ClinVar Miner

Submissions for variant NM_001321336.1(SPATA22):c.-73-12212dup (rs756198538)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000411166 SCV000485902 likely pathogenic Spongy degeneration of central nervous system 2016-02-26 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780872 SCV000918497 pathogenic Canavan Disease, Familial Form 2018-05-29 criteria provided, single submitter clinical testing Variant summary: ASPA c.244dupA (p.Met82AsnfsX8) 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. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. c.631G>T, p.Glu211X; c.693C>A, p.Tyr231X). The variant allele was found at a frequency of 7.3e-06 in 275364 control chromosomes. This frequency is lower than expected for a pathogenic variant in ASPA causing Canavan Disease (7.3e-06 vs 0.0079), allowing no conclusion about variant significance. The c.244dupA has been reported in the literature in individuals affected with a confirmed diagnosis of Canavan Disease, by the demonstration of increased levels of NAA in urine as well as aspartoacylase deficiency detected in skin fibroblasts. These data indicate that the variant is likely to be associated with disease. To our knowledge, no direct experimental evidence demonstrating an impact on protein function has been reported, although it is expected to result in a complete lack of activity (Elpeleg_1999). Other frameshifts in this region (c.244delA and c.244_245delAT) have been reported in pts with Canavan Disease with complete lack of enzymatic activity ((Zeng_2002). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000411166 SCV001251701 pathogenic Spongy degeneration of central nervous system 2020-05-03 criteria provided, single submitter clinical testing

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