19-1399793-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PP3PM2_SupportingPM3PS3PP4_Strong
This summary comes from the ClinGen Evidence Repository: The NM_000156.6:c.327G>A (p.Lys109=) variant in GAMT is a synonymous variant that alters the last nucleotide of exon 2. It is one of the most common variants associated with GAMT deficiency, accounting for 31-35% of alleles (PMID:19027335, 24268530). The variant has been previously reported in at least 30 unrelated GAMT deficiency patients, including among those with elevated urine guanidinoacetate, reduced or absent cerebral creatine peak on MRS (some of whom also have evidence of guanidinoacetate peak on MRS, and GAMT deficiency in fibroblasts (PMIDs: 8651275, 17171576, 19027335, 22019491, 23660394, 24268530, 24766785) (PP4_Strong) including at least 8 homozygotes (PMID:8651275, 11978605, 19027335, 22019491, 24268530), and in compound heterozygosity with another variant that has been classified as pathogenic by the ClinGen CCDS VCEP including c.58dupT (PMID 24766785, confirmed in trans), c.297_c.309dup13 (PMID:8651275, confirmed in trans; PMID:19027335), c.522G>A (p.Trp174Ter) (PMID:17171576, 19027335, 24268530; 3 probands), or c.36_c.37ins26 (PMID:19027335) as well as c.133T>A (p.Trp45Arg) (PMID 24268530), and c.403G>A (p.Asp135Asn) (PMID 24268530) (PM3_VeryStrong). Additional patients may be reported in the literature but the maximum evidence for PM3_VeryStrong has already been reached. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00039 (34/ 86230 alleles) in the European non-Finnish population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). The c.327G>A variant was shown by RT-PCR and RNA sequencing analysis to result in two abnormal transcripts: in one transcript, the variant resulted in a cryptic splice site in intron 2 and deletion of 146bp, and in the other transcript, the variant resulted in a 44bp insertion leading to altered splicing and skipping of exon 2 (PMID:8651275) (PS3). It is predicted to alter splicing by SpliceAI (donor loss, score 0.93) and varSEAK (splicing class 5) (PP3). There is a ClinVar entry for this variant (Variation ID: 21065). In summary, this variant meets the criteria to be classified as Pathogenic for GAMT deficiency. GAMT-specific ACMG/AMP criteria met, based on the specifications of the ClinGen Cerebral Creatine Deficiencies VCEP (Specifications Version 1.1.0): PM3_VeryStrong, PS3, PP4_Strong, PP3, PM2_Supporting.(Classification approved by the ClinGen CCDS VCEP on June 6, 2022). LINK:https://erepo.genome.network/evrepo/ui/classification/CA314804/MONDO:0012999/026
Frequency
Consequence
NM_000156.6 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GAMT | NM_000156.6 | c.327G>A | p.Lys109Lys | splice_region_variant, synonymous_variant | Exon 2 of 6 | ENST00000252288.8 | NP_000147.1 | |
| GAMT | NM_138924.3 | c.327G>A | p.Lys109Lys | splice_region_variant, synonymous_variant | Exon 2 of 5 | NP_620279.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.000164 AC: 25AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000185 AC: 32AN: 172966Hom.: 0 AF XY: 0.000173 AC XY: 16AN XY: 92628
GnomAD4 exome AF: 0.000483 AC: 681AN: 1410270Hom.: 0 Cov.: 33 AF XY: 0.000445 AC XY: 310AN XY: 697226
GnomAD4 genome 0.000164 AC: 25AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74446
ClinVar
Submissions by phenotype
Deficiency of guanidinoacetate methyltransferase Pathogenic:10Other:2
The GAMT c.327G>A (p.Lys109=) variant is reported as one of the most frequently observed pathogenic variants among patients with guanidinoacetate methyltransferase deficiency accounting for 24% of disease associated alleles (Mercimek-Mahmutoglu and Salomons 2015). Across a selection of the available literature, the p.Lys109= variant has been identified in a total of 15 individuals including four in a homozygous state and 11 in a compound heterozygous state (Stockler et al. 1996; Morris et al. 2007; Dhar et al. 2009; Comeaux et al. 2013; Mercimek-Mahmutoglu et al. 2014). Unaffected heterozygous carriers of the variant were observed in two families (Stockler et al. 1996). Control data are unavailable for this variant, which is reported at a frequency of 0.00031 in the European (non-Finnish) population of the Exome Aggregation