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NM_000156.6(GAMT):c.11_12del (p.Pro4fs) AND Deficiency of guanidinoacetate methyltransferase

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 31, 2023
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:
RCV003226645.1

Allele description [Variation Report for NM_000156.6(GAMT):c.11_12del (p.Pro4fs)]

NM_000156.6(GAMT):c.11_12del (p.Pro4fs)

Genes:
LOC130062945:ATAC-STARR-seq lymphoblastoid silent region 9707 [Gene]
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000156.6(GAMT):c.11_12del (p.Pro4fs)
HGVS:
  • NC_000019.10:g.1401468_1401469del
  • NG_009785.1:g.5088_5089del
  • NM_000156.6:c.11_12delMANE SELECT
  • NM_138924.3:c.11_12del
  • NP_000147.1:p.Pro4fs
  • NP_620279.1:p.Pro4fs
  • NC_000019.9:g.1401467_1401468del
  • NM_000156.5:c.11_12delCC
Protein change:
P4fs
Molecular consequence:
  • NM_000156.6:c.11_12del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_138924.3:c.11_12del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003922543Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Mar 31, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003922543.1

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

Description

Variant summary: GAMT c.11_12delCC (p.Pro4GlnfsX80) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 30998 control chromosomes (gnomAD). To our knowledge, no occurrence of c.11_12delCC in individuals affected with Cerebral Creatine Deficiency Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Oct 14, 2023