ClinVar Miner

Submissions for variant NM_014844.5(TECPR2):c.2330G>A (p.Ser777Asn)

gnomAD frequency: 0.00038  dbSNP: rs144849839
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000806512 SCV000946516 uncertain significance Hereditary spastic paraplegia 49 2024-12-02 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 777 of the TECPR2 protein (p.Ser777Asn). This variant is present in population databases (rs144849839, gnomAD 0.2%). 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: 651200). 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.
CeGaT Center for Human Genetics Tuebingen RCV000995260 SCV001149347 uncertain significance not provided 2022-09-01 criteria provided, single submitter clinical testing TECPR2: PM2:Supporting, BP4
Baylor Genetics RCV000806512 SCV001528890 uncertain significance Hereditary spastic paraplegia 49 2018-12-24 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
GeneDx RCV000995260 SCV001874821 uncertain significance not provided 2021-07-26 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; This variant is associated with the following publications: (PMID: 26542466)
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001849110 SCV002105926 uncertain significance Hereditary spastic paraplegia 2019-10-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005240596 SCV005884405 uncertain significance not specified 2024-12-26 criteria provided, single submitter clinical testing Variant summary: TECPR2 c.2330G>A (p.Ser777Asn) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00033 in 248962 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in TECPR2 causing Hereditary spastic paraplegia 49 (0.00033 vs 0.0011), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.2330G>A in individuals affected with Hereditary spastic paraplegia 49 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 651200). Based on the evidence outlined above, the variant was classified as uncertain significance.
Natera, Inc. RCV000806512 SCV001461379 uncertain significance Hereditary spastic paraplegia 49 2020-04-17 no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.