NM_000152.5(GAA):c.1979G>A (p.Arg660His) AND not provided

Clinical significance:Pathogenic (Last evaluated: Feb 3, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
6 submissions [Details]
Record status:
current
Accession:
RCV000256037.8

Allele description [Variation Report for NM_000152.5(GAA):c.1979G>A (p.Arg660His)]

NM_000152.5(GAA):c.1979G>A (p.Arg660His)

Gene:
GAA:alpha glucosidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.3
Genomic location:
Preferred name:
NM_000152.5(GAA):c.1979G>A (p.Arg660His)
HGVS:
  • NC_000017.11:g.80112966G>A
  • NG_009822.1:g.16411G>A
  • NM_000152.5:c.1979G>AMANE SELECT
  • NM_001079803.3:c.1979G>A
  • NM_001079804.3:c.1979G>A
  • NP_000143.2:p.Arg660His
  • NP_001073271.1:p.Arg660His
  • NP_001073272.1:p.Arg660His
  • LRG_673t1:c.1979G>A
  • LRG_673:g.16411G>A
  • NC_000017.10:g.78086765G>A
  • NM_000152.3:c.1979G>A
  • NM_001079803.2:c.1979G>A
  • P10253:p.Arg660His
Protein change:
R660H
Links:
UniProtKB: P10253#VAR_046477; dbSNP: rs374143224
NCBI 1000 Genomes Browser:
rs374143224
Molecular consequence:
  • NM_000152.5:c.1979G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079803.3:c.1979G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079804.3:c.1979G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000322397GeneDxcriteria provided, single submitter
Pathogenic
(Feb 3, 2021)
germlineclinical testing

Citation Link,

SCV000706386EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Pathogenic
(Feb 27, 2017)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link,

SCV001245692CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Pathogenic
(Nov 1, 2016)
germlineclinical testing

Citation Link,

SCV001956452Human Genetics - Radboudumc,Radboudumc - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedLikely pathogenicgermlineclinical testing

SCV001966553Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedPathogenicgermlineclinical testing

SCV002021201PerkinElmer Genomicsno assertion criteria providedPathogenic
(Jul 12, 2021)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

New GAA mutations in Japanese patients with GSDII (Pompe disease).

Pipo JR, Feng JH, Yamamoto T, Ohsaki Y, Nanba E, Tsujino S, Sakuragawa N, Martiniuk F, Ninomiya H, Oka A, Ohno K.

Pediatr Neurol. 2003 Oct;29(4):284-7.

PubMed [citation]
PMID:
14643388

The pharmacological chaperone 1-deoxynojirimycin increases the activity and lysosomal trafficking of multiple mutant forms of acid alpha-glucosidase.

Flanagan JJ, Rossi B, Tang K, Wu X, Mascioli K, Donaudy F, Tuzzi MR, Fontana F, Cubellis MV, Porto C, Benjamin E, Lockhart DJ, Valenzano KJ, Andria G, Parenti G, Do HV.

Hum Mutat. 2009 Dec;30(12):1683-92. doi: 10.1002/humu.21121.

PubMed [citation]
PMID:
19862843
See all PubMed Citations (7)

Details of each submission

From GeneDx, SCV000322397.6

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

Description

Observed in multiple individuals with glycogen storage disease type II, who harbored a second GAA variant, in the published literature (Pipo et al., 2003; Bernstein et al., 2010, Burrow et al., 2010, Palermo et al., 2012); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate a damaging effect as the variant impacts the function of the protein (Pipo et al., 2003); This variant is associated with the following publications: (PMID: 31086307, 31127727, 30559630, 33073007, 29122469, 14643388, 22555271, 22658377, 19862843, 22521436, 27649523, 21484825, 26402642, 30281819, 20472203, 20638881)

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

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000706386.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (7)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001245692.6

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

From Human Genetics - Radboudumc,Radboudumc - VKGL Data-share Consensus, SCV001956452.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001966553.1

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

From PerkinElmer Genomics, SCV002021201.1

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

Last Updated: Nov 28, 2021

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