ClinVar Miner

Submissions for variant NM_017882.3(CLN6):c.791_793CCT[1] (p.Ser265del) (rs768422260)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000187114 SCV000240689 uncertain significance not specified 2014-11-18 criteria provided, single submitter clinical testing c.794_796delCCT: p.Ser265del (S265del) in exon 7 of the CLN6 gene (NM_017882.2) The normal sequence with the bases that are deleted in braces is: TCCT{CCT}TCGC. The c.794_796delCCT variant has been reported previously in an individual with late-infantile neuronal ceroid lipofuscinosis (Sharp et al., 2003). The c.794_796delCCT variant results in an in-frame deletion of a single Serine residue at a conserved position in the seventh transmembrane domain of the CLN6 protein (Kousi et al., 2012). However, this deletion is not expected to result in protein truncation or nonsense-mediated mRNA decay. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in PME-EPI,CHILD-EPI panel(s).
Genetic Services Laboratory,University of Chicago RCV000195031 SCV000247045 pathogenic Neuronal ceroid lipofuscinosis 6 2015-05-11 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000727479 SCV000708915 uncertain significance not provided 2017-06-13 criteria provided, single submitter clinical testing
Mendelics RCV000989353 SCV001139644 pathogenic Neuronal ceroid lipofuscinosis 2019-05-28 criteria provided, single submitter clinical testing
Invitae RCV000989353 SCV001410001 likely pathogenic Neuronal ceroid lipofuscinosis 2019-11-18 criteria provided, single submitter clinical testing This variant, c.794_796del, results in the deletion of 1 amino acid(s) of the CLN6 protein (p.Ser265del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs768422260, ExAC 0.02%). Deletion of this amino acid has been observed in individual(s) with neuronal ceroid lipofuscinosis (PMID: 31029456, 19135028, 19520283, 30705896). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 205182). This variant has been reported to have conflicting or insufficient data to determine the effect on CLN6 protein function (PMID: 15265688). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Counsyl RCV000195031 SCV001132158 likely pathogenic Neuronal ceroid lipofuscinosis 6 2019-03-24 no assertion criteria provided clinical testing

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