NM_000152.5(GAA):c.752C>T (p.Ser251Leu) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Nov 22, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000497864.9

Allele description [Variation Report for NM_000152.5(GAA):c.752C>T (p.Ser251Leu)]

NM_000152.5(GAA):c.752C>T (p.Ser251Leu)

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.752C>T (p.Ser251Leu)

HGVS:

NC_000017.11:g.80107616C>T
NG_009822.1:g.11061C>T
NM_000152.5:c.752C>TMANE SELECT
NM_001079803.3:c.752C>T
NM_001079804.3:c.752C>T
NP_000143.2:p.Ser251Leu
NP_001073271.1:p.Ser251Leu
NP_001073272.1:p.Ser251Leu
LRG_673t1:c.752C>T
LRG_673:g.11061C>T
NC_000017.10:g.78081415C>T
NC_000017.10:g.78081415C>T
NM_000152.3:c.752C>T
NM_000152.4(GAA):c.752C>T
NM_000152.4:c.752C>T
P10253:p.Ser251Leu

Protein change:

S251L

Links:

UniProtKB: P10253#VAR_068578; dbSNP: rs200856561

NCBI 1000 Genomes Browser:

rs200856561

Molecular consequence:

NM_000152.5:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001079803.3:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001079804.3:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000590491	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 18, 2021)	germline	clinical testing	Citation Link,
SCV002501221	AiLife Diagnostics, AiLife Diagnostics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 28, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 31637888, 31980526, 25741868
SCV004224245	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 22, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34995642, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000590491

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jun 18, 2021)

germline

clinical testing

Citation Link,

SCV002501221

AiLife Diagnostics, AiLife Diagnostics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 28, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004224245

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 22, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Implementation of a Targeted Next-Generation Sequencing Panel for Constitutional Newborn Screening in High-Risk Neonates.

Lee H, Lim J, Shin JE, Eun HS, Park MS, Park KI, Namgung R, Lee JS.

Yonsei Med J. 2019 Nov;60(11):1061-1066. doi: 10.3349/ymj.2019.60.11.1061.

PubMed [citation]

PMID:: 31637888
PMCID:: PMC6813152

Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging.

Hou YC, Yu HC, Martin R, Cirulli ET, Schenker-Ahmed NM, Hicks M, Cohen IV, Jönsson TJ, Heister R, Napier L, Swisher CL, Dominguez S, Tang H, Li W, Perkins BA, Barea J, Rybak C, Smith E, Duchicela K, Doney M, Brar P, Hernandez N, et al.

Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):3053-3062. doi: 10.1073/pnas.1909378117. Epub 2020 Jan 24.

PubMed [citation]

PMID:: 31980526
PMCID:: PMC7022190

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000590491.4

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25466677, 29122469, 27183828, 18458862, 24513544, 29451150, 29124014, 30555256, 31637888, 31980526)

#	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 AiLife Diagnostics, AiLife Diagnostics, SCV002501221.1

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

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV004224245.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

BP4

#	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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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