ClinVar Miner

Submissions for variant NM_014918.5(CHSY1):c.1600A>T (p.Ile534Leu)

gnomAD frequency: 0.00017  dbSNP: rs141305214
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001218970 SCV001390882 uncertain significance Temtamy preaxial brachydactyly syndrome 2022-05-28 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 534 of the CHSY1 protein (p.Ile534Leu). This variant is present in population databases (rs141305214, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CHSY1-related conditions. ClinVar contains an entry for this variant (Variation ID: 947829). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.
Fulgent Genetics, Fulgent Genetics RCV001218970 SCV002794404 uncertain significance Temtamy preaxial brachydactyly syndrome 2021-09-08 criteria provided, single submitter clinical testing
Ambry Genetics RCV002562465 SCV003687169 uncertain significance Inborn genetic diseases 2021-03-17 criteria provided, single submitter clinical testing The c.1600A>T (p.I534L) alteration is located in exon 3 (coding exon 3) of the CHSY1 gene. This alteration results from a A to T substitution at nucleotide position 1600, causing the isoleucine (I) at amino acid position 534 to be replaced by a leucine (L). The p.I534L alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004757383 SCV005342826 uncertain significance CHSY1-related disorder 2024-08-19 no assertion criteria provided clinical testing The CHSY1 c.1600A>T variant is predicted to result in the amino acid substitution p.Ile534Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.040% of alleles in individuals of European (Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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