ClinVar Miner

Submissions for variant NM_000036.3(AMPD1):c.1794A>T (p.Leu598Phe)

gnomAD frequency: 0.00025  dbSNP: rs200717164
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001868286 SCV002203404 uncertain significance Muscle AMP deaminase deficiency 2025-01-14 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 631 of the AMPD1 protein (p.Leu631Phe). This variant is present in population databases (rs200717164, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with AMPD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 559257). 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 AMPD1 protein function with a positive predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV000676653 SCV002817506 uncertain significance not provided 2022-06-28 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV001868286 SCV003826250 uncertain significance Muscle AMP deaminase deficiency 2019-04-10 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005407876 SCV006072375 uncertain significance not specified 2025-03-06 criteria provided, single submitter clinical testing Variant summary: AMPD1 c.1794A>T (p.Leu598Phe) results in a non-conservative amino acid change located in the AMP deaminase domain (IPR006329) 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 0.00021 in 251408 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in AMPD1 causing Muscle AMP Deaminase Deficiency, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1794A>T in individuals affected with Muscle AMP Deaminase Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 559257). Based on the evidence outlined above, the variant was classified as uncertain significance.
Mayo Clinic Laboratories, Mayo Clinic RCV000676653 SCV000802446 uncertain significance not provided 2016-03-07 no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.