ClinVar Miner

Submissions for variant NM_173076.3(ABCA12):c.859C>T (p.Arg287Ter)

dbSNP: rs11891778
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000255175 SCV000321315 pathogenic not provided 2019-08-06 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 30916489, 25525159, 19664001, 29880184)
Invitae RCV000255175 SCV003524975 pathogenic not provided 2023-02-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg287*) in the ABCA12 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ABCA12 are known to be pathogenic (PMID: 20672373). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with congenital ichthyosis (PMID: 19664001, 29880184). ClinVar contains an entry for this variant (Variation ID: 264999). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000056334 SCV000087503 pathogenic Autosomal recessive congenital ichthyosis 4B 2009-10-01 no assertion criteria provided literature only
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000678039 SCV000803667 likely pathogenic Autosomal recessive congenital ichthyosis 4A 2018-08-13 no assertion criteria provided clinical testing The observed variant c.859C>T (p.Arg287Ter) has not been reported in 1000 Genomes and ExAC databases. The in silico prediction of the given variant is disease causing by MutationTaster2.

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