19-1401418-C-G
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3PM3_StrongPS3_SupportingPP4_Strong
This summary comes from the ClinGen Evidence Repository: The NM_000156.6:c.59G>C variant in GAMT is a missense variant predicted to cause substitution of tryptophan by serine at amino acid 20 (p.Trp20Ser). This variant has been detected in at least 9 unrelated individuals with GAMT deficiency (PMID:15651030, PMID:16855203, PMID:15108290). Of those individuals, one was compound heterozygous for the variant and a pathogenic variant, c.521G>A (p.Trp174*, in trans (PMID:16855203) and eight individuals were homozygous for the variant (PMID:15651030, PMID:16855203, PMID:15108290) (2 points total) (PM3_Strong). These individuals showed elevated plasma GAA and urine GAA (PMID:15651030, PMID:16855203, PMID:15108290), three also showed deficient (<5% wild-type) GAMT enzyme activity in lymphoblasts (PMID:15651030), and one also showed deficient (<5% wild-type) GAMT enzyme activity in fibroblasts and reduced creatine signal on brain MRS (PMID:16855203, PMID:21140503) (PP4_Strong). Expression of the variant in HeLa cells resulted in 3% wild type GAMT activity indicating that this variant may impact protein function (PMID:17336114)(PS3_Supporting). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001 (3/27420 alleles) in the European (non-Finnish) population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004); however, as this variant is covered in <50% of individuals in gnomAD v2.1.1, allele frequency estimates may not be reliable and thus PM2_Supporting is not met. The computational predictor REVEL gives a score of 0.94 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3). There is a ClinVar entry for this variant (Variation ID: 8303, 2 star review status) with 9 submitters classifying the variant as pathogenic and 1 submitter classifying the variant as likely pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for GAMT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PS3_Supporting, PM3_Strong, PP3, PP4_Strong.(Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on May 25, 2023) LINK:https://erepo.genome.network/evrepo/ui/classification/CA340769/MONDO:0012999/026
Frequency
Consequence
NM_000156.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GAMT | ENST00000252288.8 | c.59G>C | p.Trp20Ser | missense_variant | Exon 1 of 6 | 1 | NM_000156.6 | ENSP00000252288.1 | ||
| GAMT | ENST00000447102.8 | c.59G>C | p.Trp20Ser | missense_variant | Exon 1 of 5 | 2 | ENSP00000403536.2 | |||
| GAMT | ENST00000640762.1 | c.59G>C | p.Trp20Ser | missense_variant | Exon 1 of 6 | 5 | ENSP00000492031.1 |
Frequencies
GnomAD3 genomes 0.0000592 AC: 9AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000537 AC: 4AN: 74462Hom.: 0 AF XY: 0.0000928 AC XY: 4AN XY: 43098
GnomAD4 exome AF: 0.0000332 AC: 43AN: 1296552Hom.: 0 Cov.: 31 AF XY: 0.0000313 AC XY: 20AN XY: 638052
GnomAD4 genome 0.0000592 AC: 9AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74292
ClinVar
Submissions by phenotype
Deficiency of guanidinoacetate methyltransferase Pathogenic:9Other:2
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Variant summary: GAMT c.59G>C (p.Trp20Ser) results in a non-conservative amino acid change located in the Arginine N-methyltransferase 2-like domain (IPR026480) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.4e-05 in 74462 control chromosomes. c.59G>C has been reported in the literature in multiple individuals (both homozygous and compound heterozygous) affected with Guanidinoactetate methyltransferase deficiency (e.g. Mercimek-Mahmutoglu_2006, Araujo_2005). In many families it was reported to segregate with the disease (e.g. Mercimek-Mahmutoglu_2006, Araujo_2005). These data indicate that the variant is very likely to be associated with disease. GAMT activity was almost undetectable in patients homozygous for this mutation (Mercimek-Mahmutoglu_2006, Araujo_2005). Two ClinVar submitters (evaluation after 2014) cite the variant as Pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Variant interpreted as Pathogenic and reported on 07-30-2018 by GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect facilitates ClinVar submission from the Association for Creatine Deficiencies registry and does not attempt to reinterpret the variant. -
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The NM_000156.6:c.59G>C variant in GAMT is a missense variant predicted to cause substitution of tryptophan by serine at amino acid 20 (p.Trp20Ser). This variant has been detected in at least 9 unrelated individuals with GAMT deficiency (PMID: 15651030, PMID: 16855203, PMID: 15108290). Of those individuals, one was compound heterozygous for the variant and a pathogenic variant, c.521G>A (p.Trp174*, in trans (PMID: 16855203) and eight individuals were homozygous for the variant (PMID: 15651030, PMID: 16855203, PMID: 15108290) (2 points total) (PM3_Strong). These individuals showed elevated plasma GAA and urine GAA (PMID: 15651030, PMID: 16855203, PMID: 15108290), three also showed deficient (<5% wild-type) GAMT enzyme activity in lymphoblasts (PMID: 15651030), and one also showed deficient (<5% wild-type) GAMT enzyme activity in fibroblasts and reduced creatine signal on brain MRS (PMID: 16855203, PMID: 21140503) (PP4_Strong). Expression of the variant in HeLa cells resulted in 3% wild type GAMT activity indicating that this variant may impact protein function (PMID: 17336114)(PS3_Supporting). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001 (3/27420 alleles) in the European (non-Finnish) population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004); however, as this variant is covered in <50% of individuals in gnomAD v2.1.1, allele frequency estimates may not be reliable and thus PM2_Supporting is not met. The computational predictor REVEL gives a score of 0.94 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3). There is a ClinVar entry for this variant (Variation ID: 8303, 2 star review status) with 9 submitters classifying the variant as pathogenic and 1 submitter classifying the variant as likely pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for GAMT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PS3_Supporting, PM3_Strong, PP3, PP4_Strong. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on May 25, 2023) -
