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NM_000156.6(GAMT):c.459+9_459+12del AND Deficiency of guanidinoacetate methyltransferase

Germline classification:
Uncertain significance (1 submission)
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:
RCV002305515.2

Allele description [Variation Report for NM_000156.6(GAMT):c.459+9_459+12del]

NM_000156.6(GAMT):c.459+9_459+12del

Gene:
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000156.6(GAMT):c.459+9_459+12del
HGVS:
  • NC_000019.10:g.1399117GA[1]
  • NG_009785.1:g.7433CT[1]
  • NM_000156.6:c.459+9_459+12delMANE SELECT
  • NM_138924.3:c.459+9_459+12del
  • NC_000019.10:g.1399117_1399118GA[1]
  • NC_000019.9:g.1399115_1399118del
  • NC_000019.9:g.1399116GA[1]
  • NM_000156.4:c.459+9_459+12delCTCT
Links:
dbSNP: rs762239322
NCBI 1000 Genomes Browser:
rs762239322
Molecular consequence:
  • NM_000156.6:c.459+9_459+12del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_138924.3:c.459+9_459+12del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Deficiency of guanidinoacetate methyltransferase (CCDS2)
Synonyms:
CEREBRAL CREATINE DEFICIENCY SYNDROME 2
Identifiers:
MONDO: MONDO:0012999; MedGen: C0574080; Orphanet: 382; OMIM: 612736

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002600147ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen_CCDS_ACMG_Specifications_GAMT_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 providedcuration

Details of each submission

From ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen, SCV002600147.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_000156.6:c.459+9_459+12del variant in GAMT is an intronic variant that is located in intron 4 and leads to a deletion of 4 base pairs. The highest popualtion minor allele frequency in gnomAD v2.1.1 is 0.00006166 (1 in 16218 alleles) in the African population which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). The computational predictor SpliceAI suggests that this variant has no impact on the gene/gene product (BP4). There is a ClinVar entry for the variant (Variation ID: 513151). Due to conflicting evidence, this variant is classified as a variant of unknown significance for GAMT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): BP4, 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: Sep 29, 2024