ClinVar Miner

Submissions for variant NM_001128225.3(SLC39A13):c.221G>A (p.Gly74Asp)

gnomAD frequency: 0.00001  dbSNP: rs121434363
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001568112 SCV001791927 pathogenic not provided 2024-03-20 criteria provided, single submitter clinical testing Published functional studies demonstrate protein instability and rapid degredation (PMID: 25007800); Not observed at significant frequency in large population cohorts (gnomAD); 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: 18985159, 32295219, 25007800)
Labcorp Genetics (formerly Invitae), Labcorp RCV000002215 SCV002181067 uncertain significance Ehlers-Danlos syndrome, spondylocheirodysplastic type 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 74 of the SLC39A13 protein (p.Gly74Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with spondylodysplastic type Ehlers-Danlos syndrome (PMID: 18985159). It has also been observed to segregate with disease in related individuals. This variant is also known as G64D. ClinVar contains an entry for this variant (Variation ID: 2133). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects SLC39A13 function (PMID: 18985159, 25007800). 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.
OMIM RCV000002215 SCV000022373 pathogenic Ehlers-Danlos syndrome, spondylocheirodysplastic type 2008-01-01 no assertion criteria provided literature only

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