly123Ter
  • NP_001339541.1:p.Gly75Ter
  • NC_000013.10:g.100959473G>T
  • NR_148027.2:n.1424G>T
  • NR_148028.2:n.1424G>T
  • NR_148029.2:n.1346G>T
  • NR_148030.2:n.1424G>T
  • NR_148031.2:n.1340G>T
Protein change:
Molecular consequence:
  • NR_148027.2:n.1424G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148028.2:n.1424G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148029.2:n.1346G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148030.2:n.1424G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148031.2:n.1340G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000282.4:c.1312G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001127692.3:c.1234G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001178004.2:c.1312G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352605.2:c.1312G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352606.2:c.1168G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352607.2:c.1234G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352608.2:c.1090G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352609.2:c.1312G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352610.2:c.367G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352611.2:c.367G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352612.2:c.223G>T - nonsense - [Sequence Ontology: SO:0001587]


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)
SCV001587116Invitaecriteria provided, single submitter
(Apr 5, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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



Propionic acidemia: mutation update and functional and structural effects of the variant alleles.

Desviat LR, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P, Clavero S, Ugarte M.

Mol Genet Metab. 2004 Sep-Oct;83(1-2):28-37. Review.

PubMed [citation]

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, SCV001587116.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)


This sequence change creates a premature translational stop signal (p.Gly438*) in the PCCA gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PCCA-related conditions. Loss-of-function variants in PCCA are known to be pathogenic (PMID: 15464417). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 7, 2021

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