ClinVar Miner

Submissions for variant NM_000310.4(PPT1):c.535C>T (p.Arg179Cys)

gnomAD frequency: 0.00004  dbSNP: rs560471003
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000766627 SCV000242344 uncertain significance not provided 2014-12-16 criteria provided, single submitter clinical testing p.Arg179Cys (CGC>TGC): c.535 C>T in exon 5 of the PPT1 gene (NM_000310.3). The R179C variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R179C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved across species, and Cysteine is observed at this position in evolution. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in EPILEPSY,CHILD-EPI panel(s).
Athena Diagnostics RCV000188720 SCV000614762 uncertain significance not specified 2016-11-14 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000661982 SCV000784313 uncertain significance Neuronal ceroid lipofuscinosis 1 2018-03-05 criteria provided, single submitter clinical testing
Invitae RCV000661982 SCV001005829 benign Neuronal ceroid lipofuscinosis 1 2024-01-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV002345676 SCV002645092 uncertain significance Inborn genetic diseases 2020-03-18 criteria provided, single submitter clinical testing The p.R179C variant (also known as c.535C>T), located in coding exon 5 of the PPT1 gene, results from a C to T substitution at nucleotide position 535. The arginine at codon 179 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV000661982 SCV001460032 benign Neuronal ceroid lipofuscinosis 1 2020-04-30 no assertion criteria provided clinical testing

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