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NM_000642.3(AGL):c.4456del (p.Ser1486fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Aug 20, 2021)
Last evaluated:
Nov 25, 2020
Accession:
VCV000001098.14
Variation ID:
1098
Description:
1bp deletion
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NM_000642.3(AGL):c.4456del (p.Ser1486fs)

Allele ID
16137
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99916704 (GRCh38) GRCh38 UCSC
1: 100382260 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100382262del
NC_000001.11:g.99916706del
NM_000028.2:c.4456del NP_000019.2:p.Ser1486fs frameshift
... more HGVS
Protein change
S1470fs, S1486fs
Other names
-
Canonical SPDI
NC_000001.11:99916703:TTT:TT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA114758
OMIM: 610860.0005
dbSNP: rs113994134
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, multiple submitters, no conflicts Dec 20, 2019 RCV000177731.9
Pathogenic 3 criteria provided, multiple submitters, no conflicts Nov 25, 2020 RCV000723822.5
Pathogenic 1 no assertion criteria provided Sep 1, 1997 RCV000001156.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
AGL - - GRCh38
GRCh37
1284 1299

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Aug 24, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV000626759.2
Submitted: (Apr 02, 2018)
Evidence details
Comment:
This sequence change deletes 1 nucleotide from exon 33 of the AGL mRNA (c.4456delT), causing a frameshift at codon 1486. This creates a premature translational … (more)
Pathogenic
(Jun 13, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000229651.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Dec 20, 2019)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001194233.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (2)
Comment:
NM_000642.2(AGL):c.4456delT(S1486Pfs*18) is classified as pathogenic in the context of glycogen storage disease type III. Sources cited for classification include the following: PMID 9412782 and 25602008. … (more)
Pathogenic
(Nov 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001248397.6
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001804369.1
Submitted: (Aug 20, 2021)
Evidence details
Comment:
Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 47 amino acids are lost and replaced with 17 incorrect amino … (more)
pathologic
(Sep 06, 2012)
no assertion criteria provided
Method: curation
Glycogen Storage Disease Type III
Allele origin: not provided
GeneReviews
Accession: SCV000040768.1
Submitted: (Jan 08, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.
Pathogenic
(Sep 01, 1997)
no assertion criteria provided
Method: literature only
GLYCOGEN STORAGE DISEASE, TYPE IIIa
Allele origin: germline
OMIM
Accession: SCV000021306.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Natera, Inc.
Accession: SCV001460667.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Glycogen Storage Disease Type III Dagli A - 2016 PMID: 20301788
A founder AGL mutation causing glycogen storage disease type IIIa in Inuit identified through whole-exome sequencing: a case series. Rousseau-Nepton I CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne 2015 PMID: 25602008
A single-base deletion in the 3'-coding region of glycogen-debranching enzyme is prevalent in glycogen storage disease type IIIA in a population of North African Jewish patients. Parvari R European journal of human genetics : EJHG 1997 PMID: 9412782
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=AGL - - - -

Text-mined citations for rs113994134...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021