ClinVar Miner

Submissions for variant NM_012463.4(ATP6V0A2):c.78dup (p.Ser27fs) (rs745590426)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000599054 SCV000339824 pathogenic not provided 2016-02-23 criteria provided, single submitter clinical testing
GeneDx RCV000599054 SCV000709959 pathogenic not provided 2018-01-09 criteria provided, single submitter clinical testing The c.78dupC variant in the ATP6V0A2 gene has been reported previously using alternate nomenclature c.78_79insC in an individual with cutis laxa and inguinal hernia who also harbored a ATP6V0A2 missense variant, although parental studies were not performed to determine the phase of these two variants (Hucthagowder et al., 2009). The c.78dupC variant causes a frameshift starting with codon Serine 27, changes this amino acid to a Glutamine residue, and creates a premature Stop codon at position 28 of the new reading frame, denoted p.Ser27GlnfsX28. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.78dupC variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.78dupC as a pathogenic variant.
Invitae RCV000689436 SCV000817087 pathogenic ALG9 congenital disorder of glycosylation 2018-03-05 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser27Glnfs*28) in the ATP6V0A2 gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been reported in combination with another ATP6V0A2 variant in an individual affected with autosomal recessive cutis laxa type 2 (PMID: 19321599). Loss-of-function variants in ATP6V0A2 are known to be pathogenic (PMID: 18157129, 19321599). For these reasons, this variant has been classified as Pathogenic.

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