Submissions for variant NM_007254.4(PNKP):c.1029+2T>C

gnomAD frequency: 0.00115  dbSNP: rs199919568

Total submissions: 26

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000188445	SCV000242059	pathogenic	not provided	2024-07-16	criteria provided, single submitter	clinical testing	RNA studies and functional RNA analyses demonstrate a damaging effect and indicate aberrant splicing in response to c.1029+2T>C resulting predominately in skipping of exon 11, affecting the phosphatase domain and the kinase domain (PMID: 37301908, 34697416, 22508754); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 31061747, 29655203, 29720203, 29261713, 22508754, 32123317, 34697416, Fontaine2022[Preprint], 33654647, 37301908)
Genetic Services Laboratory, University of Chicago	RCV000502586	SCV000596486	likely pathogenic	Microcephaly, seizures, and developmental delay	2015-10-01	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV001085813	SCV000650110	likely benign	Developmental and epileptic encephalopathy, 12	2024-01-19	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000502586	SCV000743934	pathogenic	Microcephaly, seizures, and developmental delay	2017-07-28	criteria provided, single submitter	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000502586	SCV000745394	pathogenic	Microcephaly, seizures, and developmental delay	2017-05-31	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000502586	SCV000914850	uncertain significance	Microcephaly, seizures, and developmental delay	2017-04-27	criteria provided, single submitter	clinical testing	The PNKP c.1029+2T>C variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. A literature search was performed for the gene and cDNA change change. No publications were found based on this search. The variant is reported at a frequency of 0.00204 in the European (non-Finnish) population from the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of splice donor variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for epileptic encephalopathy. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Athena Diagnostics	RCV000188445	SCV001145114	uncertain significance	not provided	2018-11-01	criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV001196449	SCV001367057	likely pathogenic	Ataxia - oculomotor apraxia type 4	2020-04-02	criteria provided, single submitter	clinical testing	This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2.
Institute of Human Genetics, University of Leipzig Medical Center	RCV000502586	SCV001440299	likely pathogenic	Microcephaly, seizures, and developmental delay	2019-01-01	criteria provided, single submitter	clinical testing	This variant was identified as compound heterozygous.
Baylor Genetics	RCV001196449	SCV001519758	pathogenic	Ataxia - oculomotor apraxia type 4	2020-10-02	criteria provided, single submitter	clinical testing	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV001449753	SCV001653028	uncertain significance	not specified	2020-06-24	criteria provided, single submitter	clinical testing	Variant classified as Uncertain Significance - Favor Pathogenic. The c.1029+2T>C variant in PNKP has been reported in the compound heterozygous state in one individual with Ataxia with Oculomotor Apraxia Type 4 and their affected sibling (Rudenskaya 2019 PMID: 31061747). It has also been identified in 3 individuals with epilepsy (Lindy 2018 PMID: 29655203, Stanek 2018 PMID: 29720203, Coll 2017 PMID: 29261713). It has also been reported by other clinical laboratories in ClinVar (Variation ID:206401) and has been identified in 0.2% (147/70858) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. However, exon 11, which is affected by this variant, is in frame and consists of only 93 base pairs and encodes less than 10% of the PNKP protein. The PNKP gene has been definitively been associated with autosomal recessive ataxia with oculomotor apraxia and with microcephaly, seizures, and developmental delay. However, there is limited evidence regarding its association with epilepsy. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain for autosomal recessive ataxia with oculomotor apraxia. ACMG/AMP Criteria applied: PVS1_Moderate, PM3, PP1_Supporting.
Mayo Clinic Laboratories, Mayo Clinic	RCV000188445	SCV001713016	likely pathogenic	not provided	2020-02-18	criteria provided, single submitter	clinical testing	PVS1, PM2
CeGaT Center for Human Genetics Tuebingen	RCV000188445	SCV001747228	pathogenic	not provided	2024-04-01	criteria provided, single submitter	clinical testing	PNKP: PM3:Strong, PVS1:Strong, PM2:Supporting, PP1, PS3:Supporting
Revvity Omics, Revvity	RCV000188445	SCV002024696	likely pathogenic	not provided	2022-06-30	criteria provided, single submitter	clinical testing
DASA	RCV000502586	SCV002073786	likely pathogenic	Microcephaly, seizures, and developmental delay	2022-02-05	criteria provided, single submitter	clinical testing	The c.1029+2T>C variant is located in a canonical splice-site, and it is not predicted the protein reading frame alteration, however, occur in a critical region and the variant disrupts <10% of protein - PVS1_moderate. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 206401; PMID: 33654647, 31061747) - PS4_moderate. The variant is present at low allele frequencies population databases (rs199919568 – gnomAD 0.01089%; ABraOM 0.001281 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The c.1029+2T>C was detected in trans with a pathogenic variant (PMID: 31061747; 33654647) - PM3. The variant co-segregated with disease in multiple affected family members (PMID: 31061747) - PP1. In summary, the currently available evidence indicates that the variant is likely pathogenic.
