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NM_000156.6(GAMT):c.144del (p.Tyr49fs) AND Cerebral creatine deficiency syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 12, 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:
RCV003747364.2

Allele description [Variation Report for NM_000156.6(GAMT):c.144del (p.Tyr49fs)]

NM_000156.6(GAMT):c.144del (p.Tyr49fs)

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.144del (p.Tyr49fs)
HGVS:
  • NC_000019.10:g.1401337del
  • NG_009785.1:g.5221del
  • NG_197362.1:g.158del
  • NM_000156.6:c.144delMANE SELECT
  • NM_138924.3:c.144del
  • NP_000147.1:p.Tyr49fs
  • NP_620279.1:p.Tyr49fs
  • NC_000019.9:g.1401332del
  • NC_000019.9:g.1401336del
Protein change:
Y49fs
Molecular consequence:
  • NM_000156.6:c.144del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_138924.3:c.144del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Cerebral creatine deficiency syndrome (CCAD)
Synonyms:
Creatine deficiency syndromes
Identifiers:
MONDO: MONDO:0000456; MedGen: C5244016; Orphanet: 79172; OMIM: PS300352

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004506059Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 12, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Temsirolimus and rituximab in patients with relapsed or refractory mantle cell lymphoma: a phase 2 study.

Ansell SM, Tang H, Kurtin PJ, Koenig PA, Inwards DJ, Shah K, Ziesmer SC, Feldman AL, Rao R, Gupta M, Erlichman C, Witzig TE.

Lancet Oncol. 2011 Apr;12(4):361-8. doi: 10.1016/S1470-2045(11)70062-6.

PubMed [citation]
PMID:
21440503
PMCID:
PMC3106222

Characterization of seven novel mutations in seven patients with GAMT deficiency.

Item CB, Mercimek-Mahmutoglu S, Battini R, Edlinger-Horvat C, Stromberger C, Bodamer O, Mühl A, Vilaseca MA, Korall H, Stöckler-Ipsiroglu S.

Hum Mutat. 2004 May;23(5):524.

PubMed [citation]
PMID:
15108290
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004506059.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with cerebral creatine deficiency syndrome (PMID: 21440503). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr49Ilefs*65) in the GAMT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GAMT are known to be pathogenic (PMID: 15108290).

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

Last Updated: Sep 29, 2024