ClinVar Miner

Submissions for variant NM_207122.2(EXT2):c.11C>T (p.Ser4Leu)

gnomAD frequency: 0.00002  dbSNP: rs527624522
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000371317 SCV000371823 likely benign Exostoses, multiple, type 2 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Marseille Medical Genetics, U1251, Aix Marseille University, Inserm RCV000663343 SCV000783102 likely pathogenic Seizures-scoliosis-macrocephaly syndrome 2018-07-07 criteria provided, single submitter research
Invitae RCV000371317 SCV003277645 uncertain significance Exostoses, multiple, type 2 2023-12-07 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 4 of the EXT2 protein (p.Ser4Leu). This variant is present in population databases (rs527624522, gnomAD 0.03%). This missense change has been observed in individual(s) with EXT2-related conditions (PMID: 30075207). ClinVar contains an entry for this variant (Variation ID: 304572). 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.
OMIM RCV000663343 SCV000930612 pathogenic Seizures-scoliosis-macrocephaly syndrome 2020-11-06 no assertion criteria provided literature only

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