ClinVar Miner

Submissions for variant NM_006493.4(CLN5):c.155_167del (p.His52fs)

dbSNP: rs1057517134
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410399 SCV000486800 likely pathogenic Neuronal ceroid lipofuscinosis 5 2016-08-09 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003114526 SCV003787269 pathogenic Neuronal ceroid lipofuscinosis 2023-12-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.His101Profs*58) in the CLN5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CLN5 are known to be pathogenic (PMID: 20157158). This variant is present in population databases (no rsID available, gnomAD 0.001%). This variant has not been reported in the literature in individuals affected with CLN5-related conditions. ClinVar contains an entry for this variant (Variation ID: 371261). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003114526 SCV004812972 pathogenic Neuronal ceroid lipofuscinosis 2024-02-19 criteria provided, single submitter clinical testing Variant summary: CLN5 c.155_167del13 (p.His52ProfsX58) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 5.3e-06 in 188676 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.155_167del13 in individuals affected with Neuronal Ceroid-Lipofuscinosis (Batten Disease) and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 371261). Based on the evidence outlined above, the variant was classified as pathogenic.

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