Across a selection of literature, the GAMT c.59G>C (p.Trp20Ser) missense variant has been reported in a homozygous state in at least ten individuals with guanidinoacetate methyltransferase deficiency from six families, and in a compound heterozygous state in at least two additional affected individuals (Item et al. 2004; Caldeira Araujo et al. 2005; Mercimek-Mahmutoglu et al. 2006). In several families, parents of affected individuals homozygous for the p.Trp20Ser variant were found to be heterozygous carriers. Control data are not available for the p.Trp20Ser variant which is reported at a frequency of 0.000109 in the European (non-Finnish) population of the Genome Aggregation Database. GAMT activity was undetectable in lymphoblasts from affected individuals homozygous for the p.Trp20Ser variant (Caldeira Araujo et al. 2005). HeLa cells transfected with p.Trp20Ser variant GAMT showed no increase in GAMT activity in contrast to cells transfected with wild type GAMT where an increase in GAMT activity was demonstrated (Almeida et al. 2007). The p.Trp20Ser variant has been reported at a higher frequency in patients from Portugal. Screening for this variant on newborn blood spot cards in Portugal identified this variant in a heterozygous state in eight newborns (Almeida et al. 2007). A founder effect was suggested based on the results from this study. Based on the collective evidence, the p.Trp20Ser variant is classified as pathogenic for guanidinoacetate methyltransferase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
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not provided Pathogenic:2
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 significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28808834, 28055022, 19892372, 24268530, 21140503, 17336114, 15108290, 23031365, 19027335, 26003046, 16899382, 16855203, 15651030, 31589614) -
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Cerebral creatine deficiency syndrome Pathogenic:2
This sequence change replaces tryptophan, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 20 of the GAMT protein (p.Trp20Ser). This variant is present in population databases (rs80338734, gnomAD 0.01%). This missense change has been observed in individual(s) with cerebral creatine deficiency syndrome (PMID: 15108290, 15651030, 16855203, 17336114, 21140503). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 8303). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt GAMT protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GAMT function (PMID: 17336114). For these reasons, this variant has been classified as Pathogenic. -
The p.Trp20Ser variant in GAMT has been reported in at least 9 individuals with cerebral creatine deficiency syndrome (PMID: 15108290, 15651030, 16855203), segregated with disease in 4 affected relatives from 3 families (PMID: 15651030, 16855203), and has been identified in 0.01% (3/27420) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs140115503). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. Of the 9 affected individuals, 8 of those were homozygotes, which increases the likelihood that the p.Trp20Ser variant is pathogenic (PMID: 15108290, 15651030, 16855203). This variant has also been reported in ClinVar (Variation ID#: 8303) and has been interpreted as pathogenic by Illumina Clinical Services Laboratory (Illumina), Mendelics, Integrated Genetics (Laboratory Corporation of America), Invitae, GeneReviews, Natera, Inc., and OMIM. In vitro functional studies provide some evidence that the p.Trp20Ser variant may slightly impact protein function (PMID: 17336114). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein. The phenotype of individuals homozygous or compound heterozygous for this variant is highly specific for cerebral creatine deficiency syndrome based on strict biochemical investigations consistent with disease (PMID: 15651030, 15108290, 16855203). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive cerebral creatine deficiency syndrome. ACMG/AMP Criteria applied: PM3, PP3, PS3_supporting, PM2_supporting, PP4 (Richards 2015). -
Inborn genetic diseases Pathogenic:1
The p.W20S pathogenic mutation (also known as c.59G>C), located in coding exon 1 of the GAMT gene, results from a G to C substitution at nucleotide position 59. The tryptophan at codon 20 is replaced by serine, an amino acid with highly dissimilar properties. This mutation is well described as a common Portuguese founder mutation and is the second most common GAMT mutation detected in individuals with GAMT deficiency (Almeida LS et al. Mol. Genet. Metab., 2007 May;91:1-6; Mercimek-Mahmutoglu S et al. Mol. Genet. Metab., 2012 Nov;107:433-7; Sharer JD et al. Genet. Med., 2017 02;19:256-263). In addition, this mutation has been detected in the compound heterozygous and homozygous states in several individuals with GAMT deficiency (Stockler-Ipsiroglu S et al. Mol. Genet. Metab., 2014 Jan;111:16-25; Item CB et al. Hum. Mutat., 2004 May;23:524). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
See cases Pathogenic:1
ACMG classification criteria: PS4, PM2, PM3, PP3 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at