Consortium. The variant affects the last nucleotide of the splice donor site of exon 2. Experimental analysis showed the variant results in two abnormal transcripts, one from the use of a cryptic splice site in intron 2 and one resulting from skipping of exon 2. Both abnormal transcripts were identified in one compound heterozygous individual and one homozygous individual, demonstrating the effect on splicing of the variant (Stockler et al. 1996). Based on the collective evidence, the p.Lys109= 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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Variant summary: GAMT c.327G>A (p.Lys109Lys) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5 splicing donor site. These predictions are confirmed in a publication via RT-PCR analysis (though the results were not presented for evaluation; Stockler_1996). The same publication presented data showing that the activity of GAMT is significantly reduced in two patient's liver cells compared to WT, suggesting the variant affects protein function. The variant allele was found at a frequency of 0.00019 in 197356 control chromosomes. The c.327G>A variant has been reported in the literature in numerous individuals affected with Guanidinoactetate methyltransferase deficiency, both as homozygous and compound heterozygous alleles. These data indicate that the variant is very likely to be associated with disease. Additionally, in the literature it has been referred to as one of the most common mutations associated with Guanidinoactetate methyltransferase deficiency. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, both of which classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Variant interpreted as Pathogenic and reported on 12-08-2009 by GTR ID 1006. 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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Variant confirmed as disease-causing by referring clinical team -
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The NM_000156.6:c.327G>A (p.Lys109=) variant in GAMT is a synonymous variant that alters the last nucleotide of exon 2. It is one of the most common variants associated with GAMT deficiency, accounting for 31-35% of alleles (PMID: 19027335, 24268530). The variant has been previously reported in at least 30 unrelated GAMT deficiency patients, including among those with elevated urine guanidinoacetate, reduced or absent cerebral creatine peak on MRS (some of whom also have evidence of guanidinoacetate peak on MRS, and GAMT deficiency in fibroblasts (PMIDs: 8651275, 17171576, 19027335, 22019491, 23660394, 24268530, 24766785) (PP4_Strong) including at least 8 homozygotes (PMID: 8651275, 11978605, 19027335, 22019491, 24268530), and in compound heterozygosity with another variant that has been classified as pathogenic by the ClinGen CCDS VCEP including c.58dupT (PMID 24766785, confirmed in trans), c.297_c.309dup13 (PMID: 8651275, confirmed in trans; PMID: 19027335), c.522G>A (p.Trp174Ter) (PMID: 17171576, 19027335, 24268530; 3 probands), or c.36_c.37ins26 (PMID: 19027335) as well as c.133T>A (p.Trp45Arg) (PMID 24268530), and c.403G>A (p.Asp135Asn) (PMID 24268530) (PM3_VeryStrong). Additional patients may be reported in the literature but the maximum evidence for PM3_VeryStrong has already been reached. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00039 (34/ 86230 alleles) in the European non-Finnish population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). The c.327G>A variant was shown by RT-PCR and RNA sequencing analysis to result in two abnormal transcripts: in one transcript, the variant resulted in a cryptic splice site in intron 2 and deletion of 146bp, and in the other transcript, the variant resulted in a 44bp insertion leading to altered splicing and skipping of exon 2 (PMID: 8651275) (PS3). It is predicted to alter splicing by SpliceAI (donor loss, score 0.93) and varSEAK (splicing class 5) (PP3). There is a ClinVar entry for this variant (Variation ID: 21065). In summary, this variant meets the criteria to be classified as Pathogenic for GAMT deficiency. GAMT-specific ACMG/AMP criteria met, based on the specifications of the ClinGen Cerebral Creatine Deficiencies VCEP (Specifications Version 1.1.0): PM3_VeryStrong, PS3, PP4_Strong, PP3, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022). -
