ClinVar Miner

Submissions for variant NM_017882.3(CLN6):c.34G>A (p.Ala12Thr)

gnomAD frequency: 0.01081  dbSNP: rs112239768
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000675965 SCV000167774 benign not provided 2018-12-12 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 21990111, 29482223)
Eurofins Ntd Llc (ga) RCV000173024 SCV000202487 benign not specified 2015-01-29 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000173024 SCV000247043 likely benign not specified 2015-04-16 criteria provided, single submitter clinical testing
Invitae RCV000989355 SCV000290387 benign Neuronal ceroid lipofuscinosis 2024-02-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000675965 SCV000603089 benign not provided 2023-11-22 criteria provided, single submitter clinical testing
SIB Swiss Institute of Bioinformatics RCV000677327 SCV000803558 benign Ceroid lipofuscinosis, neuronal, 6A 2018-05-31 criteria provided, single submitter curation This variant is interpreted as a Benign, for Ceroid lipofuscinosis, neuronal, 6, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Ambry Genetics RCV002312552 SCV000846696 benign Inborn genetic diseases 2017-05-24 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Mendelics RCV000989355 SCV001139646 benign Neuronal ceroid lipofuscinosis 2019-05-28 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000989355 SCV001278035 uncertain significance Neuronal ceroid lipofuscinosis 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000173024 SCV002050988 likely benign not specified 2021-12-10 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000675965 SCV002822193 benign not provided 2023-11-01 criteria provided, single submitter clinical testing CLN6: PP3, BS1, BS2
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV003224161 SCV003919810 likely benign Ceroid lipofuscinosis, neuronal, 6A; Ceroid lipofuscinosis, neuronal, 6B (Kufs type) 2021-11-01 criteria provided, single submitter clinical testing CLN6 NM_017882.2 p.Ala12Thr (c.34G>A): This variant has been reported in the literature in at least 2 individuals (1 with neuronal ceroid lipofuscinosis and 1 with cerebellar ataxia) (Kousi 2012 PMID:21990111, Coutelier 2018 PMID:29482223). However, this variant is present in 1.7% (1216/67944) of European alleles including 11 homozygotes in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/15-68229551-C-T?dataset=gnomad_r3). Evolutionary conservation and computational predictive tools for this variant are unclear. This variant is present in ClinVar, with several labs classifying this variant as Likely Benign or Benign (Variation ID:136802). In summary, data on this variant suggests that this variant does not cause disease, but requires further evidence. Therefore this variant is classified as likely benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000675965 SCV000801694 uncertain significance not provided 2017-04-19 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000675965 SCV001739970 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000675965 SCV001928319 likely benign not provided no assertion criteria provided clinical testing

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