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GATM (AGAT)First nucleotideLast nucleotidelength of exon (coding nucleotides)Predicted impact of deletion of entire exonStrength of PVS1 if exon is skippedExplanationCritical residues/domains (see references*)
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Exon 1-916969In frame, deletes 23 amino acids, 5.4% of protein lengthModerateIn frame, but includes mitochondrial transit sequenceThe first 37 amino acids constitute the mitochondrial transit peptide (https://www.uniprot.org/uniprot/P50440; determined "by similarity"); amino acids 46 and 49 have a phosphoserine modification (https://www.uniprot.org/uniprot/P50440)
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Exon 270288219Out of frame -> nonsense mediated decayVery StrongOut of frame; premature stop codon and NMD predicted
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Exon 3289484196Out of frame -> nonsense mediated decayVery StrongOut of frame; premature stop codon and NMD predictedAsn98 – Binding of water molecular which is bound to ornithine and arginine (3)
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Exon 4485675191Out of frame -> nonsense mediated decayVery StrongOut of frame; premature stop codon and NMD predictedAsp170 – Hydrogen bond amidino group, helps fix arginine (substrate) to the active site; Crystal structure of p.Asp170Asn has been determined; p.Asn170Asn abolishes AGAT activity; p.Tyr203Ser, the only pathogenic missense variant (for AGAT-D) in ClinVar (Note that there are also 4 missense changes for renal fanconi syndrome)
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Exon 5676813138In frame, deletes 46 amino acids, 10.9% of protein lengthStrong or consider Very Strong if shown to be missing by RT-PCRIncludes an active site reside, Asp254Asp254 – Active site, hydrogen bonded to His303; multiple studies, including structural and mutagenesis, support that Asp254 is one of the three active site residues; the crystal structure of p.Asp254Asn has been determined and activity of this variant is reduced >2000 fold compared to wild type.
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Exon 6814978165In frame, deletes 55 amino acids, 13.0% of protein lengthStrong or consider Very Strong if shown to be missing by RT-PCRIncludes active site reside, His303, and other residue important for substrate bindingMet302 – Binding ornithine and arginine.
His303 - Binding ornithine, Hydrogen bond amidino group, active site, hydrogen bonded to D254, helps fix arg to the active site; multiple studies, including structural and mutagenesis, support that His303 is one of the three active site residues; p.His303Val abolished AGAT activity.
Asp305 - Hydrogen bonding of amidino group; p.Asp305Ala abolishes AGAT activity.
Arg322 – Binding ornithine and arginine; p.Arg322Glu reduces AGAT activity by >400 fold compared to wild type.
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Exon 7979104264Out of frame -> nonsense mediated decayVery StrongOut of frame; premature stop codon and NMD predicted
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Exon 810431159117In frame, deletes 39 amino acids, 9.2% of protein lengthModerateIncludes residues Ser354 and Ser355, which are important for substrate binding.Ser354 – Binding ornithine and arginine
Ser355 – Binding ornithine and arginine; p.Ser355Ala reduces AGAT activity by >400 fold compared to wild type.
Amino acid 385 has a N6-acetyllysine modification (https://www.uniprot.org/uniprot/P50440)
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Exon 91160*985 (1272 = last nucleotide of stop codon)113Missing last 36 amino acids, and stop codonModerate or consider upgrading if shown to be missing my RT-PCRIncludes active site reside, Cys407, and other residue important for substrate bindingGly402 - Binding of water molecular which is bound to ornithine
Cys407 – Binding ornithine, active site; multiple studies, including structural and mutagenesis, support that Cys407 is one of the three active site residues; the crystal structure of p.Cys407Ser has been determined and this variant abolishes AGAT activity (note that p.Glu233Lys was also present in the construct but not expected to impact activity).
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Total1272 nucleotides (including stop codon)423 amino acids
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*References:
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https://www.uniprot.org/uniprot/P50440
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Fritsche et al, 1997, PMID 9266688, "Substrate binding and catalysis by L-arginine :glycine amidinotransferase. A mutagenesis and crystallographic study".
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Humm et al, 1997, PMID 9148748, "Recombinant expression and isolation of human L-arginine:glycine amidinotransferase and identification of its active-site cysteine residue".
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Humm et al, 1997, PMID 9218780, "Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis"
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