ClinVar Miner

Submissions for variant NM_006031.6(PCNT):c.1032+1G>A

dbSNP: rs1569178877
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000680060 SCV000807500 pathogenic Microcephalic osteodysplastic primordial dwarfism type II 2017-09-01 criteria provided, single submitter clinical testing This splice site variant is categorized as deleterious according to ACMG guidelines (PMID:18414213) and was found once in our laboratory homozygous in a 4-year-old female with possible microcephalic primordial osteodysplastic syndrome
Labcorp Genetics (formerly Invitae), Labcorp RCV003698810 SCV004467507 likely pathogenic not provided 2023-05-13 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 561076). Disruption of this splice site has been observed in individual(s) with clinical features of microcephalic primordial osteodysplastic syndrome (PMID: 25326635). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 6 of the PCNT gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PCNT are known to be pathogenic (PMID: 18174396, 22821869).

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