NM_000152.5(GAA):c.877G>A (p.Gly293Arg) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Apr 22, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000728952.8

Allele description [Variation Report for NM_000152.5(GAA):c.877G>A (p.Gly293Arg)]

NM_000152.5(GAA):c.877G>A (p.Gly293Arg)

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.877G>A (p.Gly293Arg)

HGVS:

NC_000017.11:g.80107818G>A
NG_009822.1:g.11263G>A
NM_000152.5:c.877G>AMANE SELECT
NM_001079803.3:c.877G>A
NM_001079804.3:c.877G>A
NP_000143.2:p.Gly293Arg
NP_001073271.1:p.Gly293Arg
NP_001073272.1:p.Gly293Arg
LRG_673t1:c.877G>A
LRG_673:g.11263G>A
LRG_673p1:p.Gly293Arg
NC_000017.10:g.78081617G>A
NM_000152.3:c.877G>A
NM_000152.4:c.877G>A
NM_000152.5(GAA):c.877G>AMANE SELECT
P10253:p.Gly293Arg

Protein change:

G293R; GLY293ARG

Links:

UniProtKB: P10253#VAR_018082; OMIM: 606800.0017; dbSNP: rs121907945

NCBI 1000 Genomes Browser:

rs121907945

Molecular consequence:

NM_000152.5:c.877G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001079803.3:c.877G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001079804.3:c.877G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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putative transcriptional regulator [Methanocella arvoryzae]
putative transcriptional regulator [Methanocella arvoryzae]
gi|500973443|ref|WP_012036324.1|

Protein
gfLaeSulp
gfLaeSulp
Laetiporus sulphureus (chicken of the woods)

BioProject
gfLaeSulp1 alternate haplotype
gfLaeSulp1 alternate haplotype
Laetiporus sulphureus (chicken of the woods) genome assembly, gfLaeSulp1, alternate haplotype

BioProject

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000856579	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Jan 25, 2018)	germline	clinical testing	Citation Link,
SCV004023028	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jul 26, 2023)	germline	clinical testing	Citation Link,
SCV004934102	Genomic Research Center, Shahid Beheshti University of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 22, 2024)	unknown	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

SCV000856579

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Jan 25, 2018)

germline

clinical testing

Citation Link,

SCV004023028

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jul 26, 2023)

germline

clinical testing

Citation Link,

SCV004934102

Genomic Research Center, Shahid Beheshti University of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 22, 2024)

unknown

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	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	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 Eurofins Ntd Llc (ga), SCV000856579.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

#	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		3	not provided	not provided	not provided

From GeneDx, SCV004023028.1

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

Description

Published functional studies demonstrate a damaging effect on protein function (Hermans et al., 2004; Flanagan et al., 2009); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function and on splicing; Located in the N-terminal -sandwich domain (Kroos et al., 2012; Sugawara et al., 2009); This variant is associated with the following publications: (PMID: 34530085, 31254424, 30275481, 24590251, 29181627, 27344650, 14695532, 18429042, 15668445, 31606152, 22676651, 31510962, 29122469, 18607768, 17573812, 19862843, 22253258, 19343043)

#	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		not provided	not provided	not provided	not provided

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV004934102.1

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

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

Last Updated: Sep 29, 2024

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