ClinVar Miner

Submissions for variant NM_004369.4(COL6A3):c.5528T>C (p.Phe1843Ser)

gnomAD frequency: 0.00002  dbSNP: rs770876436
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001143249 SCV001303757 likely benign Collagen 6-related myopathy 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002032357 SCV002179042 uncertain significance Bethlem myopathy 1A 2021-09-25 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt COL6A3 protein function. ClinVar contains an entry for this variant (Variation ID: 899020). This variant is also known as p.F1236S. This missense change has been observed in individual(s) with Parkinson disease (PMID: 33964895). This variant is present in population databases (rs770876436, ExAC 0.06%). This sequence change replaces phenylalanine with serine at codon 1843 of the COL6A3 protein (p.Phe1843Ser). The phenylalanine residue is moderately conserved and there is a large physicochemical difference between phenylalanine and serine.

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