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NM_001482.3(GATM):c.*104A>G AND Arginine:glycine amidinotransferase deficiency

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jun 6, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000301010.6

Allele description [Variation Report for NM_001482.3(GATM):c.*104A>G]

NM_001482.3(GATM):c.*104A>G

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.*104A>G
HGVS:
  • NC_000015.10:g.45362005T>C
  • NG_011674.2:g.45313A>G
  • NM_001321015.2:c.*104A>G
  • NM_001482.3:c.*104A>GMANE SELECT
  • NC_000015.9:g.45654203T>C
  • NM_001482.2:c.*104A>G
Links:
dbSNP: rs886051201
NCBI 1000 Genomes Browser:
rs886051201
Molecular consequence:
  • NM_001321015.2:c.*104A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001482.3:c.*104A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000391421Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Jan 13, 2018) 		germlineclinical testing

Citation Link,

SCV002600092ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen_CCDS_ACMG_Specifications_GATM_v1.1)		Uncertain significance
(Jun 6, 2022) 		germlinecuration

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000391421.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

From ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen, SCV002600092.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_001482.3:c.*104A>G variant is a single nucleotide substitution in the 3'UTR of GATM. Because the variant is located in the 3'UTR, it is not expected to alter the amino acid sequence, and SpliceAI predicts no impact on splicing. This variant is absent in gnomAD v2.1.1 (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 316208). In summary, this variant meets the criteria to be classified as uncertain significance for AGAT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).

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

Last Updated: Apr 9, 2023