NM_000156.6(GAMT):c.59G>C (p.Trp20Ser) AND not provided

Clinical significance:Pathogenic (Last evaluated: May 28, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000986201.2

Allele description [Variation Report for NM_000156.6(GAMT):c.59G>C (p.Trp20Ser)]

NM_000156.6(GAMT):c.59G>C (p.Trp20Ser)

Gene:
GAMT:guanidinoacetate N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000156.6(GAMT):c.59G>C (p.Trp20Ser)
HGVS:
  • NC_000019.10:g.1401418C>G
  • NG_009785.1:g.5136G>C
  • NM_000156.6:c.59G>CMANE SELECT
  • NM_138924.3:c.59G>C
  • NP_000147.1:p.Trp20Ser
  • NP_620279.1:p.Trp20Ser
  • NC_000019.9:g.1401417C>G
  • NM_000156.4:c.59G>C
  • NM_000156.5:c.59G>C
  • Q14353:p.Trp20Ser
Protein change:
W20S; TRP20SER
Links:
UniProtKB: Q14353#VAR_058102; OMIM: 601240.0003; dbSNP: rs80338734
NCBI 1000 Genomes Browser:
rs80338734
Molecular consequence:
  • NM_000156.6:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138924.3:c.59G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001135124Mendelicscriteria provided, single submitter
Pathogenic
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001777342GeneDxcriteria provided, single submitter
Pathogenic
(Mar 30, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Mendelics, SCV001135124.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001777342.1

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

Description

Pathogenic founder variant in Portuguese population with a carrier frequency of 0.8% (Mercimek-Mahmutoglu et al. 2006); Published functional studies demonstrate that introduction of GAMT-W20S contructs into HeLa cells was associated with no increase of GAMT activity whereas the wild type protein resulted in increased activity (Almeida et al., 2007); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 31589614, 15651030, 17336114, 16855203, 16899382, 26003046, 19027335, 23031365, 15108290, 19892372, 21140503, 28055022, 28808834, 24268530)

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

Last Updated: Aug 27, 2021

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