ClinVar Miner

Submissions for variant NM_033109.5(PNPT1):c.407G>A (p.Arg136His)

dbSNP: rs746356243
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001585665 SCV001811021 likely pathogenic not provided 2020-06-30 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30244537, 30046113, 31752325, 28645153)
Invitae RCV001585665 SCV003524614 pathogenic not provided 2023-07-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 136 of the PNPT1 protein (p.Arg136His). This variant is present in population databases (rs746356243, gnomAD 0.02%). This missense change has been observed in individual(s) with combined oxidative phosphorylation deficiency (PMID: 28645153, 30046113, 33199448). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 587375). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PNPT1 protein function. For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV002534523 SCV003755532 uncertain significance Inborn genetic diseases 2021-03-26 criteria provided, single submitter clinical testing The c.407G>A (p.R136H) alteration is located in exon 5 (coding exon 5) of the PNPT1 gene. This alteration results from a G to A substitution at nucleotide position 407, causing the arginine (R) at amino acid position 136 to be replaced by a histidine (H). The in silico prediction for the p.R136H alteration is inconclusive. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
OMIM RCV000714514 SCV000845204 pathogenic Combined oxidative phosphorylation defect type 13 2018-10-30 no assertion criteria provided literature only
Genomics England Pilot Project, Genomics England RCV000714514 SCV001760091 likely pathogenic Combined oxidative phosphorylation defect type 13 no assertion criteria provided clinical testing

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