ClinVar Miner

Submissions for variant NM_018344.6(SLC29A3):c.401G>A (p.Arg134His)

gnomAD frequency: 0.00002  dbSNP: rs761175955
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Kariminejad - Najmabadi Pathology & Genetics Center RCV001814446 SCV001755359 likely pathogenic not provided 2021-07-10 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001882603 SCV002299691 likely pathogenic H syndrome 2023-12-11 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 134 of the SLC29A3 protein (p.Arg134His). This variant is present in population databases (rs761175955, gnomAD 0.006%). This missense change has been observed in individual(s) with histiocytosis-lymphadenopathy plus syndrome (PMID: 24894595). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1180717). 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 SLC29A3 protein function. This variant disrupts the p.Arg134 amino acid residue in SLC29A3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 20199539, 22679148, 23789599, 25967258). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
GeneDx RCV001814446 SCV003924844 uncertain significance not provided 2022-11-10 criteria provided, single submitter clinical testing 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: 24894595)

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