ClinVar Miner

Submissions for variant NM_006031.6(PCNT):c.6162_6163del (p.Lys2054fs)

gnomAD frequency: 0.00001  dbSNP: rs778391726
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000513142 SCV000609065 uncertain significance not provided 2017-02-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000513142 SCV002126292 pathogenic not provided 2024-01-19 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys2054Asnfs*58) in the PCNT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCNT are known to be pathogenic (PMID: 18174396, 22821869). This variant is present in population databases (rs778391726, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with PCNT-related conditions (PMID: 21270239). This variant is also known as 6162_6163hetdelAG (2111X). ClinVar contains an entry for this variant (Variation ID: 444579). For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003403200 SCV004105342 pathogenic PCNT-related disorder 2023-08-01 criteria provided, single submitter clinical testing The PCNT c.6162_6163delAG variant is predicted to result in a frameshift and premature protein termination (p.Lys2054Asnfs*58). This variant was reported in the compound heterozygous state in an individual with microcephalic osteodysplastic primordial dwarfism with insulin resistance (Huang-Doran et al. 2011. PubMed ID: 21270239). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/21-47835993-AAG-A). Frameshift variants in PCNT are expected to be pathogenic. This variant is interpreted as pathogenic.
GeneDx RCV000513142 SCV005396381 likely pathogenic not provided 2024-05-05 criteria provided, single submitter clinical testing Frameshift 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 significant frequency in large population cohorts (gnomAD); Observed in a patient with a reported diagnosis of MOPDII who also harbored a second variant, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes; patient specific details regarding the MOPDII features were not specified in this report (PMID: 21270239); This variant is associated with the following publications: (PMID: 21270239)

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