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NM_000156.6(GAMT):c.414_415del (p.Ser140fs) AND Cerebral creatine deficiency syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 23, 2020
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:
RCV001390318.7

Allele description [Variation Report for NM_000156.6(GAMT):c.414_415del (p.Ser140fs)]

NM_000156.6(GAMT):c.414_415del (p.Ser140fs)

Gene:
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000156.6(GAMT):c.414_415del (p.Ser140fs)
HGVS:
  • NC_000019.10:g.1399173_1399174del
  • NG_009785.1:g.7381_7382del
  • NM_000156.6:c.414_415delMANE SELECT
  • NM_138924.3:c.414_415del
  • NP_000147.1:p.Ser140fs
  • NP_620279.1:p.Ser140fs
  • NC_000019.9:g.1399171_1399172del
  • NC_000019.9:g.1399172_1399173del
Protein change:
S140fs
Links:
dbSNP: rs2144636856
NCBI 1000 Genomes Browser:
rs2144636856
Molecular consequence:
  • NM_000156.6:c.414_415del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_138924.3:c.414_415del - 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
SCV001592002Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 23, 2020) 		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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001592002.4

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

Description

This sequence change results in a premature translational stop signal in the GAMT gene (p.Ser140Glyfs*50). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 97 amino acids of the GAMT protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GAMT-related conditions. This variant disrupts the C-terminus of the GAMT protein. Other variant(s) that disrupt this region (p.Glu176*) have been determined to be pathogenic (Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024