NM_000152.5(GAA):c.1439T>C (p.Val480Ala) AND Glycogen storage disease, type II

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 27, 2021
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:: RCV000818942.5

Allele description

NM_000152.5(GAA):c.1439T>C (p.Val480Ala)

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.1439T>C (p.Val480Ala)

HGVS:

NC_000017.11:g.80110728T>C
NG_009822.1:g.14173T>C
NM_000152.5:c.1439T>CMANE SELECT
NM_001079803.3:c.1439T>C
NM_001079804.3:c.1439T>C
NP_000143.2:p.Val480Ala
NP_001073271.1:p.Val480Ala
NP_001073272.1:p.Val480Ala
LRG_673t1:c.1439T>C
LRG_673:g.14173T>C
NC_000017.10:g.78084527T>C
NM_000152.3:c.1439T>C

Protein change:

V480A

Links:

dbSNP: rs1224298513

NCBI 1000 Genomes Browser:

rs1224298513

Molecular consequence:

NM_000152.5:c.1439T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001079803.3:c.1439T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001079804.3:c.1439T>C - missense variant - [Sequence Ontology: SO:0001583]

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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protein CBFA2T1 isoform G [Homo sapiens]
protein CBFA2T1 isoform G [Homo sapiens]
gi|2052147133|ref|NP_001382138.1|

Protein
membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 iso...
membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 isoform X3 [Mus musculus]
gi|568933257|ref|XP_006535808.1|

Protein
zinc finger protein ZAT3-like [Cucurbita maxima]
zinc finger protein ZAT3-like [Cucurbita maxima]
gi|1281004588|ref|XP_022986192.1|

Protein
CBSW4729.g1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8906601 3',...
CBSW4729.g1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8906601 3', mRNA sequence
gi|133761253|gnl|dbEST|45194448|gb| 508.1|

Nucleotide
CBSW2198.b1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8904528 5',...
CBSW2198.b1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8904528 5', mRNA sequence
gi|133757689|gnl|dbEST|45190884|gb| 944.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000959580	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 27, 2021)	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

SCV000959580

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 27, 2021)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000959580.3

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

Description

This sequence change replaces valine with alanine at codon 480 of the GAA protein (p.Val480Ala). The valine residue is highly conserved and there is a small physicochemical difference between valine and alanine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with GAA-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Mar 18, 2023

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