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not provided Pathogenic:4
RNA studies indicate that this variant causes abnormal gene splicing (Stockler et al., 1996; Dhar et al., 2009); This variant is associated with the following publications: (PMID: 25852444, 28055022, 22019491, 11978605, 8651275, 24766785, 24268530, 26319512, 16855203, 28119378, 19027335, 32606525, 31980526) -
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Cerebral creatine deficiency syndrome Pathogenic:2
This sequence change affects codon 109 of the GAMT mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the GAMT protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs80338735, gnomAD 0.04%). This variant has been observed in individuals with guanidinoacetate methyltransferase deficiency (PMID: 2476685, 8651275, 22019491, 24415674). ClinVar contains an entry for this variant (Variation ID: 21065). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in an insertion of 44 nucleotides or a deletion of 146 nucleotides, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 8651275). For these reasons, this variant has been classified as Pathogenic. -
The p.Lys109= variant in GAMT has been reported in >10 individuals with cerebral creatine deficiency syndrome (PMID: 8651275, 1978605, 24268530, 1902733, 23660394), segregated with disease in 4 affected relatives from 4 families (PMID: 24268530, 19027335), and has been identified in 0.04% (34/86230) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs80338735). 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 affected individuals, at least 12 of those were homozygotes, and at least 8 were compound heterozygotes that carried reported pathogenic/likely pathogenic variants in trans or with unknown phase, which increases the likelihood that the p.Lys109= variant is pathogenic (VariationID: 328352, 431959, 8302; PMID: 8651275, 1978605, 24268530, 1902733, 23660394). This variant has also been reported in ClinVar (Variation ID#: 21065) and has been interpreted as pathogenic by Illumina Clinical Services Laboratory, (Illumina), Integrated Genetics (Laboratory Corporation of America), Cytogenetics and Genomics Lab (Cyprus Institute Of Neurology and Genetics), Fulgent Genetics, GeneDx, Invitae, GeneReviews, Natera, Inc. In vitro functional studies provide evidence that the p.Lys109= variant impacts protein function (PMID: 8651275). However, these types of assays may not accurately represent biological function. This variant is located in the last three bases of the exon, which is part of the 3’ splice region. Computational tools do suggest an impact to splicing. 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: 23660394, 22019491, 24766785, 8651275, 19027335). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive cerebral creatine deficiency syndrome. ACMG/AMP Criteria applied: PM3_strong, PS3, PP3, PM2_supporting, PP4 (Richards 2015). -
Inborn genetic diseases Pathogenic:1
The c.327G>A (p.K109K) alteration is located in coding exon 2 of the GAMT gene. This alteration consists of a G to A substitution at nucleotide position 327. This nucleotide substitution does not change the lysine at codon 109. However, this change occurs in the last base pair of coding exon 2, which makes it likely to have some effect on normal mRNA splicing. Based on data from the Genome Aggregation Database (gnomAD) database, the GAMT c.327G>A alteration was observed in 0.02% (38/204352) of total alleles studied, with a frequency of 0.04% (34/86230) in the European (non-Finnish) subpopulation. This mutation was identified in 30/82 alleles in a cohort of individuals with guanidinoacetate methyltransferase deficiency including numerous homozygous individuals (Stockler-Ipsiroglu, 2014). This alteration was detected in the homozygous state, and in conjunction with another alteration in GAMT, in multiple other individuals with GAMT-related cerebral creatine deficiency syndrome (Mercimek-Mahmutoglu, 2006; Morris, 2007; Yolda, 2021; Kritioti, 2021; Libell, 2023). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the available evidence, this alteration is classified as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at