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NM_000642.3(AGL):c.1384del (p.Trp461_Val462insTer)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 22, 2020
Accession:
VCV000189080.7
Variation ID:
189080
Description:
1bp deletion
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NM_000642.3(AGL):c.1384del (p.Trp461_Val462insTer)

Allele ID
186641
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99876556 (GRCh38) GRCh38 UCSC
1: 100342112 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100342114del
NC_000001.11:g.99876558del
NG_012865.1:g.31475del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:99876555:GGG:GG
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA274354
dbSNP: rs786204678
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Oct 22, 2020 RCV000169486.8
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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
Likely pathogenic
(Dec 09, 2014)
criteria provided, single submitter
Method: literature only
Glycogen storage disease type III
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220939.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (1)
Pathogenic
(Nov 30, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000916429.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: AGL c.1384delG (p.Val462X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Oct 22, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV000818823.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change creates a premature translational stop signal (p.Val462*) in the AGL gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Natera, Inc.
Accession: SCV001454507.1
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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Molecular analysis of the AGL gene: identification of 25 novel mutations and evidence of genetic heterogeneity in patients with Glycogen Storage Disease Type III. Goldstein JL Genetics in medicine : official journal of the American College of Medical Genetics 2010 PMID: 20648714
Distinct mutations in the glycogen debranching enzyme found in glycogen storage disease type III lead to impairment in diverse cellular functions. Cheng A Human molecular genetics 2009 PMID: 19299494

Text-mined citations for rs786204678...

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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