NM_000642.3(AGL):c.1996_1999delinsT (p.His666_Gln667delinsTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 14, 2016
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:: RCV000330238.1

Allele description [Variation Report for NM_000642.3(AGL):c.1996_1999delinsT (p.His666_Gln667delinsTer)]

NM_000642.3(AGL):c.1996_1999delinsT (p.His666_Gln667delinsTer)

Gene:

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

Variant type:

Indel

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.1996_1999delinsT (p.His666_Gln667delinsTer)

HGVS:

NC_000001.11:g.99881172_99881175delinsT
NG_012865.1:g.36089_36092delinsT
NM_000028.3:c.1996_1999delCATCinsT
NM_000642.3:c.1996_1999delinsTMANE SELECT
NM_000643.3:c.1996_1999delCATCinsT
NM_000644.3:c.1996_1999delCATCinsT
NM_000646.3:c.1948_1951delCATCinsT
NM_001425325.1:c.1996_1999delCATCinsT
NM_001425326.1:c.1996_1999delCATCinsT
NM_001425327.1:c.1795_1798delCATCinsT
NM_001425328.1:c.1792_1795delCATCinsT
NM_001425329.1:c.1792_1795delCATCinsT
NM_001425332.1:c.1618_1621delCATCinsT
NP_000019.2:p.His666_Gln667delinsTer
NP_000019.2:p.His666_Tyr1001delinsTer
NP_000633.2:p.His666_Gln667delinsTer
NP_000634.2:p.His666_Gln667delinsTer
NP_000634.2:p.His666_Tyr1001delinsTer
NP_000635.2:p.His666_Gln667delinsTer
NP_000635.2:p.His666_Tyr1001delinsTer
NP_000637.2:p.His650_Gln651delinsTer
NP_000637.2:p.His650_Tyr985delinsTer
NP_001412254.1:p.His666_Tyr1001delinsTer
NP_001412255.1:p.His666_Asp1001delinsTer
NP_001412256.1:p.His599_Tyr934delinsTer
NP_001412257.1:p.His598_Tyr933delinsTer
NP_001412258.1:p.His598_Gln933delinsTer
NP_001412261.1:p.His540_Tyr875delinsTer
NC_000001.10:g.100346728_100346731delinsT
NM_000028.2:c.1996_1999delinsT
NM_000642.2:c.1996_1999delCATCinsT
NM_000643.2:c.1996_1999delinsT
NM_000644.2:c.1996_1999delinsT
NM_000646.2:c.1948_1951delinsT

Links:

dbSNP: rs886042008

NCBI 1000 Genomes Browser:

rs886042008

Molecular consequence:

NM_000028.3:c.1996_1999delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_000642.3:c.1996_1999delinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_000643.3:c.1996_1999delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_000644.3:c.1996_1999delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_000646.3:c.1948_1951delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_001425325.1:c.1996_1999delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_001425326.1:c.1996_1999delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_001425327.1:c.1795_1798delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_001425328.1:c.1792_1795delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_001425329.1:c.1792_1795delCATCinsT - nonsense - [Sequence Ontology: SO:0001587]
NM_001425332.1:c.1618_1621delCATCinsT - 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
SCV000330835	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Sep 14, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330835

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Sep 14, 2016)

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, SCV000330835.6

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

Description

The c.1996_1999delCATCinsT pathogenic variant in the AGL gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1996_1999delCATCinsT causes a frameshift, changing codon Histidine 666 to a premature Stop codon, denoted p.His666Ter. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. As an alternate mechanism, this variant is also predicted to destroy the splice donor site in intron 15. The c.1996_1999delCATCinsT variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.1996_1999delCATCinsT as a pathogenic variant.

#	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: Nov 20, 2023

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