ClinVar Genomic variation as it relates to human health

The c.1295_1298+6del (NM_007254.3 c.1295_1298+6delCCAGGTAGCG) variant in PNKP has been reported in the compound heterozygous state in 1 individual with microcephaly with early onset seizures (MCSZ), in 1 individual with motor neuropathy, and in 2 individuals with ataxia with oculomotor apraxia and segregated with disease in 2 affected relatives from 1 family (Previtali 2019 PMID: 31167812, Kalasova 2019 PMID: 31041400, da Costa 2022 PMID: 35426160). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 159788) and has been identified in 0.06% (3/4832) of South Asian and 0.0029% (2/68006) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). This variant is a deletion of ten nucleotides at the exon 14/intron 14 boundary, thereby destroying the canonical splice donor site in intron 14. It is predicted to cause altered splicing, leading to an abnormal or absent protein. Biallelic loss of function of the PNKP gene has been associated with ataxia with oculomotor apraxia. Functional studies in patient fibroblasts provide some evidence that this variant reduced protein expression and activity and were more susceptible to single strand breaks due to reduced repair activity (Kalasova 2019 PMID: 31041400, Kalasova 2020 PMID: 32504494). In summary, the c.1295_1298+6delCCAGGTAGCG variant in PNKP meets criteria to be classified as pathogenic for PNKP-related disorders, such as autosomal recessive ataxia with oculomotor apraxia, and autosomal recessive microcephaly, seizures and developmental delay. ACMG/AMP Criteria applied: PVS1, PM3_Strong, PP1, PS3_Supporting.

Variant summary: PNKP c.1295_1298+6del10 is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site. The variant allele was found at a frequency of 6.8e-05 in 175710 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in PNKP causing PNKP-Related Disorders, allowing no conclusion about variant significance. The variant, c.1295_1298+6del10, has been reported in the literature in multiple individuals affected with PNKP-Related Disorders ranging from microcephaly with early onset seizures to oculomotor apraxia and Charcot-Marie-Tooth type 2 (CMT2) disease (e.g. Previtali_2019, Kalasova_2020, daCosta_2022). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, and demonstrated strongly reduced protein level and reduced function in patient derived cells (Kalasova_2020). The following publications have been ascertained in the context of this evaluation (PMID: 31167812, 32504494, 35426160). ClinVar contains an entry for this variant (Variation ID: 159788). Based on the evidence outlined above, the variant was classified as pathogenic.

The c.1295_1298+6delCCAGGTAGCG mutation in the PNKP gene results in the deletion of ten nucleotides at the exon 14/intron 14 boundary, thereby destroying the canonical splice donor site in intron 14. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product if the message is used for protein translation. Although this mutation has not been previously reported to our knowledge, it is considered a disease-causing mutation.The variant is found in CHILD-EPI,EPILEPSY panel(s).

This variant results in the deletion of part of exon 14 (c.1295_1298+6del) of the PNKP 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 PNKP are known to be pathogenic (PMID: 20118933, 25728773). This variant is present in population databases (rs587784366, gnomAD 0.03%). This variant has been observed in individual(s) with PNKP-related conditions (PMID: 31167812). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 159788). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects PNKP function (PMID: 32504494). For these reasons, this variant has been classified as Pathogenic.