NM_000642.3(AGL):c.16C>T (p.Gln6Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Dec 12, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000675315.3

Allele description [Variation Report for NM_000642.3(AGL):c.16C>T (p.Gln6Ter)]

NM_000642.3(AGL):c.16C>T (p.Gln6Ter)

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.16C>T (p.Gln6Ter)
HGVS:
  • NC_000001.11:g.99851058C>T
  • NG_012865.1:g.5975C>T
  • NM_000028.2:c.16C>T
  • NM_000642.3:c.16C>TMANE SELECT
  • NM_000643.2:c.16C>T
  • NM_000644.2:c.16C>T
  • NM_000646.2:c.-176C>T
  • NP_000019.2:p.Gln6Ter
  • NP_000633.2:p.Gln6Ter
  • NP_000634.2:p.Gln6Ter
  • NP_000635.2:p.Gln6Ter
  • NC_000001.10:g.100316614C>T
  • NM_000642.2:c.16C>T
Protein change:
Q6*; GLN6TER
Links:
OMIM: 610860.0002; dbSNP: rs113994126
NCBI 1000 Genomes Browser:
rs113994126
Molecular consequence:
  • NM_000646.2:c.-176C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000028.2:c.16C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000642.3:c.16C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000643.2:c.16C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000644.2:c.16C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000227162EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Pathogenic
(Jun 13, 2014)
germlineclinical testing

Citation Link,

SCV000800980Mayo Clinic Laboratories, Mayo Clinicno assertion criteria providedPathogenic
(Mar 23, 2017)
unknownclinical testing

SCV001765379GeneDxcriteria provided, single submitter
Pathogenic
(Dec 12, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000227162.5

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV000800980.1

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

From GeneDx, SCV001765379.1

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 20648714, 8755644, 23430490)

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

Last Updated: Nov 27, 2021

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