ClinVar Miner

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

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Total submissions: 9
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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 pathogenic Neuronal ceroid lipofuscinosis 2020-10-01 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 type 6 (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). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CLN6 protein function (PMID: 15265688). For these reasons, this variant has been classified as Pathogenic.
Centre for Inherited Metabolic Diseases, Karolinska University Hospital RCV000195031 SCV001571377 pathogenic Neuronal ceroid lipofuscinosis 6 2021-04-13 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000727479 SCV001713713 uncertain significance not provided 2019-04-07 criteria provided, single submitter clinical testing
Kasturba Medical College, Manipal University RCV000195031 SCV001786701 likely pathogenic Neuronal ceroid lipofuscinosis 6 criteria provided, single submitter clinical testing
Counsyl RCV000195031 SCV001132158 likely pathogenic Neuronal ceroid lipofuscinosis 6 2019-03-24 no assertion criteria provided clinical testing

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