ClinVar Miner

Submissions for variant NM_014844.5(TECPR2):c.3466G>A (p.Ala1156Thr)

gnomAD frequency: 0.00013  dbSNP: rs200844941
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000811792 SCV000952078 uncertain significance Hereditary spastic paraplegia 49 2022-05-21 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 1156 of the TECPR2 protein (p.Ala1156Thr). This variant is present in population databases (rs200844941, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TECPR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 655585). 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001849114 SCV002105944 uncertain significance Hereditary spastic paraplegia 2016-12-12 criteria provided, single submitter clinical testing
Ambry Genetics RCV004028743 SCV004963803 uncertain significance Inborn genetic diseases 2024-02-27 criteria provided, single submitter clinical testing The c.3466G>A (p.A1156T) alteration is located in exon 16 (coding exon 15) of the TECPR2 gene. This alteration results from a G to A substitution at nucleotide position 3466, causing the alanine (A) at amino acid position 1156 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV004768677 SCV005378470 uncertain significance not provided 2023-11-21 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Natera, Inc. RCV000811792 SCV001454396 uncertain significance Hereditary spastic paraplegia 49 2020-04-17 no assertion criteria provided clinical testing

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