ClinVar Miner

Submissions for variant NM_001253852.3(AP4B1):c.1526T>C (p.Met509Thr)

gnomAD frequency: 0.00001  dbSNP: rs1043676103
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002316863 SCV000850644 uncertain significance Inborn genetic diseases 2017-05-18 criteria provided, single submitter clinical testing The p.M509T variant (also known as c.1526T>C), located in coding exon 9 of the AP4B1 gene, results from a T to C substitution at nucleotide position 1526. The methionine at codon 509 is replaced by threonine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen RCV000994076 SCV001147383 uncertain significance not provided 2017-06-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002534959 SCV003211460 uncertain significance Hereditary spastic paraplegia 47 2022-07-15 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 509 of the AP4B1 protein (p.Met509Thr). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with AP4B1-related conditions. ClinVar contains an entry for this variant (Variation ID: 589638). 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. 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.
Genome-Nilou Lab RCV002534959 SCV004050649 uncertain significance Hereditary spastic paraplegia 47 2023-04-11 criteria provided, single submitter clinical testing

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