NM_000642.3(AGL):c.118C>T (p.Gln40Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 22, 2017
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:: RCV000579304.1

Allele description [Variation Report for NM_000642.3(AGL):c.118C>T (p.Gln40Ter)]

NM_000642.3(AGL):c.118C>T (p.Gln40Ter)

Gene:

AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.118C>T (p.Gln40Ter)

HGVS:

NC_000001.11:g.99861538C>T
NG_012865.1:g.16455C>T
NM_000028.3:c.118C>T
NM_000642.3:c.118C>TMANE SELECT
NM_000643.3:c.118C>T
NM_000644.3:c.118C>T
NM_000646.3:c.70C>T
NM_001425325.1:c.118C>T
NM_001425326.1:c.118C>T
NM_001425327.1:c.118C>T
NM_001425328.1:c.118C>T
NM_001425329.1:c.118C>T
NP_000019.2:p.Gln40Ter
NP_000019.2:p.Gln40Ter
NP_000633.2:p.Gln40Ter
NP_000634.2:p.Gln40Ter
NP_000634.2:p.Gln40Ter
NP_000635.2:p.Gln40Ter
NP_000635.2:p.Gln40Ter
NP_000637.2:p.Gln24Ter
NP_000637.2:p.Gln24Ter
NP_001412254.1:p.Gln40Ter
NP_001412255.1:p.Gln40Ter
NP_001412256.1:p.Gln40Ter
NP_001412257.1:p.Gln40Ter
NP_001412258.1:p.Gln40Ter
NC_000001.10:g.100327094C>T
NM_000028.2:c.118C>T
NM_000642.2:c.118C>T
NM_000643.2:c.118C>T
NM_000644.2:c.118C>T
NM_000646.2:c.70C>T

Protein change:

Q24*

Links:

dbSNP: rs771961377

NCBI 1000 Genomes Browser:

rs771961377

Molecular consequence:

NM_000028.3:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000642.3:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000643.3:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000644.3:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000646.3:c.70C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425325.1:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425326.1:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425327.1:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425328.1:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425329.1:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000680764	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Sep 22, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000680764

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Sep 22, 2017)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000680764.2

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

Description

The Q40X nonsense variant in the AGL gene has been reported previously in individuals with glycogen storage disease type III who were also found to harbor a second AGL gene variant (Austin et al., 2012; Li et al., 2014 ). The Q40X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In summary, we interpret this variant 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		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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