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NM_000642.3(AGL):c.3764A>G (p.Asn1255Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Aug 31, 2021)
Last evaluated:
Dec 22, 2020
Accession:
VCV000456497.6
Variation ID:
456497
Description:
single nucleotide variant
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NM_000642.3(AGL):c.3764A>G (p.Asn1255Ser)

Allele ID
448502
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99910775 (GRCh38) GRCh38 UCSC
1: 100376331 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100376331A>G
NC_000001.11:g.99910775A>G
NG_012865.1:g.65692A>G
... more HGVS
Protein change
N1255S, N1239S
Other names
-
Canonical SPDI
NC_000001.11:99910774:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00260 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00170
The Genome Aggregation Database (gnomAD) 0.00147
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00192
1000 Genomes Project 0.00260
Links
ClinGen: CA967210
dbSNP: rs138134718
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 31, 2019 RCV000556035.4
Uncertain significance 1 criteria provided, single submitter Dec 22, 2020 RCV001591194.3
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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
1281 1296

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV000626739.4
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Dec 22, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001814288.1
Submitted: (Aug 31, 2021)
Evidence details
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to … (more)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs138134718...

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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 06, 2021