ClinVar Miner

Submissions for variant NM_052989.3(IFT122):c.3263A>G (p.Tyr1088Cys)

gnomAD frequency: 0.00001  dbSNP: rs774343448
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000334995 SCV000440846 uncertain significance Cranioectodermal dysplasia 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV000334995 SCV002164670 uncertain significance Cranioectodermal dysplasia 1 2021-11-15 criteria provided, single submitter clinical testing 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. 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 disruptive. ClinVar contains an entry for this variant (Variation ID: 343264). This variant has not been reported in the literature in individuals affected with IFT122-related conditions. This variant is present in population databases (rs774343448, gnomAD 0.009%). This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 1139 of the IFT122 protein (p.Tyr1139Cys).
Fulgent Genetics, Fulgent Genetics RCV000334995 SCV002783556 uncertain significance Cranioectodermal dysplasia 1 2022-04-15 criteria provided, single submitter clinical testing

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