NM_004563.3(PCK2):c.577C>T (p.Arg193Ter) AND not provided

Clinical significance:Uncertain significance (Last evaluated: May 9, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000732852.2

Allele description [Variation Report for NM_004563.3(PCK2):c.577C>T (p.Arg193Ter)]

NM_004563.3(PCK2):c.577C>T (p.Arg193Ter)

Genes:
NRL:neural retina leucine zipper [Gene - OMIM - HGNC]
PCK2:phosphoenolpyruvate carboxykinase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q11.2
Genomic location:
Preferred name:
NM_004563.3(PCK2):c.577C>T (p.Arg193Ter)
HGVS:
  • NC_000014.9:g.24098591C>T
  • NG_008162.2:g.9318C>T
  • NM_001018073.2:c.577C>T
  • NM_004563.3:c.577C>T
  • NP_001018083.2:p.Arg193Ter
  • NP_004554.3:p.Arg193Ter
  • NC_000014.8:g.24567800C>T
  • NM_004563.2:c.577C>T
Protein change:
R193*
Links:
dbSNP: rs753706965
NCBI 1000 Genomes Browser:
rs753706965
Molecular consequence:
  • NM_004563.3:c.577C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000620559GeneDxcriteria provided, single submitter
Uncertain significance
(May 9, 2018)
germlineclinical testing

Citation Link,

SCV000860847EGL Genetic Diagnostics,Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Apr 9, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000620559.2

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

Description

The R193X variant in the PCK2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R193X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret R193X as a variant of uncertain significance.

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

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000860847.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 19, 2019

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