Ambry Genetics	RCV002381633	SCV002694485	pathogenic	Inborn genetic diseases	2022-01-05	criteria provided, single submitter	clinical testing	The c.1029+2T>C intronic variant results from a T to C substitution two nucleotides after exon 11 (coding exon 10) of the PNKP gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, direct evidence is unavailable. Based on data from gnomAD, the PNKP c.1029+2T>C alteration has an overall frequency of 0.11% (190/178830) total alleles studied. The highest observed frequency was 0.21% (147/70858) of European (non-Finnish) alleles. This alteration has been reported in the compound heterozygous state in individuals with a spectrum of presentations including PNKP-related neurodevelopmental disorder and ataxia-oculomotor apraxia 4 (AOA4) (Freitas, 2021; Rudenskaya, 2019). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the available evidence, this alteration is classified as pathogenic.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	RCV003224209	SCV003920336	likely pathogenic	Charcot-Marie-Tooth disease type 2B2; Microcephaly, seizures, and developmental delay; Ataxia - oculomotor apraxia type 4	2022-04-29	criteria provided, single submitter	clinical testing	This variant has been reported in the literature in the compound heterozygous state in at least 2 individuals with features of ataxia with oculomotor apraxia type 4 (AOA4) segregating with disease in 2 affected family members. This variant has also been identified in the heterozygous state in at least 3 individuals with epilepsy; however, at least 1 author has called into question the pathogenicity of this variant (Coll 2017 PMID:29261713, Stanek 2018 PMID:29720203, Lindy 2018 PMID:29655203, Rudenskaya 2019 PMID:310617747, Freitas 2021 PMID:33654647). This variant is present in the Genome Aggregation Database (Highest reported MAF 0.2% (127/65136) (https://gnomad.broadinstitute.org/variant/19-49862369-A-G?dataset=gnomad_r3). This variant is present in ClinVar, with several labs classifying this variant as Pathogenic or Likely Pathogenic; however, at least 1 laboratory has submitted a classification of Likely Benign for this variant (Variation ID:206401). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. RNA studies predict that this variant will impact the protein with altered splicing (Wai 2020 PMID:32123317). However, these studies may not accurately represent in vivo biological function. Of note, this variant alters the consensus splice sequence (+/- 1,2) which is predicted to result in an absent or abnormal protein. Loss of function variants are a known mechanism of disease for this gene (Dumitrache 2017 PMID:27125728). However, this variant is expected to alter exon 11; this exon is in frame and represents less than 10% of the total protein. In summary, data on this variant is highly suspicious for disease, but requires further evidence for pathogenicity. Therefore, this variant is classified as likely pathogenic.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000502586	SCV003922343	uncertain significance	Microcephaly, seizures, and developmental delay	2023-05-02	criteria provided, single submitter	curation	The heterozygous c.1029+2T>C variant in PNKP was identified by our study in 1 individual with microcephaly, seizures, and intellectual disability (Broad Institute Rare Genomes Project). The significance of the c.1029+2T>C variant is uncertain. If you have any additional information about functional evidence we encourage you to reach out to us.
Genetics and Molecular Pathology, SA Pathology	RCV003447514	SCV004175334	likely pathogenic	Microcephaly, seizures, and developmental delay; Ataxia - oculomotor apraxia type 4	2023-02-13	criteria provided, single submitter	clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV001196449	SCV005086751	likely pathogenic	Ataxia - oculomotor apraxia type 4	2023-07-17	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with ataxia-oculomotor apraxia 4 (MIM#616267), and microcephaly, seizures, and developmental delay (MIM#613402). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (190 heterozygotes, 0 homozygotes). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0704 - Another canonical splice site variant comparable to the one identified in this case has limited previous evidence for pathogenicity. A different variant in the same splice site (c.1029+1G>A) has been reported as pathogenic (ClinVar). (SP) 0808 - Previous reports of pathogenicity for this variant are conflicting. The variant has been previously reported in two brothers affected with Ataxia-culomotor apraxia 4 (MIM#616267) (PMID: 31061747). It has also been reported in multiple patients with microcephaly, seizures and developmental delay (MIM#613402) and have conflicting classifications from likely benign to pathogenic (ClinVar, PMID: 29720203, 30398534, 29261713). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Clinical Genetics Laboratory, Skane University Hospital Lund	RCV000188445	SCV005197216	pathogenic	not provided	2022-12-27	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000188445	SCV001741120	pathogenic	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000188445	SCV001952864	likely pathogenic	not provided		no assertion criteria provided	clinical testing
Diagnostic Laboratory, Strasbourg University Hospital	RCV002274937	SCV002562838	likely pathogenic	Abnormal cerebral morphology		no assertion criteria provided	clinical testing
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	RCV000502586	SCV004041699	likely pathogenic	Microcephaly, seizures, and developmental delay	2023-10-09	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004539746	SCV004762633	uncertain significance	PNKP-related disorder	2024-02-12	no assertion criteria provided	clinical testing	The PNKP c.1029+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in the compound heterozygous state in at least five individuals with severe progressive microcephaly, hypotonia, developmental delays, and ataxia-oculomotor apraxia type 4 (Neuser et al. 2021. PubMed ID: 34697416; Rudenskaya et al. 2019. PubMed ID: 31061747; Freitas et al. 2021. PubMed ID: 33654647). Functional studies confirm that this variant causes aberrant splicing by skipping exon 11, resulting in an in-frame deletion of amino acids 313-343 (Wai et al. 2020. PubMed ID: 32123317). This variant is reported in 0.21% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations regarding it pathogenicity in ClinVar, ranging from pathogenic to likely pathogenic to uncertain significance to likely benign (https://www.ncbi.nlm.nih.gov/clinvar/variation/206401/). Loss of function is a known mechanism of disease for PNKP, and other splice altering changes have been reported as causative; however these other pathogenic variants are all found at lower frequency in gnomAD (Human Gene Mutation Database). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.