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NM_001482.3(GATM):c.61G>A (p.Gly21Arg) AND Arginine:glycine amidinotransferase deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 14, 2021
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:
RCV002039315.5

Allele description [Variation Report for NM_001482.3(GATM):c.61G>A (p.Gly21Arg)]

NM_001482.3(GATM):c.61G>A (p.Gly21Arg)

Genes:
LOC130056991:ATAC-STARR-seq lymphoblastoid silent region 6406 [Gene]
GATM:glycine amidinotransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q21.1
Genomic location:
Preferred name:
NM_001482.3(GATM):c.61G>A (p.Gly21Arg)
HGVS:
  • NC_000015.10:g.45378393C>T
  • NG_011674.2:g.28925G>A
  • NM_001321015.2:c.-318-1574G>A
  • NM_001482.3:c.61G>AMANE SELECT
  • NP_001473.1:p.Gly21Arg
  • NC_000015.9:g.45670591C>T
Protein change:
G21R
Links:
dbSNP: rs903485357
NCBI 1000 Genomes Browser:
rs903485357
Molecular consequence:
  • NM_001321015.2:c.-318-1574G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001482.3:c.61G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Arginine:glycine amidinotransferase deficiency (CCDS3)
Synonyms:
AGAT deficiency; Creatine deficiency syndrome due to AGAT deficiency; GATM deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012996; MedGen: C2675179; Orphanet: 35704; OMIM: 612718

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002112144Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 14, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002112144.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with GATM-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces glycine with arginine at codon 21 of the GATM protein (p.Gly21Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024