ClinVar Miner

Submissions for variant NM_001848.3(COL6A1):c.2560C>T (p.Arg854Cys)

gnomAD frequency: 0.00003  dbSNP: rs771987341
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001948185 SCV002201583 benign Bethlem myopathy 1A 2025-01-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV002560582 SCV003749822 uncertain significance Inborn genetic diseases 2022-12-21 criteria provided, single submitter clinical testing The c.2560C>T (p.R854C) alteration is located in exon 35 (coding exon 35) of the COL6A1 gene. This alteration results from a C to T substitution at nucleotide position 2560, causing the arginine (R) at amino acid position 854 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV003136326 SCV003828564 uncertain significance not provided 2019-08-08 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004690184 SCV005185547 likely benign not specified 2024-05-06 criteria provided, single submitter clinical testing Variant summary: COL6A1 c.2560C>T (p.Arg854Cys) results in a non-conservative amino acid change located in the von Willebrand factor, type A domain (IPR002035) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.8e-05 in 1609974 control chromosomes. The observed variant frequency is approximately 144 fold of the estimated maximal expected allele frequency for a pathogenic variant in COL6A1 causing Collagen Type VI-Related Disorders phenotype (4.8e-07), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.2560C>T in individuals affected with Collagen Type VI-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1428029). Based on the evidence outlined above, the variant was classified as likely benign.

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