ClinVar Miner

Submissions for variant NM_130849.4(SLC39A4):c.295G>A (p.Ala99Thr)

gnomAD frequency: 0.00001  dbSNP: rs182506368
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000999109 SCV001155561 likely pathogenic not provided 2019-06-01 criteria provided, single submitter clinical testing
Invitae RCV000999109 SCV004295965 likely pathogenic not provided 2023-11-20 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 99 of the SLC39A4 protein (p.Ala99Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with acrodermatitis enteropathica (PMID: 21762381, 36479285). 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: 810336). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SLC39A4 function (PMID: 27321477). 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.

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