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NM_000156.6(GAMT):c.182G>A (p.Gly61Glu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Dec 28, 2020)
Last evaluated:
May 6, 2019
Accession:
VCV000328350.5
Variation ID:
328350
Description:
single nucleotide variant
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NM_000156.6(GAMT):c.182G>A (p.Gly61Glu)

Allele ID
332705
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1399938 (GRCh38) GRCh38 UCSC
19: 1399937 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.1399938C>T
NC_000019.9:g.1399937C>T
NM_000156.6:c.182G>A MANE Select NP_000147.1:p.Gly61Glu missense
... more HGVS
Protein change
G61E
Other names
-
Canonical SPDI
NC_000019.10:1399937:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00012
1000 Genomes Project 0.00100
Exome Aggregation Consortium (ExAC) 0.00035
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Links
dbSNP: rs77168423
ClinGen: CA9043773
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, single submitter Jan 12, 2018 RCV000289407.3
Uncertain significance 1 criteria provided, single submitter Aug 27, 2018 RCV000480090.2
Uncertain significance 1 criteria provided, single submitter May 6, 2019 RCV000550292.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAMT - - GRCh38
GRCh37
331 375

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 27, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000569738.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
A variant of uncertain significance has been identified in the GAMT gene. The G61E variant has not been published as a pathogenic variant, nor has … (more)
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of guanidinoacetate methyltransferase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000410915.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(May 06, 2019)
criteria provided, single submitter
Method: clinical testing
Cerebral creatine deficiency syndrome
Allele origin: germline
Invitae
Accession: SCV000659563.3
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glycine with glutamic acid at codon 61 of the GAMT protein (p.Gly61Glu). The glycine residue is highly conserved and there is … (more)
Uncertain significance
(Jan 07, 2020)
no assertion criteria provided
Method: clinical testing
Guanidinoacetate methyltransferase deficiency
Allele origin: germline
Natera, Inc.
Accession: SCV001460088.1
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

Text-mined citations for rs77168423...

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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 Aug 27, 2021