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PCK1, 12-BP DEL, NT369 AND Phosphoenolpyruvate carboxykinase deficiency, cytosolic

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 12, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000509050.5

Allele description [Variation Report for PCK1, 12-BP DEL, NT369]

PCK1, 12-BP DEL, NT369

Gene:
PCK1:phosphoenolpyruvate carboxykinase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
20q13.31
Preferred name:
PCK1, 12-BP DEL, NT369
HGVS:
    Nucleotide change:
    12-BP DEL, NT369
    Links:
    OMIM: 614168.0002

    Condition(s)

    Name:
    Phosphoenolpyruvate carboxykinase deficiency, cytosolic (PCKDC)
    Synonyms:
    PCK1 DEFICIENCY, CYTOSOLIC; PEPCK DEFICIENCY, CYTOSOLIC
    Identifiers:
    MONDO: MONDO:0009866; MedGen: C5574905; Orphanet: 2880; OMIM: 261680

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV000606823OMIM
    no assertion criteria provided
    		Pathogenic
    (Apr 12, 2023)     		germlineliterature only

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

    Citations

    PubMed

    Cytosolic phosphoenolpyruvate carboxykinase deficiency presenting with acute liver failure following gastroenteritis.

    Santra S, Cameron JM, Shyr C, Zhang L, Drögemöller B, Ross CJ, Wasserman WW, Wevers RA, Rodenburg RJ, Gupte G, Preece MA, van Karnebeek CD.

    Mol Genet Metab. 2016 May;118(1):21-7. doi: 10.1016/j.ymgme.2016.03.001. Epub 2016 Mar 4.

    PubMed [citation]
    PMID:
    26971250

    Details of each submission

    From OMIM, SCV000606823.4

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedliterature only PubMed (1)

    Description

    In a 9-month-boy, born of third-cousin parents from a multiply consanguineous Pakistani family, who presented with transient acute liver failure and biochemical patterns suggestive of disturbed urea cycle (PCKDC; 261680), Santra et al. (2016) identified homozygosity for a 12-bp deletion (chr20.56,140,097-56,140,107, GRCh37) in the PCK1 gene, resulting in deletion of 4 highly conserved amino acids (GlyValProLeuVal123Val) within the N-terminal phosphoenolpyruvate carboxykinase domain, adjacent to a putative GTP-binding domain. The deletion segregated fully with disease in the family and was not found in an in-house database of more than 430 exomes or the dbSNP (build 142), NHLBI Exome Variant Server, or ExAC databases. Analysis of transfected COS-1 cells showed that PCK1-deletion mutant PEPCK activity was significantly reduced compared to wildtype, similar to empty vector.

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

    Last Updated: Apr 23, 2023