NM_000152.5(GAA):c.1819_1836del (p.Gly607_His612del) AND Glycogen storage disease, type II

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 6, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004549031.1

Allele description [Variation Report for NM_000152.5(GAA):c.1819_1836del (p.Gly607_His612del)]

NM_000152.5(GAA):c.1819_1836del (p.Gly607_His612del)

Gene:

GAA:alpha glucosidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_000152.5(GAA):c.1819_1836del (p.Gly607_His612del)

Other names:

p.Gly607_His612del

HGVS:

NC_000017.11:g.80112642_80112659del
NG_009822.1:g.16087_16104del
NM_000152.5:c.1819_1836delMANE SELECT
NM_001079803.3:c.1819_1836del
NM_001079804.3:c.1819_1836del
NM_001406741.1:c.1819_1836del
NM_001406742.1:c.1819_1836del
NP_000143.2:p.Gly607_His612del
NP_000143.2:p.Gly607_His612del
NP_001073271.1:p.Gly607_His612del
NP_001073272.1:p.Gly607_His612del
NP_001393670.1:p.Gly607_His612del
NP_001393671.1:p.Gly607_His612del
LRG_673t1:c.1819_1836del18
LRG_673:g.16087_16104del
LRG_673p1:p.Gly607_His612del
NC_000017.10:g.78086441_78086458del
NM_000152.3:c.1819_1836del18

Molecular consequence:

NM_000152.5:c.1819_1836del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001079803.3:c.1819_1836del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001079804.3:c.1819_1836del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406741.1:c.1819_1836del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406742.1:c.1819_1836del - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

Name:: Glycogen storage disease, type II (GSD2)
Synonyms:: ACID ALPHA-GLUCOSIDASE DEFICIENCY; GLYCOGENOSIS, GENERALIZED, CARDIAC FORM; GSD II; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009290; MedGen: C0017921; Orphanet: 365; OMIM: 232300

Recent activity

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hypothetical protein [Acinetobacter baumannii]
hypothetical protein [Acinetobacter baumannii]
gi|757519277|ref|WP_042782860.1|

Protein
MULTISPECIES: 30S ribosomal protein S21 [Candidatus Palauibacter]
MULTISPECIES: 30S ribosomal protein S21 [Candidatus Palauibacter]
gi|2580057165|ref|WP_310756486.1|

Protein
Microbe sample from Spirosoma arboris
Microbe sample from Spirosoma arboris

biosample
Microbe sample from Hufsiella ginkgonis
Microbe sample from Hufsiella ginkgonis

biosample
Targeting enhancer switching overcomes non-genetic drug resistance in acute myel...
Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [RNA-seq]
Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [RNA-seq]

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005043135	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 6, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005043135

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 6, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV005043135.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (1)

Description

A heterozygous 18 base pair deletion in exon 13 of the GAA gene that results in deletion of amino acid from codon 607_612. The observed variant c.1819_1836del (p.Gly607_His612del) has not been reported in the 1000 genomes and gnomAD databases. The in silico prediction of the variant is damaging by MutationTaster2 and DANN. In summary, the variant meets our criteria to be classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 26, 2024

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Relating variation to medicine