NM_000642.3(AGL):c.4456del (p.Ser1486fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Nov 25, 2020)

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:
RCV000723822.5

Allele description [Variation Report for NM_000642.3(AGL):c.4456del (p.Ser1486fs)]

NM_000642.3(AGL):c.4456del (p.Ser1486fs)

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.4456del (p.Ser1486fs)
HGVS:
  • NC_000001.11:g.99916706del
  • NG_012865.1:g.71623del
  • NM_000028.2:c.4456del
  • NM_000642.3:c.4456delMANE SELECT
  • NM_000643.2:c.4456del
  • NM_000644.2:c.4456del
  • NM_000646.2:c.4408del
  • NP_000019.2:p.Ser1486fs
  • NP_000633.2:p.Ser1486fs
  • NP_000634.2:p.Ser1486fs
  • NP_000635.2:p.Ser1486fs
  • NP_000637.2:p.Ser1470fs
  • NC_000001.10:g.100382262del
  • NM_000642.2:c.4455delT
  • NM_000642.2:c.4456del
  • NM_000642.2:c.4456delT
  • NM_000642.3:c.4456delTMANE SELECT
Protein change:
S1470fs
Links:
OMIM: 610860.0005; dbSNP: rs113994134
NCBI 1000 Genomes Browser:
rs113994134
Molecular consequence:
  • NM_000028.2:c.4456del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.4456del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.2:c.4456del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.2:c.4456del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.2:c.4408del - frameshift variant - [Sequence Ontology: SO:0001589]
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
SCV000229651EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Pathogenic
(Jun 13, 2014)
germlineclinical testing

Citation Link,

SCV001248397CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Nov 1, 2018)
germlineclinical testing

Citation Link,

SCV001804369GeneDxcriteria provided, single submitter
Pathogenic
(Nov 25, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000229651.5

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001248397.6

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

From GeneDx, SCV001804369.1

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

Description

Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 47 amino acids are lost and replaced with 17 incorrect amino acids (Stenson et al., 2014);; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31661040, 28888851, 25388549, 25602008, 27460348, 9412782)

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

Last Updated: Nov 27, 2021

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