ClinVar Miner

Submissions for variant NM_001136472.2(LITAF):c.88A>T (p.Asn30Tyr)

gnomAD frequency: 0.00001  dbSNP: rs368574479
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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 RCV000816653 SCV000394840 uncertain significance Charcot-Marie-Tooth disease type 1C 2018-01-12 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000816653 SCV000957170 uncertain significance Charcot-Marie-Tooth disease type 1C 2024-08-19 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 30 of the LITAF protein (p.Asn30Tyr). This variant is present in population databases (rs368574479, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with LITAF-related conditions. ClinVar contains an entry for this variant (Variation ID: 317788). 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 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000816653 SCV005878976 uncertain significance Charcot-Marie-Tooth disease type 1C 2024-04-19 criteria provided, single submitter clinical testing The LITAF c.88A>T; p.Asn30Tyr variant (rs368574479), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 317788). This variant is only observed on one allele in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.551). Due to limited information, the clinical significance of this variant is uncertain at this time.

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