ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.2095-21_2095-10del (rs772869377)

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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 RCV000725930 SCV000340601 uncertain significance not provided 2016-04-11 criteria provided, single submitter clinical testing
GeneDx RCV000725930 SCV000709889 uncertain significance not provided 2017-11-14 criteria provided, single submitter clinical testing The c.2095-21_2095-10del12 variant in the PEX6 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant reduces the quality of the splice acceptor site in intron 10, and may cause abnormal gene splicing. The c.2095-21_2095-10del12 variant is observed in 8/33582 (0.024%) alleles from individuals of Latino background, in large population cohorts (Lek et al., 2016). We interpret c.2095-21_2095-10del12 as a variant of uncertain significance.
Invitae RCV000639508 SCV000761083 likely pathogenic Peroxisome biogenesis disorders, Zellweger syndrome spectrum 2019-09-13 criteria provided, single submitter clinical testing This sequence change falls in intron 10 of the PEX6 gene. It does not directly change the encoded amino acid sequence of the PEX6 protein. 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 observed in several individuals affected with Zellweger syndrome (PMID: 15542397, Invitae). This variant has been reported in individuals in the Leiden Open-source Variation Database (PMID: 21520333). ClinVar contains an entry for this variant (Variation ID: 286981). Experimental studies have shown that this variant disrupts mRNA splicing (PMID: 21520333). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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